Articles de revues : « S –ITS rDNA »

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Lin, Pingping, Xuguang Hu, Li Xue, Xinyi Li, Ping Wang, Xinwang Zhao, Muqing Zhang, Zuhu Deng et Fan Yu. « Identification of Sugarcane S. spontaneum (Poaceae) Germplasm : Evidence from rDNA-ITS and rDNA Locus Analyses ». Agronomy 12, n^o 12 (14 décembre 2022) : 3167. http://dx.doi.org/10.3390/agronomy12123167.

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Sugarcane is a major crop for sugar production around the world. The complexity of the sugarcane genome creates challenges for the use of both conventional and molecular breeding methods to improve sugarcane at a genetic level. DNA sequencing is an important tool to assess how the genus Saccharum and the genera of the Saccharum complex are interrelated. Here, we identify the kinship of Nepal2013-6 (Saccharum spontaneum, x = 10) using a tetra-primer amplification refractory mutation system (ARMS) PCR. Based on rDNA-ITS sequence analysis, the accession Nepal2013-6 falls within a single cluster with S. spontaneum (Yunnan82-114 and SES208), which is consistent with the previous results. Moreover, fluorescence in situ hybridization (FISH) results indicate that the 5S rDNA spots are consistent with the chromosomal ploidy in the analytical Saccharum materials, whereas 35S rDNA has similar or fewer sites than the ploidy. Therefore, 5S rDNA FISH patterns would be more suitable than 35S rDNA for chromosomal ploidy analysis in S. spontaneum with varied basic chromosome number x = 8, 9, 10. Altogether, these results indicate that the rDNA sequences will be a useful marker for further rapidly identifying the relationship and ploidy of S. spontaneum in sugarcane breeding.

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Chang, Chin-Feng, Cheng-Hsu Yao, Shuh-Sen Young, Savitree Limtong, Rungluk Kaewwichian, Nantana Srisuk et Ching-Fu Lee. « Candida gosingica sp. nov., an anamorphic ascomycetous yeast closely related to Scheffersomyces spartinae ». International Journal of Systematic and Evolutionary Microbiology 61, n^o 3 (1 mars 2011) : 690–94. http://dx.doi.org/10.1099/ijs.0.020511-0.

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During surveys on yeast diversity in forest soils from Taiwan and Thailand, ten yeast strains isolated from different samples were found to have similar molecular and physiological characteristics. Sequence analysis of small subunit (SSU) rDNA, the D1/D2 domain of large subunit (LSU) rDNA and internal transcribed spacer (ITS)-5.8S rDNA demonstrated that these strains were closely related to Scheffersomyces spartinae. The novel strains could be differentiated from S. spartinae by a 0.9 % sequence divergence (5 substitutions, 0 gaps) in the D1/D2 domain of LSU rDNA, a 1.5 % divergence (8 substitutions, 0 gaps) in the ITS-5.8S rDNA and a 0.7 % divergence (12 substitutions, 2 gaps) in the SSU rDNA. The novel strains also showed specific patterns of electrophoretic karyotypes that differed from that of S. spartinae. Therefore, a novel yeast species, Candida gosingica sp. nov., is proposed to accommodate these strains. The type strain SJ7S11T (=BCRC 23194T=CBS 11433T) was assigned and deposited in the Bioresource Collection and Research Center (BCRC), Food Industry Development and Research Institute, Hsinchu, Taiwan, and Centraalbureau voor Schimmelcultures (CBS), Utrecht, The Netherlands.

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McGrath, J. Mitchell, et John P. Helgeson. « Differential behavior of Solanum brevidens ribosomal DNA loci in a somatic hybrid and its progeny with potato ». Genome 41, n^o 3 (1 juin 1998) : 435–39. http://dx.doi.org/10.1139/g98-039.

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Fluorescence in situ hybridization was used to characterize loci encoding ribosomal RNA (rDNA) among parents and progeny of a somatic fusion between tetraploid Solanum tuberosum (potato) and diploid Solanum brevidens. As expected, four major sites of hybridization to rDNA loci were evident in the tetraploid parent species, two in the diploid parent species, and six in the hexaploid somatic fusion plant. Two of the loci in the somatic fusion plant showed differential signals relative to the other four, which were interpreted as a delayed condensation of sites harboring the rDNA loci. This delayed condensation was heritable to the first backcross generation of the somatic hybrid crossed with potato. In the second backcross generation, differential condensation was not evident. However, a heterochromatic isochromosome was observed whose presence was correlated with a S. brevidens specific marker linked with the rDNA locus. It is suggested that the S. brevidens rDNA loci are preferentially affected in the somatic hybrid and its progeny, and that the delayed condensation may have contributed to the formation of the isochromosome.Key words: introgression, recombination, isochromosome, in situ hybridization.

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Yue-Qin, Chen, Wang Ning, Zhou Hui et Qu Liang-Hu. « Differentiation of Medicinal Cordyceps Species by rDNA ITS Sequence Analysis ». Planta Medica 68, n^o 7 (juillet 2002) : 635–39. http://dx.doi.org/10.1055/s-2002-32892.

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Deng, Cheng Xun, Mei Yue, Ling Wang et Yu Hui Li. « Molecular Identification of a Strain Acidithiobacillus Ferrooxidans and its Biological Characteristics ». Advanced Materials Research 402 (novembre 2011) : 3–6. http://dx.doi.org/10.4028/www.scientific.net/amr.402.3.

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A strain of Acidithiobacillus ferrooxidans designated S t1 was isolated and identified from the acid mine drainage of Tianmashan Coal Mine, Tongling county, Anhui province. Its morphological, physiological and biochemical characters, growth conditions of pH value and temperature, 16S rDNA sequence and the phylogenetic tree was studied. Results showed that the bacteria strains from different sites have divergence at the curve of pH and Eh values during the enriching culture. The isolated strain S t1 grew in a pH rang from 2.0 to 3.0 and temperature 25 to 35°C with over 98％similarity toAcidithiobacillus ferrooxidansin 16S rDNA sequence.

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Wu, Zhipeng, Jun Sun, Junjie Hu, Jingling Song, Shuangsheng Deng, Niuping Zhu, Yurong Yang et Jianping Tao. « Morphological and Molecular Characterization, and Demonstration of a Definitive Host, for Sarcocystis masoni from an Alpaca (Vicugna pacos) in China ». Biology 11, n^o 7 (6 juillet 2022) : 1016. http://dx.doi.org/10.3390/biology11071016.

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Only 18S rDNA sequences of Sarcocystis spp. in South American camelids (SACs) are deposited in GenBank as references, and the definitive host of S. masoni in SACs is still unclear. Here, S. masoni sarcocysts detected in an alpaca (Vicugna pacos) in China were investigated with the aid of light (LM) and transmission electron (TEM) microscopy, and characterized using four genetic markers, i.e., 18S rDNA, 28S rDNA and ITS, and the mitochondrial cox1. Additionally, the life cycle of the parasite was completed via experimental animal infection. Under LM, S. masoni sarcocysts exhibited numerous 1.3–2.1 μm conical protrusions. Under TEM, the sarcocyst wall contained conical, cylindrical, or irregular-shaped villar protrusions, similar to type 9j. Two dogs (Canis familiaris) fed S. masoni sarcocysts shed sporocysts with a prepatent period of 8–9 days. The newly obtained 18S rDNA sequences showed 98.4–100% identity with those of S. masoni in SACs previously deposited in GenBank. Interestingly, the newly obtained sequences of 18S rDNA and mitochondrial cox1 shared 99.6–100% and 98.2–98.5% identity, respectively, with those of S. cameli in dromedary camels (Camelus dromedaries). Phylogenetic analysis based on sequences of 18S rDNA, 28S rDNA, or mitochondrial cox1 revealed that S. masoni has a close relationship with Sarcocystis spp. in ruminants. The relationship between S. masoni and S. cameli deserves to be further clarified in the future.

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Rodionov, A. V., K. S. Dobryakova, N. N. Nosov, A. A. Gnutikov, E. O. Punina, A. A. Kriukov et V. S. Shneyer. « Polymorphism of ITS sequences in 35S rRNA genes in Elymus dahuricus aggregate species : two cryptic species ? » Vavilov Journal of Genetics and Breeding 23, n^o 3 (14 mai 2019) : 287–95. http://dx.doi.org/10.18699/vj19.493.

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Nuclear ribosomal internal transcribed spacer (ITS) sequences were sequenced for 23 species and subspecies of Elymus sensu lato collected in Russia. The Neighbor-Net analysis of ITS sequences suggested that there are four ribotypes called Core Northern St-rDNA, Core Southern St-rDNA, Northern dahuricus St-rDNA and Southern dahuricus St-rDNA. The Core Southern variant of St-rDNA is closely related to rDNA of diploid Pseudoroegneria stipifolia (PI 313960) and P. spicata (PI 547161). The Core Northern St-rDNA is closely related to rDNA of P. cognata (PI 531720), a diploid species of Kyrgyzstan carrying StY variant of the St genome. The Core Northern St-rDNA is widespread among the Elymus species of Siberia and the Far East, including Yakutia and Chukotka. The Core Southern St-ribotype is typical of southern Elymus and Pseudoroegneria of the South Caucasus, Primorye, Pakistan, and South Korea. The Northern dahuricus St-ribotype and Southern dahuricus St-ribotype are derivatives of the Core Northern and Core Southern St-ribotypes, correspondingly. Both of them were found in all four studied species of the E. dahuricus aggregate: E. dahuricus Turcz. ex Griseb., E. franchetii Kitag., E. excelsus Turcz. ex Griseb. and Himalayan E. tangutorum (Nevski) Hand.-Mazz. In other words, there are at least two population groups (two races) of the Elymus dahuricus aggregate species that consistently differ in their ITS-sequences in Siberia, the Far East and Northern China. Each contains all morphological forms, which taxonomists now attribute either to different species of E. dahuricus aggr. (E. dahuricus sensu stricto, E. franchetii, E. tangutorum, E. excelsus) or subspecies of Campeiostachys dahurica (Turcz. ex Griseb.) B.R. Baum, J.L. Yang et C.C. Yen. At the moment it is unknown if there are any morphological differences between plants carrying either Northern or Southern dahuricus rDNA. Probably, they are cryptic species, but it is certain that if differences in morphology between the two races exist, they are not associated with signs that are now considered taxonomically significant and are used to separate E. dahuricus s. s., E. franchetii, E. tangutorum, and E. excelsus.

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Ding, Xiaoyu, Luosan Xu, Zhengtao Wang, Kaiya Zhou, Hong Xu et Yiquan Wang. « Authentication of Stems of Dendrobium officinale by rDNA ITS Region Sequences ». Planta Medica 68, n^o 2 (février 2002) : 191–92. http://dx.doi.org/10.1055/s-2002-20239.

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Xu, Hong, Zhengtao Wang, Xiaoyu Ding, Kaiya Zhou et Luoshan Xu. « Differentiation ofDendrobiumSpecies used as ”Huangcao Shihu” by rDNA ITS Sequence Analysis ». Planta Medica 72, n^o 1 (décembre 2006) : 89–92. http://dx.doi.org/10.1055/s-2005-916228.

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Smith, Donna S., Hélène Rocheleau, Julie T. Chapados, Cathryn Abbott, Sharon Ribero, Scott A. Redhead, C. André Lévesque et Solke H. De Boer. « Phylogeny of the Genus Synchytrium and the Development of TaqMan PCR Assay for Sensitive Detection of Synchytrium endobioticum in Soil ». Phytopathology® 104, n^o 4 (avril 2014) : 422–32. http://dx.doi.org/10.1094/phyto-05-13-0144-r.

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Potato wart, caused by the fungal pathogen Synchytrium endobioticum, is a serious disease with the potential to cause significant economic damage. The small subunit (SSU) and internal transcribed spacer (ITS) ribosomal DNA (rDNA) were sequenced for several Synchytrium spp., showing a high rate of variability for both of these markers among the different species and monophyly of the genus within phylum Chytridiomycota. The intergenic nontranscribed spacer (IGS) of rDNA was sequenced for different pathotypes and showed no intraspecific variation within S. endobioticum, similar to the other rDNA markers from this study. To facilitate screening for the pathogen in soil, three TaqMan polymerase chain reaction (PCR) assays were developed from SSU, ITS, and IGS rDNA sequences to detect S. endobioticum sporangia in the chloroform-flotation fraction of sieved soil extracts. In the screening portion of the method, a first TaqMan assay targeting the SSU rDNA was developed with positive results that were further confirmed with amplicon melt analysis. A synthetic reaction control cloned into a plasmid was incorporated into the procedure, facilitating the validation of negative results. The presence of the reaction control did not adversely affect the efficiency of the SSU target amplification. A second TaqMan assay targeting the ITS-1 region was developed as a confirmatory test. There was 100% accordance between the SSU and ITS-1 TaqMan assays. Utilizing these two assays in tandem achieved good specificity for S. endobioticum, generating negative results with the cloned SSU and ITS-1 regions from all 14 other Synchytrium spp. considered. Spike recovery experiments indicated that these assays, targeting the SSU and ITS-1 rDNA regions, developed from a phylogeny dataset of the genus, could reliably detect a single sporangium in the chloroform flotation fraction of a soil extract. Good correlation between microscopic detection of sporangia and PCR results in both positive and negative soil samples was dually demonstrated for both the SSU and ITS-1 assays.

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Martín, María P., Scott LaGreca et H. Thorsten Lumbsch. « Molecular phylogeny of Diploschistes inferred from ITS sequence data ». Lichenologist 35, n^o 1 (janvier 2003) : 27–32. http://dx.doi.org/10.1006/lich.2002.0427.

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AbstractThe phylogeny of the genus Diploschistes was investigated using nucleotide sequences of the nuclear ITS rDNA region (ITS1, ITS2 and 5.8S rDNA). Sequences of 22 Diploschistes species were aligned to those of six other species of Thelotremataceae, Graphis scripta and Aspicilia cinerea, with the last used as an outgroup. The alignment was analysed cladistically using maximum parsimony. In the most parsimonious trees, Diploschistes is monophyletic, with D. ocellatus being a sister group to the remaining Diploschistes spp. (= Diploschistes s. str.). A previous cladistic analysis of morphological data suggested an evolutionary trend within the genus from perithecioid to urceolate ascomata. The present ITS data suggest the opposite: perithecioid ascomata are apparently an apomorphic character within the genus, with the actinostomus group forming a derived monophyletic clade. However, the topology within Diploschistes s. str. Lacks strong bootstrap support.

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Zhu, Yanqing, Yong Wang, Boxiang Tao, Jinhua Han, Hong Chen, Qinfang Zhu, Ling Huang et al. « Nucleolar GTPase Bms1 displaces Ttf1 from RFB-sites to balance progression of rDNA transcription and replication ». Journal of Molecular Cell Biology 13, n^o 12 (13 novembre 2021) : 902–17. http://dx.doi.org/10.1093/jmcb/mjab074.

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Abstract 18S, 5.8S, and 28S ribosomal RNAs (rRNAs) are cotranscribed as a pre-ribosomal RNA (pre-rRNA) from the rDNA by RNA polymerase I whose activity is vigorous during the S-phase, leading to a conflict with rDNA replication. This conflict is resolved partly by replication-fork-barrier (RFB)-sites sequences located downstream of the rDNA and RFB-binding proteins such as Ttf1. However, how Ttf1 is displaced from RFB-sites to allow replication fork progression remains elusive. Here, we reported that loss-of-function of Bms1l, a nucleolar GTPase, upregulates rDNA transcription, causes replication-fork stall, and arrests cell cycle at the S-to-G2 transition; however, the G1-to-S transition is constitutively active characterized by persisting DNA synthesis. Concomitantly, ubf, tif-IA, and taf1b marking rDNA transcription, Chk2, Rad51, and p53 marking DNA-damage response, and Rpa2, PCNA, Fen1, and Ttf1 marking replication fork stall are all highly elevated in bms1l mutants. We found that Bms1 interacts with Ttf1 in addition to Rc1l. Finally, we identified RFB-sites for zebrafish Ttf1 through chromatin immunoprecipitation sequencing and showed that Bms1 disassociates the Ttf1‒RFB complex with its GTPase activity. We propose that Bms1 functions to balance rDNA transcription and replication at the S-phase through interaction with Rcl1 and Ttf1, respectively. TTF1 and Bms1 together might impose an S-phase checkpoint at the rDNA loci.

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Reinoso, Elina, Silvana Dieser, Luis Calvinho, Cristina Bogni et Liliana Odierno. « Phenotyping and genotyping of streptococci in bovine milk in Argentinean dairy herds ». Acta Veterinaria Hungarica 58, n^o 3 (1 septembre 2010) : 287–95. http://dx.doi.org/10.1556/avet.58.2010.3.2.

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Most veterinary and milk hygiene laboratories identify streptococci and enterococci based on serological and biochemical tests. The analysis of 16S rDNA was suggested to be used for more exact identification; however, its use has not been considered so far in monitoring studies. The objective of the present study was to compare a conventional phenotypic method with restriction fragment length polymorphism analysis of 16S rDNA (16S rDNA RFLP) for identification of streptococci isolated from composite milk samples collected in connection with intramammary infection (IMI) in six Argentinean dairy farms. Composite milk samples (n = 1223) from cows belonging to six herds were collected for bacteriological analysis. Twelve reference strains and fifty streptococci or streptococcuslike isolates were identified to species level by the API 20 Strep system, conventional biochemical tests and 16S rDNA RFLP in a blind assay. The remaining streptococci or streptococcus-like isolates (n = 40) were identified to the species level both by 16S rDNA RFLP and conventional biochemical tests. As indicated by Kappa values, agreement between the 16S rDNA RFLP and the conventional scheme for identification ofStreptococcus agalactiae, S. dysgalactiae, S. uberis, S. equinusandEnterococcus faecaliswas 0.91, 0.73, 0.92, 0.81 and 0.85, respectively. Together with the less frequently isolated streptococcal species, the conventional scheme correctly identified 77 out of 90 isolates (85.5%). Thus, the use of 16S rDNA RFLP is considered valuable for monitoring studies due to its affordable cost for standard laboratories.

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Leitch, A. R., W. Mosgoller, M. Shi et J. S. Heslop-Harrison. « Different patterns of rDNA organization at interphase in nuclei of wheat and rye ». Journal of Cell Science 101, n^o 4 (1 avril 1992) : 751–57. http://dx.doi.org/10.1242/jcs.101.4.751.

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The physical location of the rDNA repeating units (25 S, 18 S and 5.8 S rRNA genes and the intergenic spacer sequences) was investigated in rye (Secale cereale L.) and wheat (Triticum aestivum L.) root tip meristematic cells by in situ hybridization using light and electron microscopy. The rDNA sequences are organized differently in the two related and intercrossable species. In rye (2n = 14, one pair of chromosomes with nucleolar organizing regions, NORs), two condensed blocks of rDNA-containing chromatin occurred in each interphase nucleus. The blocks were associated with the periphery of nucleoli and a single-labelled, decondensed rDNA fibre extended into the nucleolus from the block. We term this expression pattern terminal decondensation. In wheat (2n = 6x = 42, five pairs of chromosomes with NORs), inactive condensed labelled chromatin was found unassociated with nucleoli. Active NORs had some condensed rDNA associated with the nucleolar periphery, but, in contrast to rye, condensed rDNA was also found within the nucleolus. The condensed labelled rDNA in wheat nucleoli was visible as fluorescent foci in the light microscope and labelled condensed chromatin in the electron microscope. Its absence in rye shows that condensed rDNA need not be present in active plant nucleoli. Diffuse labelled sites of rDNA, likely to represent actively transcribed rDNA, were found in both rye and wheat. Active rDNA loci in wheat have many expressed segments separated by unexpressed, condensed, rDNA-fragmented decondensation-while each locus in rye has a single, unexpressed perinucleolar condensed block of rRNA genes. Thus the positions of actively transcribed genes within the tandem arrays of rDNA at each locus are fundamentally different in the two cereals. The NOR chromosome appeared to extend through the nucleolus, and active rDNA sequences did not loop out from chromatin into the nucleolus as is frequently described in nucleolar models.

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Saluja, Puja, et G. S. Prasad. « Cryptococcus rajasthanensis sp. nov., an anamorphic yeast species related to Cryptococcus laurentii, isolated from Rajasthan, India ». International Journal of Systematic and Evolutionary Microbiology 57, n^o 2 (1 février 2007) : 414–18. http://dx.doi.org/10.1099/ijs.0.64543-0.

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Two novel anamorphic yeast strains (S-15LT and 3-C1) were isolated from the inflorescences of plants collected in two different towns in Rajasthan State, India. Sequencing of the D1/D2 domains of the large-subunit (LSU) rDNA and the internal transcribed spacer (ITS) regions suggested they are strains of the same species. Phenotypic characteristics such as the absence of fermentation, the absence of sexual structures and ballistoconidia, the assimilation of myo-inositol and d-glucuronate, and positive Diazonium blue B and urease reactions indicated that these strains belong to the genus Cryptococcus. The novel strains differed from Cryptococcus laurentii in six physiological tests and differed from other related species in more than six tests. A phylogenetic analysis of the sequences of the D1/D2 domains of the LSU rDNA and the ITS regions placed these strains in the Bulleromyces clade within the order Tremellales, with C. laurentii as their closest described relative. The novel strains showed 1.6 and 7.5 % divergence in the D1/D2 domain of the LSU rDNA and ITS regions, respectively, with respect to C. laurentii. The divergence from other species was more than 3 % for the D1/D2 domain and more than 9 % for the ITS region. On the basis of the phenotypic and molecular data, strains S-15LT and 3-C1 represent a novel species within the genus Cryptococcus, for which the name Cryptococcus rajasthanensis sp. nov. is proposed. The type strain is S-15LT (=MTCC 7075T=CBS 10406T).

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VIRTUDAZO, Eric V., Hitoshi NAKAMURA et Makoto KAKISHIMA. « Phylogenetic Analysis of Sugarcane Rusts Based on Sequences of ITS, 5.8 S rDNA and D1/D2 Regions of LSU rDNA ». Journal of General Plant Pathology 67, n^o 1 (février 2001) : 28–36. http://dx.doi.org/10.1007/pl00012983.

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Sánchez-Gorostiaga, Alicia, Carlos López-Estraño, Dora B. Krimer, Jorge B. Schvartzman et Pablo Hernández. « Transcription Termination Factor reb1p Causes Two Replication Fork Barriers at Its Cognate Sites in Fission Yeast Ribosomal DNA In Vivo ». Molecular and Cellular Biology 24, n^o 1 (1 janvier 2004) : 398–406. http://dx.doi.org/10.1128/mcb.24.1.398-406.2004.

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ABSTRACT Polar replication fork barriers (RFBs) near the 3′ end of the rRNA transcriptional unit are a conserved feature of ribosomal DNA (rDNA) replication in eukaryotes. In the mouse, in vivo studies indicate that the cis-acting Sal boxes required for rRNA transcription termination are also involved in replication fork blockage. On the contrary, in the budding yeast Saccharomyces cerevisiae, the rRNA transcription termination factors are not required for RFBs. Here we characterized the rDNA RFBs in the fission yeast Schizosaccharomyces pombe. S. pombe rDNA contains three closely spaced polar replication barriers named RFB1, RFB2, and RFB3 in the 3′ to 5′ order. The transcription termination protein reb1 and its two binding sites, present at the 3′ end of the coding region, were required for fork arrest at RFB2 and RFB3 in vivo. On the other hand, fork arrest at the strongest RFB1 barrier was independent of the above transcription termination factors. Therefore, RFB2 and RFB3 resemble the barriers present in the mouse rDNA, whereas RFB1 is similar to the budding yeast RFBs. These results suggest that during evolution, cis- and trans-acting factors required for rRNA transcription termination became involved in replication fork blockage also. S. pombe is suggested to be a transitional species in which both mechanisms coexist.

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Sousa, Aretuza, Julia Bechteler, Eva M. Temsch et Susanne S. Renner. « Different from tracheophytes, liverworts commonly have mixed 35S and 5S arrays ». Annals of Botany 125, n^o 7 (17 février 2020) : 1057–64. http://dx.doi.org/10.1093/aob/mcaa027.

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Abstract Background and Aims Unlike other nuclear genes in eukaryotes, rDNA genes (5S and 35S loci) are present in numerous copies per cell and, when stained, can therefore provide basic information about genome organization. In tracheophytes (vascular plants), they are usually located on separate chromosomes, the so-called S-type organization. An analysis of 1791 species of land plants suggested that S-type arrays might be ancestral in land plants, while linked (L-type) organization may be derived. However, no outgroup and only a handful of ferns and bryophytes were included. Methods We analysed genome sizes and the distribution of telomere, 5S and 35S rDNA FISH signals in up to 12 monoicous or dioicous species of liverworts from throughout a phylogeny that includes 287 of the 386 currently recognized genera. We also used the phylogeny to plot chromosome numbers and the occurrence of visibly distinct sex chromosomes. Key Results Chromosome numbers are newly reported for the monoicous Lejeunea cavifolia and for females of the dioicous Scapania aequiloba. We detected sex-related differences in the number of rDNA signals in the dioicous Plagiochila asplenioides and Frullania dilatata. In the latter, the presence of two UU chromosomes in females and additional 5S-35S rDNA loci result in a haploid genome 0.2082 pg larger than the male genome; sex-specific genome differences in the other dioicous species were small. Four species have S-type rDNA, while five species have mixed L-S rDNA organization, and transitions may have occurred multiple times, as suggested by rDNA loci not being conserved among closely related species of Pellia. All species shared an Arabidopsis-like telomere motif, and its detection allowed verification of the chromosome number of Radula complanata and chromosome rearrangements in Aneura pinguis and P. asplenioides, the latter also showing sex-specific interstitial telomere repeats. Conclusions The S and L rDNA arrangements appear to have evolved repeatedly within liverworts, even in the same species. Evidence for differential accumulation of rDNA between the sexes so far is limited.

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Howard, Caroline, Paul Bremner, Mark Fowler, Belinda Isodo, Nigel Scott et Adrian Slater. « Molecular Identification ofHypericum perforatumby PCR Amplification of the ITS and 5.8S rDNA Region ». Planta Medica 75, n^o 08 (4 mars 2009) : 864–69. http://dx.doi.org/10.1055/s-0029-1185397.

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GRUHN, GÉRALD, PABLO ALVARADO, NILS HALLENBERG, MÉLANIE ROY et RÉGIS COURTECUISSE. « Contribution to the taxonomy of Sistotremastrum (Trechisporales, Basidiomycota) and the description of two new species, S. fibrillosum and S. aculeocrepitans ». Phytotaxa 379, n^o 1 (27 novembre 2018) : 27. http://dx.doi.org/10.11646/phytotaxa.379.1.2.

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Two new species of Sistotremastrum collected in French West Indies and French Guyana are described and illustrated. Morphological studies and molecular sequence data from two ribosomal DNA regions (ITS and 28S rDNA) support the recognition of S. fibrillosum and S. aculeocrepitans, two species characterized by their hyphal cords and basidia with 4 sterigmata.

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Reid, A. P., et W. M. Hominick. « Cloning of the rDNA repeat unit from a British entomopathogenic nematode (Steinernematidae) and its potential for species identification ». Parasitology 107, n^o 5 (décembre 1993) : 529–36. http://dx.doi.org/10.1017/s0031182000068104.

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SUMMARYThe entire ribosomal DNA repeat unit of a steinernematid species (Nashes isolate) was cloned as three separate EcoR I fragments in the plasmid pUC18. An equimolar cocktail of these three clones was used to identify Steinernema species on Southern blots as each species displays its own unique restriction fragment length polymorphisms. The clones also identified two new species isolated in a soil survey of coastal regions of Britain. One of the clones (pSn4.0) can detect length heterogeneities in the rDNA repeat unit of various isolates of some of the species, particularly the most common in the United Kingdom, S. feltiae. These differences in the rDNA repeat unit length remained constant over several years for one isolate of S. feltiae, but were different for each of the geographical isolates studied to date.

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Gromicho, Marta, Maria Manuela Coelho, Maria Judite Alves et Maria João Collares-Pereira. « Cytogenetic analysis of Anaecypris hispanica and its relationship with the paternal ancestor of the diploid-polyploid Squalius alburnoides complex ». Genome 49, n^o 12 (décembre 2006) : 1621–28. http://dx.doi.org/10.1139/g06-121.

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The karyotype of the endangered fish Anaecypris hispanica was revisited using advanced cytogenetic techniques to elucidate its putative relationship with the paternal ancestor of the hybrid complex Squalius alburnoides and to clarify some of the recently described cytogenetic patterns of the complex. The results of chromomycin A3 and Ag staining, as well as fluorescent in situ hybridization with 28S and 5S rDNA and the (TTAGGG)n telomeric probes, were compared with the patterns observed in specimens of the all-male nonhybrid lineage of S. alburnoides complex, which is considered to reconstitute the nuclear genome of the probably extinct paternal ancestor. Several cytogenetic features observed in A. hispanica specimens were indeed shared by S. alburnoides nuclear nonhybrid males, supporting the hypothesis of a close evolutionary link between A. hispanica and the paternal ancestor of the complex. The genomic rearrangements involving 28S rDNA sites previously described in the S. alburnoides complex and in its maternal ancestor ( S. pyrenaicus ) were not detected in A. hispanica; they are, therefore, probably due to mechanisms related to hybridization and polyploidy.

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Dantas, Katia Cristina, Roseli S. Freitas, Adriana Pardini Vicentini Moreira, Marcos Vinicius da Silva, Gil Benard, Cidia Vasconcellos et Paulo Ricardo Criado. « The use of nested Polymerase Chain Reaction (nested PCR) for the early diagnosis of Histoplasma capsulatum infection in serum and whole blood of HIV-positive patients* ». Anais Brasileiros de Dermatologia 88, n^o 1 (février 2013) : 141–43. http://dx.doi.org/10.1590/s0365-05962013000100025.

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The aim of the study was to detect the rDNA sequences and their regions in Histoplasma capsulatum, which could be considered species-specific and used as a molecular method for this diagnosis by the technique of nested polymerase chain reaction (nested PCR), employing specific sequences (primers) for H. capsulatum: 18S rDNA region (HC18), 100 kDa (HC100) and the sequence 5.8 S-ITS rDNA (HC5.8). The PCR sequences HC18, HC100 and HC5.8 resulted in a specificity of 100%. The molecular assays may increase the specificity, sensitivity and speed in the diagnosis of Histoplasmosis.

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Sullivan, Matt, Liam Holt et David O. Morgan. « Cyclin-Specific Control of Ribosomal DNA Segregation ». Molecular and Cellular Biology 28, n^o 17 (30 juin 2008) : 5328–36. http://dx.doi.org/10.1128/mcb.00235-08.

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ABSTRACT Following chromosome duplication in S phase of the cell cycle, the sister chromatids are linked by cohesin. At the onset of anaphase, separase cleaves cohesin and thereby initiates sister chromatid separation. Separase activation results from the destruction of its inhibitor, securin, which is triggered by a ubiquitin ligase called the anaphase-promoting complex (APC). Here, we show in budding yeast that securin destruction and, thus, separase activation are not sufficient for the efficient segregation of the repetitive ribosomal DNA (rDNA). We find that rDNA segregation also requires the APC-mediated destruction of the S-phase cyclin Clb5, an activator of the protein kinase Cdk1. Mutations that prevent Clb5 destruction are lethal and cause defects in rDNA segregation and DNA synthesis. These defects are distinct from the mitotic-exit defects caused by stabilization of the mitotic cyclin Clb2, emphasizing the importance of cyclin specificity in the regulation of late-mitotic events. Efficient rDNA segregation, both in mitosis and meiosis, also requires APC-dependent destruction of Dbf4, an activator of the protein kinase Cdc7. We speculate that the dephosphorylation of Clb5-specific Cdk1 substrates and Dbf4-Cdc7 substrates drives the resolution of rDNA in early anaphase. The coincident destruction of securin, Clb5, and Dbf4 coordinates bulk chromosome segregation with segregation of rDNA.

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Panahandeh, Yousef, Ebrahim Pourjam, Ali Roshan-Bakhsh et Majid Pedram. « First record of the genus Sakia Khan, 1964 (Nematoda : Tylenchidae) from Iran, with proposal of Sakia arboris n. sp. » Nematology 20, n^o 5 (2018) : 449–60. http://dx.doi.org/10.1163/15685411-00003150.

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Summary The genus Sakia is recorded from Iran for the first time and Sakia arboris n. sp., recovered from two geographical points in northern Iran, is described. The new species is characterised by its smooth cuticle under light microscopy (LM), absence of lateral fields, head continuous with body contour, flattened lip region, 9.3 (9.0-10.0) μm long stylet, vulva at 60.2 (59.3-61.3)%, bilobed spermatheca, 117 (102-128) μm long tail, and 14.3 (14-15) μm long spicules. By lacking lateral fields, the new species comes close to three known species of the genus, namely: S. alii, S. castori and S. indica. Molecular phylogenetic analyses using sequences of the near full-length fragment of the small subunit of ribosomal DNA (18S rDNA) and the D2-D3 expansion segments of the large subunit ribosomal DNA (28S rDNA) were performed using Bayesian inference (BI) and maximum likelihood (ML) methods. In the reconstructed Bayesian tree using the 18S rDNA sequence of the type population, the new species occupied a position in a clade including two isolates of Sakia sp. and some species of Lelenchus, with maximal BPP and high ML BS values (1.00/99%). In the reconstructed 28S rDNA phylogenetic tree, two newly sequenced isolates of S. arboris n. sp. formed a well-supported clade with Lelenchus spp.

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James, Timothy Y., Jean-Marc Moncalvo, Sean Li et Rytas Vilgalys. « Polymorphism at the Ribosomal DNA Spacers and Its Relation to Breeding Structure of the Widespread Mushroom Schizophyllum commune ». Genetics 157, n^o 1 (1 janvier 2001) : 149–61. http://dx.doi.org/10.1093/genetics/157.1.149.

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Abstract The common split-gilled mushroom Schizophyllum commune is found throughout the world on woody substrates. This study addresses the dispersal and population structure of this fungal species by studying the phylogeny and evolutionary dynamics of ribosomal DNA (rDNA) spacer regions. Extensive sampling (n = 195) of sequences of the intergenic spacer region (IGS1) revealed a large number of unique haplotypes (n = 143). The phylogeny of these IGS1 sequences revealed strong geographic patterns and supported three evolutionarily distinct lineages within the global population. The same three geographic lineages were found in phylogenetic analysis of both other rDNA spacer regions (IGS2 and ITS). However, nested clade analysis of the IGS1 phylogeny suggested the population structure of S. commune has undergone recent changes, such as a long distance colonization of western North America from Europe as well as a recent range expansion in the Caribbean. Among all spacer regions, variation in length and nucleotide sequence was observed between but not within the tandem rDNA repeats (arrays). This pattern is consistent with strong within-array and weak among-array homogenizing forces. We present evidence for the suppression of recombination between rDNA arrays on homologous chromosomes that may account for this pattern of concerted evolution.

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Junéra, H. R., C. Masson, G. Géraud, J. Suja et D. Hernandez-Verdun. « Involvement of in situ conformation of ribosomal genes and selective distribution of upstream binding factor in rRNA transcription. » Molecular Biology of the Cell 8, n^o 1 (janvier 1997) : 145–56. http://dx.doi.org/10.1091/mbc.8.1.145.

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The distribution of the ribosomal genes (rDNA) and the upstream binding factor (UBF), correlatively with their RNA transcripts, was investigated in G1, S-phase, and G2. rDNA was distributed in nucleoli, with alternate sites of clustered and dispersed genes. UBF was found associated with some but not all clustered genes and proportionally more with dispersed genes. It was distributed in several foci that were more numerous and heterogeneous in size during G2 than G1. We suggest that UBF associated with rDNA during S-phase because its nucleolar amount increased during that time and remained stable in G2. 5,6-Dichloro-1-beta-D-ribofuranosylbenzimidazole treatment indicated a similar amount of UBF per transcription unit, and consequently heterogeneous size of the UBF foci can represent a variable number of transcription units per foci. Direct visualization of the transcripts demonstrated that only part of UBF is associated with active transcription and that rDNA distribution varied with transcription. We propose that in the same rDNA locus three types of configuration coexist that are correlated with gene activity: 1) clustered genes without UBF; 2) clustered genes with UBF, of which some are associated with transcription; and 3) dispersed genes with UBF and transcription. These results support the hypothesis that rDNA transcription involved several steps of regulation acting successively and locally in the same locus to promote the repressed clustered genes to become actively transcribed dispersed genes.

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Leskinen, Elina, et Cecilia Alstr�m-Rapaport. « Molecular phylogeny ofSalicaceae and closely relatedFlacourtiaceae : Evidence from 5.8 S, ITS 1 and ITS 2 of the rDNA ». Plant Systematics and Evolution 215, n^o 1-4 (1999) : 209–27. http://dx.doi.org/10.1007/bf00984656.

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Hanssen, Felix, Niko Wischnewski, Ute Moreth et Elisabeth A. Magel. « Molecular Identification of Fitzroya Cupressoides, Sequoia Sempervirens, and Thuja Plicata Wood Using Taxon-Specific RDNA-ITS Primers ». IAWA Journal 32, n^o 2 (2011) : 273–84. http://dx.doi.org/10.1163/22941932-90000057.

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The nuclear ribosomal DNA internal transcribed spacer (rDNA-ITS) region was PCR amplified and sequenced from the wood of three specimens of Fitzroya cupressoides, nine specimens of Sequoia sempervirens, and ten specimens of Thuja plicata. The full lengths of the ITS regions are 1110 bp for F. cupressoides, 1096 bp for S. sempervirens, and 1138 bp for T. plicata, and thus in the range of 975 bp to 1125 bp which is reported for members of the Cupressaceae. Length variation of ITS regions is due to differences in the length of the spacer region ITS1. Intraspecific variations of the sequences of rDNA-ITS regions were one bp in F. cupressoides, and 18 bp in S. sempervirens and T. plicata. Based on the interspecific sequence divergence of the ITS region, taxon-specific primers were designedfor the detection of F. cupressoides, S. sempervirens and T. plicata. The primer sequences were selected from the highly divergent ITS1 spacer. The specificity of the primers was checked by lengths and sequence of the amplicons, and the primers detected the target organism, solely, across 40 conifer species. Our data establish the molecular basis for DNA-based wood identification in these species.

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Lawrimore, Josh, Daniel Kolbin, John Stanton, Muznah Khan, Solenn C. de Larminat, Colleen Lawrimore, Elaine Yeh et Kerry Bloom. « The rDNA is biomolecular condensate formed by polymer–polymer phase separation and is sequestered in the nucleolus by transcription and R-loops ». Nucleic Acids Research 49, n^o 8 (9 avril 2021) : 4586–98. http://dx.doi.org/10.1093/nar/gkab229.

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Abstract The nucleolus is the site of ribosome biosynthesis encompassing the ribosomal DNA (rDNA) locus in a phase separated state within the nucleus. In budding yeast, we find the rDNA locus and Cdc14, a protein phosphatase that co-localizes with the rDNA, behave like a condensate formed by polymer–polymer phase separation, while ribonucleoproteins behave like a condensate formed by liquid-liquid phase separation. The compaction of the rDNA and Cdc14’s nucleolar distribution are dependent on the concentration of DNA cross-linkers. In contrast, ribonucleoprotein nucleolar distribution is independent of the concentration of DNA cross-linkers and resembles droplets in vivo upon replacement of the endogenous rDNA locus with high-copy plasmids. When ribosomal RNA is transcribed from the plasmids by Pol II, the rDNA–binding proteins and ribonucleoprotein signals are weakly correlated, but upon repression of transcription, ribonucleoproteins form a single, stable droplet that excludes rDNA-binding proteins from its center. Degradation of RNA–DNA hybrid structures, known as R-loops, by overexpression of RNase H1 results in the physical exclusion of the rDNA locus from the nucleolar center. Thus, the rDNA locus is a polymer–polymer phase separated condensate that relies on transcription and physical contact with RNA transcripts to remain encapsulated within the nucleolus.

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Gong, Li, Wei Shi, Min Yang et Xiaoyu Kong. « Marked intra-genomic variation and pseudogenes in the ITS1-5.8S-ITS2 rDNA of Symphurus plagiusa (Pleuronectiformes : Cynoglossidae) ». Animal Biology 68, n^o 4 (2018) : 353–65. http://dx.doi.org/10.1163/15707563-17000134.

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Abstract The eukaryotic ribosomal DNA (rDNA) cluster consists of multiple copies of three genes (18S, 5.8S, and 28S rDNA) and two internal transcribed spacers (ITS1 and ITS2). In recent years, an increasing number of rDNA sequence polymorphisms have been identified in numerous species. In the present study, we provide 33 complete ITS (ITS1-5.8S-ITS2) sequences from two Symphurus plagiusa individuals. To the best of our knowledge, these sequences are the first detailed information on ITS sequences in Pleuronectiformes. Here, two divergent types (Type A and B) of the ITS1-5.8S-ITS2 rDNA sequence were found, which mainly differ in sequence length, GC content, nucleotide diversity (π), secondary structure and minimum free energy. The ITS1-5.8S-ITS2 rDNA sequence of Type B was speculated to be a putative pseudogene according to pseudogene identification criteria. Cluster analysis showed that sequences from the same type clustered into one group and two major groups were formed. The high degree of ITS1-5.8S-ITS2 sequence polymorphism at the intra-specific level indicated that the S. plagiusa genome has evolved in a non-concerted evolutionary manner. These results not only provide useful data for ribosomal pseudogene identification, but also further contribute to the study of rDNA evolution in teleostean genomes.

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POURSAFAR, ALIREZA, YOUBERT GHOSTA et MOHAMMAD JAVAN-NIKKHAH. « An emended description of Stemphylium amaranthi with its first record for Iran mycobiota ». Phytotaxa 371, n^o 2 (27 septembre 2018) : 93. http://dx.doi.org/10.11646/phytotaxa.371.2.3.

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Stemphylium amaranthi was originally described from the leaves of Amaranthus retroflexous in China based only on asexual morphological characteristics. New collections of S. amaranthi from wheat and barley plants with symptoms of black (sooty) head mould in Golestan and Qazvin Provinces, Iran, revealed abundant formation of a sexual morph. The morphological identification was confirmed by sequences obtained from ITS-rDNA and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genomic loci. New information on the sexual morph of S. amaranthi is provided and the species circumscription is emended. Wheat and barley are reported as new substrates for S. amaranthi, and this species is recorded for the first time in Iran.

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Carneiro, Andréa Almeida, Eliane Aparecida Gomes, Claudia Teixeira Guimarães, Fernando Tavares Fernandes, Newton Portilho Carneiro et Ivan Cruz. « Molecular characterization and pathogenicity of isolates of Beauveria spp. to fall armyworm ». Pesquisa Agropecuária Brasileira 43, n^o 4 (avril 2008) : 513–20. http://dx.doi.org/10.1590/s0100-204x2008000400010.

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The objective of this work was to evaluate the pathogenicity of 24 Beauveria isolates to Spodoptera frugiperda larvae, and characterize them molecularly through rDNA-ITS sequencing and RAPD markers. Sequencing of rDNA-ITS fragments of 570 bp allowed the identification of isolates as B. bassiana or B. brongniarti by sequence comparison to GenBank. Sixty seven polymorphic RAPD fragments were capable to differentiate 20 among 24 Beauveria isolates, grouping them according to the derived host insect and to pathogenicity against maize fall armyworm larvae. Three RAPD markers were highly associated to the pathogenicity against S. frugiperda, explaining up to 67% of the phenotypic variation. Besides identification and molecular characterization of Beauveria isolates, ITS sequence and RAPD markers proved to be very useful in selecting the isolates potentially effective against S. frugiperda larvae and in monitoring field release of these microorganisms in biocontrol programs.

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Gentile, Gabriele, Alessandra della Torre, Bertha Maegga, Jeffrey R. Powell et Adalgisa Caccone. « Genetic Differentiation in the African Malaria Vector, Anopheles gambiae s.s., and the Problem of Taxonomic Status ». Genetics 161, n^o 4 (1 août 2002) : 1561–78. http://dx.doi.org/10.1093/genetics/161.4.1561.

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Abstract Of the seven recognized species of the Anopheles gambiae complex, A. gambiae s.s. is the most widespread and most important vector of malaria. It is becoming clear that, in parts of West Africa, this nominal species is not a single panmictic unit. We found that the internal transcribed spacer (ITS) of the X-linked rDNA has two distinct sequences with three fixed nucleotide differences; we detected no heterozygotes at these three sites, even in areas of sympatry of the two ITS types. The intergenic spacer (IGS) of this region also displays two distinct sequences that are in almost complete linkage disequilibrium with the distinct ITS alleles. We have designated these two types as S/type I and M/type II. These rDNA types correspond at least partly to the previously recognized chromosomal forms. Here we expand the geographic range of sampling to 251 individuals from 38 populations. Outside of West Africa, a single rDNA type, S/type I, corresponds to the Savanna chromosomal form. In West Africa, both types are often found in a single local sample. To understand if these findings might be due to unusual behavior of the rDNA region, we sequenced the same region for 46 A. arabiensis, a sympatric sibling species. No such distinct discontinuity was observed for this species. Autosomal inversions in one chromosome arm (2R), an insecticide resistance gene on 2L, and this single X-linked region indicate at least two genetically differentiated subpopulations of A. gambiae. Yet, rather extensive studies of other regions of the genome have failed to reveal genetic discontinuity. Evidently, incomplete genetic isolation exists within this single nominal species.

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Baturo-Ciesniewska, Anna, Carol L. Groves, Kenneth A. Albrecht, Craig R. Grau, David K. Willis et Damon L. Smith. « Molecular Identification ofSclerotinia trifoliorumandSclerotinia sclerotiorumIsolates from the United States and Poland ». Plant Disease 101, n^o 1 (janvier 2017) : 192–99. http://dx.doi.org/10.1094/pdis-06-16-0896-re.

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Symptoms of clover rot caused by Sclerotinia trifoliorum or S. sclerotiorum are identical, making differentiation and identification of the causal species difficult and time consuming. Polymerase chain reaction (PCR) amplification and nucleotide sequencing were used to examine 40 isolates of S. trifoliorum (29 from Poland, 11 from the United States) and 55 isolates of S. sclerotiorum (26 from Poland, 29 from the United States). We determined that amplification of the β-tubulin and calmodulin genes with TU1/TU2/TU3 and SscadF1/SscadR1 PCR primers and the presence of introns and single-nucleotide polymorphisms (SNP) within the ribosomal DNA (rDNA) as detected with NS1/NS8 and internal transcribed spacer (ITS)1/ITS4 PCR primers are effective for rapidly and accurately differentiating between the two species of Sclerotinia. In addition, our research revealed a lack of intraspecies variation within S. sclerotiorum isolates from the United States and Poland using these same molecular markers. We detected a relatively high degree of intraspecies variability among isolates of S. trifoliorum from the United States and Poland using the presence of introns and SNP within the rDNA. SNP and nuclear small-subunit rDNA analyses revealed distinct groups of S. trifoliorum among the isolates used in this study. The results of this study provide useful information for clover breeders and pathologists looking to develop clover varieties with durable resistance.

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Komaki, Hisayuki, et Tomohiko Tamura. « Differences at Species Level and in Repertoires of Secondary Metabolite Biosynthetic Gene Clusters among Streptomyces coelicolor A3(2) and Type Strains of S. coelicolor and Its Taxonomic Neighbors ». Applied Microbiology 1, n^o 3 (18 novembre 2021) : 573–85. http://dx.doi.org/10.3390/applmicrobiol1030037.

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Streptomyces coelicolor A3(2) is used worldwide for genetic studies, and its complete genome sequence was published in 2002. However, as the whole genome of the type strain of S. coelicolor has not been analyzed, the relationship between S. coelicolor A3(2) and the type strain is not yet well known. To clarify differences in their biosynthetic potential, as well as their taxonomic positions, we sequenced whole genomes of S. coelicolor NBRC 12854T and type strains of its closely related species—such as Streptomyces daghestanicus, Streptomyces hydrogenans, and Streptomyces violascens—via PacBio. Biosynthetic gene clusters for polyketides and non-ribosomal peptides were surveyed by antiSMASH, followed by bioinformatic analyses. Type strains of Streptomyces albidoflavus, S. coelicolor, S. daghestanicus, S. hydrogenans, and S. violascens shared the same 16S rDNA sequence, but S. coelicolor A3(2) did not. S. coelicolor A3(2) and S. coelicolor NBRC 12854T can be classified as Streptomycesanthocyanicus and S. albidoflavus, respectively. In contrast, S. daghestanicus, S. hydrogenans, and S. violascens are independent species, despite their identical 16S rDNA sequences. S. coelicolor A3(2), S. coelicolor NBRC 12854T, S. daghestanicus NBRC 12762T, S. hydrogenans NBRC 13475T, and S. violascens NBRC 12920T each harbor specific polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters in their genomes, whereas PKS and NRPS gene clusters are well conserved between S. coelicolor A3(2) and S. anthocyanicus JCM 5058T, and between S. coelicolor NBRC 12854T and S. albidoflavus DSM 40455T, belonging to the same species. These results support our hypothesis that the repertoires of PKS and NRPS gene clusters are different between different species.

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Chakrabarti, Rajarshi, Sulagna Sanyal, Amit Ghosh, Kaushik Bhar, Chandrima Das et Anirban Siddhanta. « Phosphatidylinositol-4-phosphate 5-Kinase 1α Modulates Ribosomal RNA Gene Silencing through Its Interaction with Histone H3 Lysine 9 Trimethylation and Heterochromatin Protein HP1-α ». Journal of Biological Chemistry 290, n^o 34 (7 juillet 2015) : 20893–903. http://dx.doi.org/10.1074/jbc.m114.633727.

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Phosphoinositide signaling has been implicated in the regulation of numerous cellular processes including cytoskeletal dynamics, cellular motility, vesicle trafficking, and gene transcription. Studies have also shown that nuclear phosphoinositide(s) regulates processes such as mRNA export, cell cycle progression, gene transcription, and DNA repair. We have shown previously that the nuclear form of phosphatidylinositol-4-phosphate 5-kinase 1α (PIP5K), the enzyme responsible for phosphatidylinositol 4,5-bisphosphate synthesis, is modified by small ubiquitin-like modifier (SUMO)-1. In this study, we have shown that due to the site-specific Lys to Ala mutations of PIP5K at Lys-244 and Lys-490, it is unable to localize in the nucleus and nucleolus, respectively. Furthermore, by using chromatin immunoprecipitation assays, we have observed that PIP5K associates with the chromatin silencing complex constituted of H3K9me3 and heterochromatin protein 1α at multiple ribosomal DNA (rDNA) loci. These interactions followed a definite cyclical pattern of occupancy (mostly G1) and release from the rDNA loci (G1/S) throughout the cell cycle. Moreover, the immunoprecipitation results clearly demonstrate that PIP5K SUMOylated at Lys-490 interacts with components of the chromatin silencing machinery, H3K9me3 and heterochromatin protein 1α. However, PIP5K does not interact with the gene activation signature protein H3K4me3. This study, for the first time, demonstrates that PIP5K, an enzyme actively associated with lipid modification pathway, has additional roles in rDNA silencing.

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Gnutikov, Alexander A., Nikolai N. Nosov, Tatiana M. Koroleva, Elizaveta O. Punina, Nina S. Probatova, Victoria S. Shneyer et Alexander V. Rodionov. « Origin of the Rare Hybrid Genus ×Trisetokoeleria Tzvelev (Poaceae) According to Molecular Phylogenetic Data ». Plants 11, n^o 24 (15 décembre 2022) : 3533. http://dx.doi.org/10.3390/plants11243533.

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In our article, we analyzed new data on the origin of the hybrid genus ×Trisetokoeleria. According to the morphological criteria ×T. jurtzevii is a hybrid between Koeleria asiatica s. l. and Trisetum spicatum, ×T. taimyrica, and originated from Koeleria asiatica s. l. and Trisetum subalpestre, ×T. gorodkowii, a hybrid between Koeleria asiatica and Trisetum ruprechtianum. Later ×T. taimyrica was transferred to Koeleria. Parental taxa are prone to active hybridization themselves, thus, new methods of next-generation sequencing (NGS) were needed to clarify the relationships of these genera. For NGS we used the fragment 18S rDNA (part)–ITS1–5.8S rDNA (totally 441 accessions). We analyzed ITS1–5.8S rDNA–ITS2 region, trnL–trnF and trnK–rps16 from eight samples of the five species, using the Sanger method: ×Trisetokoeleria jurtzevii, ×T. taimyrica, Koeleria asiatica, Sibirotrisetum sibiricum (=Trisetum sibiricum), and Trisetum spicatum. We also studied the pollen fertility of ×Trisetokoeleria and its possible progenitors. Our data partly contradicted previous assumptions, based on morphological grounds, and showed us a picture of developed introgression within and between Koeleria and Trisetum. ×T. jurtzevii, a totally sterile hybrid formed rather recently. We can suppose that ×T. jurtzevii is a hybrid between K. asiatica and some Trisetum s. str. Species, but not T. spicatum. ×T. gorodkowii, a hybrid in the stage of primary stabilization; it has one unique ribotype related to T. spicatum s. l. The second parental species is unrelated to Trisetum ruprechtianum. ×T. taimyrica and is a stabilized hybrid species; it shares major ribotypes with the T. spicatum/T. wrangelense group and has a minor fraction of rDNA related to genus Deyeuxia s. l.

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CLAUSI, MIRELLA, DIEGO LEONE et SERGEI E. SPIRIDONOV. « HAPLOTYPE DIVERSITY OF STEINERNEMA FELTIAE (NEMATODA : STEINERNEMATIDAE) IN EURASIA ». Redia 103 (1 décembre 2020) : 133–36. http://dx.doi.org/10.19263/redia-103.20.21.

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Phylogenetic analysis of ITS rDNA sequences of the entomopathogenic nematode Steinernema feltiae Filipjev, 1934 (Wouts, Mráček, Gerdin and Bedding, 1982) was used to infer intraspecific genetic variability of this rhabditid nematode. Nucleotide intraspecific differences among S. feltiae isolates reached the level of 19 base pairs per ITS rDNA region, i.e. up to 2.9%. Several weakly or moderately supported intraspecific clades were detected. Sicilian and Swiss isolates of S. feltiae were found clustering together. Swiss strain ‘St. Bernard’ has been isolated on the St. Bernardino mountain pass in Switzerland in 2000. Phylogenetic relationships among S. feltiae isolates were inferred by using three different methods (maximum parsimony, neighbor joining and maximum likelihood). The topologies of the phylogenetic trees were identical and thus only ML tree is presented. ML tree revealed that S. feltiae isolates from Israel and Armenia grouped at the basal position of the tree, while in the spanning network obtained with POPART software, Iranian and Ukrainian isolates were the closest to the outgroup. In all methods of analyses, the European and Siberian strains of S. feltiae occupied terminal positions. Thus, further studies on the intraspecific genetic variability of entomopathogenic nematodes is needed.

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Moya, Patricia, Pavel Škaloud, Salvador Chiva, Francisco J. García-Breijo, José Reig-Armiñana, Lucie Vančurová et Eva Barreno. « Molecular phylogeny and ultrastructure of the lichen microalga Asterochloris mediterranea sp. nov. from Mediterranean and Canary Islands ecosystems ». International Journal of Systematic and Evolutionary Microbiology 65, Pt_6 (1 juin 2015) : 1838–54. http://dx.doi.org/10.1099/ijs.0.000185.

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The microalgae of the genus Asterochloris are the preferential phycobionts in Cladonia, Lepraria and Stereocaulon lichens. Recent studies have highlighted the hidden diversity of the genus, even though phycobionts hosting species of the genus Cladonia in Mediterranean and Canarian ecosystems have been poorly explored. Phylogenetic analyses were made by concatenation of the sequences obtained with a plastid – LSU rDNA – and two nuclear – internal transcribed spacer (ITS) rDNA and actin – molecular markers of the phycobionts living in several populations of the Cladonia convoluta-Cladonia foliacea complex, Cladonia rangiformis and Cladonia cervicornis s. str. widely distributed in these areas in a great variety of substrata and habitats. A new strongly supported clade was obtained in relation to the previously published Asterochloris phylogenies. Minimum genetic variation was detected between our haplotypes and other sequences available in the GenBank database. The correct identification of the fungal partners was corroborated by the ITS rDNA barcode. In this study we provide a detailed characterization comprising chloroplast morphology, and ultrastructural and phylogenetic analyses of a novel phycobiont species, here described as Asterochloris mediterranea sp. nov. Barreno, Chiva, Moya et Škaloud. A cryopreserved holotype specimen has been deposited in the Culture Collection of Algae of Charles University in Prague, Czech Republic (CAUP) as CAUP H 1015. We suggest the use of a combination of several nuclear and plastid molecular markers, as well as ultrastructural (transmission electron and confocal microscopy) techniques, both in culture and in the symbiotic state, to improve novel species delimitation of phycobionts in lichens.

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López-Núñez, Juan Carlos, Kathryn Plichta, Carmenza E. Góngora-Botero et S. Patricia Stock. « A new entomopathogenic nematode, Steinernema colombiense n. sp. (Nematoda : Steinernematidae), from Colombia ». Nematology 10, n^o 4 (2008) : 561–74. http://dx.doi.org/10.1163/156854108784513879.

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Abstract A new entomopathogenic nematode, Steinernema colombiense n. sp., is described from Colombia. Morphological, molecular (28S and ITS rDNA sequence data) and cross-hybridisation studies were used for diagnostics and identification purposes. In addition, 28S and ITS rDNA sequence data were used to assess evolutionary relationships of the new species with other Steinernema spp. Morphological diagnostic features for S. colombiense n. sp. include morphometric features of the third-stage infective juvenile, including body length of 636 (549-732) μm, narrow body diam. (31 (22-36) μm), position of the excretory pore (35 (31-40) μm), tail length (41 (32-53) μm), D% = 29 (25-33) and E% = 205 (138-284). In addition, males of first and second generations are characterised by the morphology of the spicules and gubernaculum, the number and arrangement of the genital papillae and the excretory pore position (at 67 (56-76) and 54 (46-63) μm, for first and second generations, respectively). In addition to these traits, 28S and ITS rDNA sequences analyses both showed this species to be a distinct and unique entity.

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Qiu, J. H., Y. Lou, Y. Zhang, Q. C. Chang, Z. X. Liu, H. Duan, D. H. Guo, D. Z. Gao, D. M. Yue et C. R. Wang. « Sequence variability in internal transcribed spacers of nuclear ribosomal DNA among isolates of the oxyurid nematodes Syphacia obvelata and Aspiculuris tetraptera from mice reared in laboratories in China ». Journal of Helminthology 90, n^o 1 (9 janvier 2015) : 81–85. http://dx.doi.org/10.1017/s0022149x1400087x.

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AbstractThis study examined sequence variability in internal transcribed spacers (ITS) of nuclear ribosomal DNA among Syphacia obvelata and Aspiculuris tetraptera isolates from laboratory mice from different geographical locations in China. ITS1, 5.8S and ITS2 rDNA were amplified separately from adult S. obvelata and A. tetraptera individuals by polymerase chain reaction (PCR), and the amplicons were subjected to sequencing from both directions. The lengths of the sequences of ITS1, 5.8S and ITS2 rDNA from both nematodes were 314 bp and 456 bp, 157 bp, and 273 bp and 419 bp, respectively. The intraspecific sequence variations in S. obvelata ITS1 were 0–0.3%. For A. tetraptera they were 0–0.7% in ITS1 and 0–1.0% in ITS2. However, the interspecific sequence differences among members of the infraorder Oxyuridomorpha were significantly higher, being 54.0–65.5% for ITS1 and 55.3–64.1% for ITS2. Phylogenetic analysis based on the combined partial sequences of ITS1 and ITS2 using three inference methods – Bayesian inference, maximum likelihood and maximum parsimony – revealed that all the S. obvelata and A. tetraptera samples formed independent monophyletic groups. Syphacia obvelata was closer to Syphacia muris than to A. tetraptera, consistent with morphological classification. These results demonstrate that ITS1 and ITS2 rDNA sequences are useful markers for population genetic studies of oxyurid nematodes.

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Schmidt, Olaf, et Ute Moreth. « Identification of the Dry Rot Fungus, Serpula lacrymans, and the Wild Merulius, S. himantioides, by Amplified Ribosomal DNA Restriction Analysis (ARDRA) ». Holzforschung 53, n^o 2 (1 mars 1999) : 123–28. http://dx.doi.org/10.1515/hf.1999.020.

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SummaryIsolates of the dry rot fungus,Serpula lacrymans, and of the morphologically similar wild merulius,S. himantioides, were investigated by amplified ribosomal DNA restriction analysis (ARDRA) of the internal transcribed spacer (ITS) region to prove this method as diagnosis tool for the economically important indoor rot fungi. The technique uses the polymerase chain reaction (PCR) to amplify the relatively variable sequences of the ITS region arranged between the highly conserved portions of the 18S and 28S RNA genes of the nuclear ribosomal DNA (rDNA) repeat unit. Subsequent digestion of the amplicon with restriction endonucleases may exhibit differences at species and subspecies level. Using the universal ITS 1/ITS 4 primer combination, the ITS region of all isolates ofS. lacrymansandS. himantioideswas amplified. The size of the amplified products was about 630bp in both species, as estimated from agarose gel electrophoresis. Digestion of the amplicon with the endonuclease pairsAluI/HhaI andAvaII/MboII, respectively, revealed identical rDNA-ITS fragments for the isolates of both species, indicating their genetic relationship. On the other hand, digestion withBglI/HinfI andHaeIII/TaqI, respectively, separated the fungi by means of different fragment patterns. Thus, ARDRA-ITS proved to be suited for the identification of both fungi.

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Spiridonov, Sergei, Dieter Sturhan et Zdeněk Mráček. « Steinernema silvaticum sp. n. (Rhabditida : Steinernematidae), a new entomopathogenic nematode from Europe ». Nematology 7, n^o 2 (2005) : 227–41. http://dx.doi.org/10.1163/1568541054879629.

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AbstractSteinernema silvaticum sp. n. is described from woodland soil near Berlin, Germany. The species is quite common in European woodlands, being found in forest soil all over Germany, in Belgium, the Czech Republic, The Netherlands, Sweden and the UK. It was previously reported as Steinernema sp. 'B' in Germany and the Czech Republic, and as Steinernema sp. 'B3' in UK, Belgian and Dutch surveys. Third-stage infective juveniles are mainly characterised by a straight body of medium length (means = 700–900 μm), lateral fields with eight equal ridges (with appearance of nine parallel, equally spaced lines under light microscope), rather broad, flatly rounded and continuous cephalic region, excretory pore at level of mid-pharynx and average hyaline tail portion constituting ca half total tail length; males with mucronate tail, yellowish spicules of ca 50 μm length and wide manubria; females with short conoid tail with pointed non-mucronate tip. According to the ITS rDNA sequences, S. silvaticum sp. n. belongs to the 'feltiae-kraussei-oregonense' group of Steinernema species, although it is closest to S. kraussei. The new species shows a high level of nucleotide differences in ITS rDNA sequences from other steinernematid species and can be easily distinguished from S. kraussei, S. feltiae, S. oregonense, S. weiseri and S. jollieti by morphological characters of the infective juveniles and males.

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Nakayama, Celeste Mutuko, Eliana Feldberg et Luiz Antonio Carlos Bertollo. « Karyotype differentiation and cytotaxonomic considerations in species of Serrasalmidae (Characiformes) from the Amazon basin ». Neotropical Ichthyology 10, n^o 1 (2012) : 53–58. http://dx.doi.org/10.1590/s1679-62252012000100005.

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Six species of Serrasalmidae from the central Amazon, representatives of the genera Serrasalmus (S. elongatus, S. maculatus, S. cf. rhombeus, and S. rhombeus), Pygocentrus (P. nattereri), and Colossoma (C. macropomum), were analyzed regarding the distribution of the Ag-NORs, C-positive heterochromatin and 18S and 5S rRNA genes on the chromosomes. All specimens had 2n = 60 chromosomes, except S. cf. rhombeus, with 2n = 58, and C. macropomum with 2n = 54 chromosomes. The Ag-NORs were multiple and located on the short arms of subtelo-acrocentric chromosomes in all Serrasalmus species and in P. nattereri, but were found on metacentric chromosomes in C. macropomum. The 18S rDNA sites were usually coincident with Ag-NORs, although some species had a higher number and/or a distinct localization of these sites. C-positive heterochromatin was preferentially situated in centromeric regions, remarkably on metacentric pair number 7 in all Serrasalmus species and number 3 in P. nattereri, which beared a conspicuous proximal C-band on the long arms. The 5S rDNA sites were detected in a single chromosomal pair in all species. In Serrasalmus and P. nattereri, this pair was the number 7 and 3, respectively, thereby revealing its co-localization with the conspicuous heterochromatic band. However, in C. macropomum, only one homologue (probably belonging to pair number 12) exhibited 5S rDNA sites on the short arms, close to the centromere. The present data revealed reliable cytotaxonomic markers, enabling the evaluation of karyotype differentiation and interrelationships among Serrasalmidae, as well as the probable occurrence of a species complex in S. rhombeus.

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Ki, Jang-Seu, Dae-Sik Hwang, Kyoungsoon Shin, Won Duk Yoon, Donghyun Lim, Young Shil Kang, Yoon Lee et Jae-Seong Lee. « Recent moon jelly (Aurelia sp.1) blooms in Korean coastal waters suggest global expansion : examples inferred from mitochondrial COI and nuclear ITS-5.8S rDNA sequences ». ICES Journal of Marine Science 65, n^o 3 (11 mars 2008) : 443–52. http://dx.doi.org/10.1093/icesjms/fsn018.

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AbstractKi, J-S., Hwang, D-S., Shin, K., Yoon, W. D., Lim, D., Kang, Y. S., Lee, Y., and Lee, J-S. 2008. Recent moon jelly (Aurelia sp.1) blooms in Korean coastal waters suggest global expansion: examples inferred from mitochondrial COI and nuclear ITS-5.8S rDNA sequences. – ICES Journal of Marine Science, 65: 443–452. The moon jelly Aurelia was found recently in Korean coastal environments, and its dense blooms caused economic losses for fisheries and power plants. The species is tentatively recognized as Aurelia aurita; yet, its identity and origin remain elusive. To find reliable molecular evidence for its identity, we determined the DNA sequence of the mitochondrial cytochrome c oxidase subunit I gene and nuclear ITS-5.8S rDNA of specimens collected from different Korean locations. We compared the nuclear and mitochondrial DNA data among specimens and demonstrated that all Korean Aurelia have an identical genotype. BLAST searches demonstrated that the Korean Aurelia matched the previously designated Aurelia sp.1. Parsimony and relevant phylogenetic analyses of the genus Aurelia demonstrated that the genotypes of Korean, Japanese, and Californian Aurelia sp.1 were nearly identical (>99.6% similarity), whereas they were significantly different (<84.1% similarity) from other Aurelia. This suggests that Aurelia sp.1, which occur in the three regions, are descendants of a single population and may have dispersed from one location. However, the dispersal time and origin of Aurelia sp.1 still remain uncertain.

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Ashrafi, Kaveh, Stephen S. Lin, Jill K. Manchester et Jeffrey I. Gordon. « Sip2p and its partner Snf1p kinase affect aging in S. cerevisiae ». Genes & ; Development 14, n^o 15 (1 août 2000) : 1872–85. http://dx.doi.org/10.1101/gad.14.15.1872.

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For a number of organisms, the ability to withstand periods of nutrient deprivation correlates directly with lifespan. However, the underlying molecular mechanisms are poorly understood. We show that deletion of the N-myristoylprotein, Sip2p, reduces resistance to nutrient deprivation and shortens lifespan in Saccharomyces cerevisiae. This reduced lifespan is due to accelerated aging, as defined by loss of silencing from telomeres and mating loci, nucleolar fragmentation, and accumulation of extrachromosomal rDNA. Genetic studies indicate that sip2Δ produces its effect on aging by increasing the activity of Snf1p, a serine/threonine kinase involved in regulating global cellular responses to glucose starvation. Biochemical analyses reveal that as yeast age, hexokinase activity increases as does cellular ATP and NAD+ content. The change in glucose metabolism represents a new correlate of aging in yeast and occurs to a greater degree, and at earlier generational ages in sip2Δ cells. Sip2p and Snf1p provide new molecular links between the regulation of cellular energy utilization and aging.

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Koppenhöfer, Albrecht, et S. Patricia Stock. « Steinernema scarabaei n. sp. (Rhabditida : Steinernematidae), a natural pathogen of scarab beetle larvae (Coleoptera : Scarabaeidae) from New Jersey, USA ». Nematology 5, n^o 2 (2003) : 191–204. http://dx.doi.org/10.1163/156854103767139680.

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AbstractSteinernema scarabaei n. sp. (Rhabditida: Steinernematidae) is a new entomopathogenic nematode isolated from larvae of the scarab beetles Anomala(= Exomala)orientalis and Popillia japonica from turfgrass in New Jersey, USA. Morphology, hybridisation and molecular studies indicated the distinctness of S. scarabaei n. sp. from other Steinernema spp. Distinctive diagnostic characters include: the presence of a mucronated tail in both first generation adults; the presence of a ventrally bifurcated mucro in the first generation female tail; the size and shape of the spicules and gubernaculum and the arrangement of the genital papillae of the male; third-stage infective juvenile with total body length of 890-959 μm and lateral field with eight longitudinal ridges. RFLP analysis of the ITS region of rDNA showed S. scarabaei n. sp. to be distinct from 50 other Steinernema species and isolates. In addition, phylogenetic interpretation of sequence data from the LSU of rDNA provided further evidence for autapomorphies and separate species status for S. scarabaei n. sp.

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Zouhar, M., M. Marek, J. Lucinio et P. Ryšánek. « Using point mutations in rDNA for differentiation of bioraces of Ditylenchus dipsaci from the Czech Republic ». Plant Protection Science 38, SI 2 - 6th Conf EFPP 2002 (31 décembre 2017) : 358–60. http://dx.doi.org/10.17221/10490-pps.

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Ditylenchus dipsaci is one of the most harmful parasitic nematodes in Central Europe. It is able to survive for long time in soil without its host plants and that is why it belongs to organisms with quarantine importance. Nothing is known about D. dipsaci distribution in the Czech Republic. The aim of the study was to collect samples of D. dipsaci from the Czech Republic and to identify them by molecular methods. Region of rDNA including 3'end of 18 S gene, ITS1, 5,8 S gene, ITS2 and 5'end of 26 S gene was amplified using general primers designed according to the DNA sequence of Caenorhabditis elegans. The amplicon (900 bp) was analyzed by RFLP and SSCP. Restriction endonucleases Eco R1, Hinc II and Alu 1 can be used for differentiation of certain bioraces of D. dipsaci. At the same time methods for DNA extraction from plant material and contaminated soil were optimized.

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Kim, Seung-Chul, Christina T. Lu et Brendan J. Lepschi. « Phylogenetic positions of Actites megalocarpa and Sonchus hydrophilus (Sonchinae : Asteraceae) based on ITS and chloroplast non-coding DNA sequences ». Australian Systematic Botany 17, n^o 1 (2004) : 73. http://dx.doi.org/10.1071/sb03019.

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Phylogenetic positions of the Australian endemic taxa Actites megalocarpa and Sonchus hydrophilus within the subtribe Sonchinae were determined on the basis of ITS sequences of nuclear rDNA and the psbA–trnH(GUG) intergenic spacer of chloroplast DNA. Both ITS and cpDNA phylogenies suggest that the monotypic genus Actites is not closely related to the members of Sonchus section Asperi, as previously suggested. Rather, this study indicates that it is more closely related to the members of Sonchus sections Maritimi (S.�maritimus) and Arvenses (S. arvensis). It also suggests that S. maritimus from section Maritimi is one of the closest relatives of Actites in Australia, although an alternative origin from section Arvenses is possible. Actites and Embergeria, once treated as congeneric taxa, appear to have originated independently in Australia and New Zealand, respectively. Sonchus hydrophilus is closely related to the S. asper complex, S. oleraceus and S. kirkii. This study suggests that S. kirkii may be involved in the origin of S. hydrophilus in Australia.

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