Relevant bibliographies by topics / Mitogenomes

Academic literature on the topic 'Mitogenomes'

Author: Grafiati
Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Mitogenomes"

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Burzyński, Artur, and Marianna Soroka. "Complete paternally inherited mitogenomes of two freshwater mussels Unio pictorum and Sinanodonta woodiana (Bivalvia: Unionidae)." PeerJ 6 (September 11, 2018): e5573. http://dx.doi.org/10.7717/peerj.5573.

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Freshwater bivalves from the family Unionidae usually have two very divergent mitogenomes, inherited according to the doubly uniparental model. The early divergence of these two mitogenomic lineages gives a unique opportunity to use two mitogenomic data sets in a single phylogenetic context. However, the number of complete sequences of the maternally inherited mitogenomes of these animals available in GenBank greatly exceeds that of the paternally inherited mitogenomes. This is a problem for phylogenetic reconstruction because it limits the use of both mitogenomic data sets. Moreover, since long branch attraction phenomenon can bias reconstructions if only a few but highly divergent taxa are considered, the shortage of the faster evolving paternally inherited mitogenome sequences is a real problem. Here we provide, for the first time, complete sequences of the M mitogenomes sampled from Polish populations of two species: native Unio pictorum and invasive Sinanodonta woodiana. It increases the available set of mitogenomic pairs to 18 species per family, and allows unambiguous reconstruction of phylogenetic relationships among them. The reconstructions based on M and F mitogenomes which were separated for many millions of years, and subject to differing evolutionary dynamics, are fully congruent.
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Li, Shu-Yi, Yan-Min Zhao, Bing-Xin Guo, Chen-Hong Li, Bing-Jiao Sun, and Xiao-Long Lin. "Comparative Analysis of Mitogenomes of Chironomus (Diptera: Chironomidae)." Insects 13, no. 12 (December 16, 2022): 1164. http://dx.doi.org/10.3390/insects13121164.

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(1) Background: Chironomids are biological indicators, playing an important role in monitoring and assessing the changes in water ecosystems. Mitochondrial genomes have been widely applied as a molecular marker to analyze the taxonomy and phylogeny of insects. However, knowledge of the mitogenomes of Chironomus species is scarce at present, which limits our understanding of the evolutionary relationships among Chironomus. (2) Methods: In our study, the mitogenomes and their basic structure of 12 Chironomus species and one Microchironomus species were newly sequenced. Combined with reported mitogenomes, a total of 15 mitogenomes of Chironomus were selected for a comparative mitogenomic analysis and phylogenetic reconstruction of Chironomus. (3) Results: Each mitogenome of the Chironomus species has the typical 37 genes and a control region. The basic structure of the whole mitogenomes of Chironomus species is relatively conservative, and the genetic arrangements stay the same as the ancestral mitogenome. (4) Conclusions: Our study enriches the library of mitogenomes of chironomids and provides a valuable resource for understanding the evolutionary history of Chironomus.
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Yang, Chao, Xiaojuan Du, Yuxin Liu, Hao Yuan, Qingxiong Wang, Xiang Hou, Huisheng Gong, et al. "Comparative mitogenomics of the genus Motacilla (Aves, Passeriformes) and its phylogenetic implications." ZooKeys 1109 (July 1, 2022): 49–65. http://dx.doi.org/10.3897/zookeys.1109.81125.

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The genus Motacilla belongs to Motacillidae (Passeriformes), where mitochondrial features are poorly understood and phylogeny is controversial. Whole mitochondrial genome (mitogenome) data and large taxon sampling are considered to be ideal strategies to obtain this information. We generated four complete mitogenomes of M. flava, M. cinerea, M. alba and Dendronanthus indicus, and made comparative analyses of Motacilla species combined with mitogenome data from GenBank, and then reconstructed phylogenetic trees based on 37 mitochondrial genes. The mitogenomes of four mitogenome sequences exhibited the same gene order observed in most Passeriformes species. Comparative analyses were performed among all six sampled Motacilla mitogenomes. The complete mitogenomes showed A-skew and C-skew. Most protein-coding genes (PCGs) start with an ATG codon and terminate with a TAA codon. The secondary structures of RNAs were similar among Motacilla and Dendronanthus. All tRNAs except for trnS(agy) could be folded into classic clover-leaf structures. Three domains and several conserved boxes were detected. Phylogenetic analysis of 90 mitogenomes of Passeriformes using maximum likelihood (ML) and Bayesian inference (BI) revealed that Motacilla was a monophyletic group. Among Motacilla species, M. flava and M. tschutschensis showed closer relationships, and M. cinerea was located in a basal position within Motacilla. These data provide important information for better understanding the mitogenomic characteristics and phylogeny of Motacilla.
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Miao, Yujing, Haimei Chen, Wanqi Xu, Chang Liu, and Linfang Huang. "Cistanche Species Mitogenomes Suggest Diversity and Complexity in Lamiales-Order Mitogenomes." Genes 13, no. 10 (October 4, 2022): 1791. http://dx.doi.org/10.3390/genes13101791.

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The extreme diversity and complexity of angiosperms is well known. Despite the fact that parasitic plants are angiosperms, little is known about parasitic plant mitogenomic diversity, complexity, and evolution. In this study, we obtained and characterized the mitogenomes of three Cistanche species (holoparasitic plants) from China to compare the repeats, segment duplication and multi-copy protein-coding genes (PCGs), to clarify the phylogenetic and evolution relationship within the Lamiales order, and to identify the mitochondrial plastid insertions (MTPT) in Cistanche mitogenomes. The results showed that the mitogenome sizes of the three Cistanche species ranged from 1,708,661 to 3,978,341 bp. The Cistanche species genome encodes 75–126 genes, including 37–65 PCGs, 31–58 tRNA genes and 3–5 rRNA genes. Compared with other Lamiales and parasitic species, the Cistanche species showed extremely high rates of multi-copy PCGs, ranging from 0.13 to 0.58 percent of the total number of PCGs. In addition, 37–133 Simple Sequence Repeat (SSRs) were found in these three mitogenomes, the majority of which were the mononucleotides Adenine/Thymine. The interspersed repeats contained forward and palindromic repeats. Furthermore, the segment-duplication sequence size ranged from 199,584 to 2,142,551 bp, accounting for 24.9%, 11.7% and 53.9% of the Cistanche deserticola, Cistanche salsa and Cistanche tubulosa mitogenome, respectively. Furthermore, the Ka/Ks analysis suggested that the atp4, ccmB, ccmFc and matR were probably positively selected during Lamiales evolution. The Cistanche plastome suggested the presence of MTPT. Moreover, 6–12 tRNA, 9–15 PCGs fragments and 3 rRNA gene fragments in the Cistanche mitogenomes were found in the MTPT regions. This work reports the Cistanche species mitogenome for the first time, which will be invaluable for study the mitogenome evolution of Orobanchaceae family.
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Ma, Yan, and Ying Miao. "Mitogenomic Comparison of the Mole Crickets Gryllotalpidae with the Phylogenetic Implications (Orthoptera: Ensifera)." Insects 13, no. 10 (October 11, 2022): 919. http://dx.doi.org/10.3390/insects13100919.

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Owing to limited molecular data, the phylogenetic position of the family Gryllotalpidae is still controversial in the infraorder Gryllidea. Mitochondrial genome (mitogenome) plays a crucial role in reconstructing phylogenetic relationships and revealing the molecular evolution of insects. However, only four mitogenomes have been reported in Gryllotalpidae to date. Herein, we obtained the first mitogenomes of Gryllotalpa henana Cai & Niu, 1998 and the Chinese G. orientalis Burmeister, 1838, made a detailed comparison of all mitogenomes available in Gryllotalpidae and reconstructed the phylogeny of Gryllidea based on mitogenomes using Bayesian inference (BI) and maximum likelihood (ML) methods. The results show that the complete mitogenome sequences of G. henana (15,504 bp) and G. orientalis (15,497 bp) are conserved, both exhibiting the double-stranded circular structure, typical gene content and the ancestral insect gene arrangement. The complete mitogenome of G.henana exhibits the lowest average AT content ever detected in Gryllotalpidae, and even Gryllidea. The gene nad2 of both species has atypical initiation codon GTG. All tRNAs exhibit typical clover-leaf structure, except for trnS1 lacking the dihydrouridine (DHU) arm. A potential stem–loop structure, containing a (T)n(TC)2(T)n sequence, is detected in the control region of all gryllotalpids investigated and is likely related to the replication initiation of the minority strand. The phylogenetic analyses recover the six families of Gryllidea as Gryllotalpidae + (Myrmecophilidae + (Mogoplistidae + (Trigonidiidae + (Phalangopsidae + Gryllidae)))), similar to the trees based on transcriptomic and mitogenomic data. However, the trees are slightly different from the multilocus phylogenies, which show the sister-group relationship of Gryllotalpidae and Myrmecophilidae. The contradictions between mitogenomic and multilocus trees are briefly discussed.
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Yang, Mingsheng, Bingyi Hu, Lin Zhou, Xiaomeng Liu, Yuxia Shi, Lu Song, Yunshan Wei, and Jinfeng Cao. "First mitochondrial genome from Yponomeutidae (Lepidoptera, Yponomeutoidea) and the phylogenetic analysis for Lepidoptera." ZooKeys 879 (October 9, 2019): 137–56. http://dx.doi.org/10.3897/zookeys.879.35101.

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The complete mitochondrial genome (mitogenome) of Yponomeuta montanatus is sequenced and compared with other published yponomeutoid mitogenomes. The mitogenome is circular, 15,349 bp long, and includes the typical metazoan mitochondrial genes (13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes) and an A + T-rich region. All 13 protein-coding genes use a typical start codon ATN, the one exception being cox1, which uses CGA across yponomeutoid mitogenomes. Comparative analyses further show that the secondary structures of tRNAs are conserved, including loss of the Dihydorouidine (DHU) arm in trnS1 (AGN), but remarkable nucleotide variation has occurred mainly in the DHU arms and pseudouridine (TψC) loops. A + T-rich regions exhibit substantial length variation among yponomeutoid mitogenomes, and conserved sequence blocks are recognized but some of them are not present in all species. Multiple phylogenetic analyses confirm the position of Y. montanatus in Yponomeutoidea. However, the superfamily-level relationships in the Macroheterocera clade in Lepidoptera recovered herein show considerable difference with that recovered in previous mitogenomic studies, raising the necessity of extensive phylogenetic investigation when more mitogenomes become available for this clade.
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Sinn, Brandon T., and Craig F. Barrett. "Ancient Mitochondrial Gene Transfer between Fungi and the Orchids." Molecular Biology and Evolution 37, no. 1 (August 29, 2019): 44–57. http://dx.doi.org/10.1093/molbev/msz198.

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Abstract The mitochondrial genomes (mitogenomes) of plants are known to incorporate and accumulate DNA from intra- and extracellular donors. Despite the intimate relationships formed between flowing plants (angiosperms) and fungi, lengthy fungal-like sequence has not been identified in angiosperm mitogenomes to date. Here, we present multiple lines of evidence documenting horizontal gene transfer (HGT) between the mitogenomes of fungi and the ancestors of the orchids, plants that are obligate parasites of fungi during their early development. We show that the ancestor of the orchids acquired an ∼270-bp fungal mitogenomic region containing three transfer RNA genes. We propose that the short HGT was later replaced by a second HGT event transferring >8 kb and 14 genes from a fungal mitogenome to that of the ancestor of the largest orchid subfamily, Epidendroideae. Our results represent the first evidence of genomic-scale HGT between fungal and angiosperm mitogenomes and demonstrate that the length intergenic spacer regions of angiosperm mitogenomes can effectively fossilize the genomic remains of ancient, nonplant organisms.
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Teske, Peter R. "Mitochondrial genome announcements need to consider existing short sequences from closely related species to prevent taxonomic errors." Conservation Genetics Resources 13, no. 3 (May 21, 2021): 359–65. http://dx.doi.org/10.1007/s12686-021-01214-7.

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AbstractThe reconstruction of complete mitochondrial genomes (mitogenomes) has considerable potential to clarify species relationships in cases where morphological analysis and DNA sequencing of individual genes are inconclusive. However, the trend to use only mitogenomes for the phylogenies presented in mitogenome announcements carries the inherent risk that the study species’ taxonomy is incorrect because no mitogenomes have yet been reconstructed for its sister species. Here, I illustrate this problem using the mitogenomes of two seahorses, Hippocampus capensis and H. queenslandicus. Both specimens used for mitogenome reconstruction originated from traditional Chinese medicine markets rather than native habitats. Although mitogenome phylogenies placed these specimens correctly among the seahorses from which mitogenomes were available at the time, incorporating single-marker sequence from closely related species into the phylogenies revealed that both mitogenomes are problematic. The mitogenome of the endemic South African H. capensis did not cluster among single-marker DNA sequences of seahorses from the species’ native habitat, but among sequences submitted under the names H. casscsio, H. fuscus and H. kuda that originated from all over the Indo-Pacific, including China. Phylogenetic placement of the mitogenome of H. queenslandicus within a cluster of seahorses that also included H. spinosissimus confirms an earlier finding that H. queenslandicus is a synonym of H. spinosissimus, a widespread Indo-Pacific species that also occurs in China. It is recommended that mitogenome announcements incorporate available single-marker sequences of closely related species, not only mitogenomes. The reconstruction of mitogenomes can exacerbate taxonomic confusion if existing information is ignored.
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Li, Qiang, Ting Zhang, Lijiao Li, Zhijie Bao, Wenying Tu, Peng Xiang, Qian Wu, Ping Li, Mei Cao, and Wenli Huang. "Comparative Mitogenomic Analysis Reveals Intraspecific, Interspecific Variations and Genetic Diversity of Medical Fungus Ganoderma." Journal of Fungi 8, no. 8 (July 26, 2022): 781. http://dx.doi.org/10.3390/jof8080781.

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Ganoderma species are widely distributed in the world with high diversity. Some species are considered to be pathogenic fungi while others are used as traditional medicine in Asia. In this study, we sequenced and assembled four Ganoderma complete mitogenomes, including G. subamboinense s118, G. lucidum s37, G. lingzhi s62, and G. lingzhi s74. The sizes of the four mitogenomes ranged from 50,603 to 73,416 bp. All Ganoderma specimens had a full set of core protein-coding genes (PCGs), and the rps3 gene of Ganoderma species was detected to be under positive or relaxed selection. We found that the non-conserved PCGs, which encode RNA polymerases, DNA polymerases, homing endonucleases, and unknown functional proteins, are dynamic within and between Ganoderma species. Introns were thought to be the main contributing factor in Ganoderma mitogenome size variation (p < 0.01). Frequent intron loss/gain events were detected within and between Ganoderma species. The mitogenome of G. lucidum s26 gained intron P637 in the cox3 gene compared with the other two G. lucidum mitogenomes. In addition, some rare introns in Ganoderma were detected in distinct Basidiomycetes, indicating potential gene transfer events. Comparative mitogenomic analysis revealed that gene arrangements also varied within and between Ganoderma mitogenomes. Using maximum likelihood and Bayesian inference methods with a combined mitochondrial gene dataset, phylogenetic analyses generated identical, well-supported tree topologies for 71 Agaricomycetes species. This study reveals intraspecific and interspecific variations of the Ganoderma mitogenomes, which promotes the understanding of the origin, evolution, and genetic diversity of Ganoderma species.
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Zhang, Dong, Hong Zou, Ivan Jakovlić, Shan G. Wu, Ming Li, Jin Zhang, Rong Chen, Wen X. Li, and Gui T. Wang. "Mitochondrial Genomes of Two Thaparocleidus Species (Platyhelminthes: Monogenea) Reveal the First rRNA Gene Rearrangement among the Neodermata." International Journal of Molecular Sciences 20, no. 17 (August 28, 2019): 4214. http://dx.doi.org/10.3390/ijms20174214.

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Phylogenetic framework for the closely related Ancylodiscoidinae and Ancyrocephalinae subfamilies remains contentious. As this issue was never studied using a large molecular marker, we sequenced the first two Ancylodiscoidinae mitogenomes: Thaparocleidus asoti and Thaparocleidus varicus. Both mitogenomes had two non-coding regions (NCRs) that contained a number of repetitive hairpin-forming elements (RHE). Due to these, the mitogenome of T. asoti (16,074 bp) is the longest among the Monogenea; especially large is its major NCR, with 3500 bp, approximately 1500 bp of which could not be sequenced (thus, the total mitogenome size is ≈ 17,600 bp). Although RHEs have been identified in other monopisthocotyleans, they appear to be independently derived in different taxa. The presence of RHEs may have contributed to the high gene order rearrangement rate observed in the two mitogenomes, including the first report of a transposition of rRNA genes within the Neodermata. Phylogenetic analyses using mitogenomic dataset produced Dactylogyrinae embedded within the Ancyrocephalinae (paraphyly), whereas Ancylodiscoidinae formed a sister-group with them. This was also supported by the gene order analysis. 28S rDNA dataset produced polyphyletic Dactylogyridae and Ancyrocephalinae. The phylogeny of the two subfamilies shall have to be further evaluated with more data.
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Dissertations / Theses on the topic "Mitogenomes"

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Shen, Hong. "Mitogenomic analysis of decapod phylogeny." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2012. http://dx.doi.org/10.18452/16505.

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Für eine umfassende Untersuchung der Phylogenie der Decapoda wurden von mir die mitochondrialen Genome von 13 Dekapoden sequenziert. Zusammen mit den in der GenBank verfügbaren Sequenzen von 31 Dekapoden und dem von der Universität Bonn zur Verfügung gestellten mitochondrialen Genom von Dromia personata deckt dieser Datensatz alle großen Teilgruppen der Decapoda ab. Maximum likelihood (ML)-Analysen und Bayesian inference (BI)-Analysen der Nucleotidsequenzen und Aminosäuresequenzen ergaben bezüglich der Verwandtschaft der hochrangigen Taxa ähnliche Topologien: (((((((Anomala, Brachyura), Thalassinida: Gebiidea) Thalassinida: Axiidea), Astacidea), Achelata), Stenopodidea), Caridea), Dendrobranchiata). Gleichwohl wurde mit den Polychelida ein problematisches Taxon mit ungewissen Verwandtschaftsbeziehungen identifiziert. Auf der Eben der Unterordnungen sind die Thalassinida paraphyletisch, was mit einigen morphologischen und einigen jüngeren molekularen Studien konsistent ist, alle anderen gebräuchlichen Taxa sind monophyletisch. Es handelt sich um eine Inversion, die sich vom S-E-F tRNA cluster bis zum I-Q-M tRNA cluster erstreckt und in Procambarus fallax f. virginalis und Homarus gammarus auftritt. Im Vergleich mit dem Genarrangement des Limulus polyphemus zeigen beide Astaciden in dieser Region exakt dieselbe Inversion wie der Priapulide Priapulus caudatus, die daher innerhalb der Ecdysozoa als konvergent angenommen werden muss. Auch neben dieser Inversion innerhalb der Astacidea zeigen die Genarrangements aller verfügbaren Dekapoden mehrere interessante Eigenschaften. Um die beobachteten einzigartigen genomischen Eigenschaften zu erklären, schlage ich mit dem „inversion triggered duplication“ Model ein neues Modell für Gen-Rearrangements vor.
For a comprehensive study of decapod phylogeny at the mitochondrial genome level, I have sequenced the mitochondrial genome of 13 decapods. Together with available sequences of 31 decapods from GenBank, and the mitochondrial genome of Dromia personata provided by the Bonn University, the dataset now cover all major decapod taxa. Maximum likelihood (ML) and Bayesian inference (BI) of the nucleotide and amino acid datasets reveal similar topologies at the higher level relationships: (((((((Anomala, Brachyura), Thalassinida: Gebiidea) Thalassinida: Axiidea), Astacidea), Achelata), Stenopodidea), Caridea), Dendrobranchiata). Nevertheless, one problematic taxon, Polychelida, with ambiguous affinities is recognized. At the lower level, most taxa are monophyletic, whereas the Thalassinida is paraphyletic, which is consistent with some morphological and molecular results. An inversion spanning from S-E-F tRNA cluster to the I-Q-M tRNA cluster occurred in Procambarus fallax f. virginalis, Homarus gammarus, and one priapulid Priapulus caudatus. Compared with the gene arrangement of the horseshoe crab Limulus polyphemus, both astacids and the priapulid exhibit the same inversion, which is therefore supposed to be a convergent event of the clade Astacidea and Priapulida among Ecdysozoa. Other than this notable feature observed in astacids, the gene arrangements in all available decapods show some interesting characters. To explain these unique genomic features observed here, a new gene rearrangement model is proposed, which is called the “inversion triggered duplication” model.
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Briscoe, Andrew G. "Advancing mitogenomics : a case study in the Araneae." Thesis, Bangor University, 2013. https://research.bangor.ac.uk/portal/en/theses/advancing-mitogenomics--a-case-study-in-the-araneae(f642bbb7-75fa-49ea-a59d-23274019e8fa).html.

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Tabata, Ryouichi. "The origin, history and mitogenome evolution of fishes in Lake Biwa." 京都大学 (Kyoto University), 2016. http://hdl.handle.net/2433/215345.

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Van, de Paer Céline. "Diversité structurelle et évolution contrastée des génomes cytoplasmiques des plantes à fleurs : une approche phylogénomique chez les Oleaceae." Thesis, Toulouse 3, 2017. http://www.theses.fr/2017TOU30228/document.

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Chez les plantes, la dynamique structurelle et l'évolution concertée des génomes nucléaire et cytoplasmiques restent peu documentées. L'objectif de cette thèse était d'étudier la diversité structurelle et l'évolution des mitogénomes et des plastomes chez les Oleaceae à l'aide d'une approche de phylogénomique. Nous avons d'abord assemblé des mitogénomes à partir de données de séquençage de faible couverture, obtenues à partir de matériel frais et d'herbier. Une grande variation de structure du mitogénome a été observée chez l'olivier, et un gène chimérique potentiellement associé à un type de stérilité mâle a été identifié. Enfin, nous avons étudié l'évolution des plastomes et des gènes mitochondriaux chez les Oleaceae. Une accélération de l'évolution du plastome a été observée dans deux lignées indépendantes. Ce changement de trajectoire évolutive pourrait être la conséquence d'une transmission occasionnelle de plastes par le pollen, modifiant les pressions sélectives sur certains gènes
In plants, the structural dynamics and concerted evolution of nuclear and cytoplasmic genomes are poorly understood. The objective of this thesis was to study the structural diversity and evolution of mitogenomes and plastomes in the family Oleaceae with a phylogenomic approach. First, we assembled mitogenomes from low-coverage sequencing data obtained from live and herbarium material. Considerable structural variation of mitogenomes was observed in the olive, and a chimeric gene potentially associated to a type of male sterility was detected. Finally, we studied the evolution of plastomes and mitochondrial genes in the Oleaceae. Accelerated evolution of plastomes was observed in two independent lineages. This change of evolutionary rate could be the consequence of an occasional transmission of plastids with pollen, modifying selective pressures on some genes
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Garbutt, James. "The complete mitogenome of two Australian lampreys: mordacia mordax and mordacia praecox." Thesis, Garbutt, James (2015) The complete mitogenome of two Australian lampreys: mordacia mordax and mordacia praecox. Honours thesis, Murdoch University, 2015. https://researchrepository.murdoch.edu.au/id/eprint/30595/.

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As one of only two surviving outgroups to all jawed vertebrates, lampreys (Petromyzontiformes) can provide important information in our understanding of early vertebrate evolution. However, with many phylogenetic aspects of lamprey evolution still uncertain, the ability to use contemporary lampreys in this role depends on robust phylogenetic hypotheses regarding the interrelationship of the three lamprey families, as well as the relationship between lampreys and hagfishes. To achieve this, complete mitogenome data of Southern Hemisphere lampreys is required. Another contentious issue in lamprey taxonomy is the status of paired species. Whilst many studies have focused on Northern Hemisphere species pairs, this study is the first to compare Mordacia mordax and Mordacia praecox, two lamprey species endemic to Australia and the only species pair in the Southern Hemisphere. The complete mitochondrial genome of Mordacia mordax and Mordacia praecox was determined twice independently, in a single shotgun sequencing run on an Ion Torrent PGM, and using a combination of Sanger sequencing of short range PCR products and Roche 454 GS Junior pyrosequencing of long range PCR products. Both of the mitogenomes contain the 37 typical vertebrate genes. Their gene order and contents are identical to those of previously described lamprey mitogenomes, with the exception of a novel tandem repeat array located between Cyt b and tRNA proline. The tandem repeat array, referred to as NCIII, contains pseudogenes of tRNA proline and phenylalanine, indicating that it has arisen by tandem duplication of the tRNA proline – phenylalanine region. Characterisation of NCIII revealed that the number of repeat copies was polymorphic between individuals of both species, and was a source of both intra-individual and inter-individual variation. Consistent with other studies of lamprey species pairs, the mitogenome of M. mordax and M. praecox are nearly identical. Phylogenetic analyses were carried out using the newly determined mitogenomes, together with five additional lamprey species and two hagfishes. Most tree topologies obtained strongly support the hypothesis that Petromyzontidae plus Geotriidae are a clade whose sister group is Mordaciidae. Additionally, lamprey divergence times were estimated by a temporally-calibrated phylogenetic analysis that included 20 vertebrate mitogenomes and was done using nine well-established fossil calibration points. The recovered topology strongly supported the hypothesis that lampreys separated from hagfishes about 409 MYA, and that lamprey divergence involved the early radiation of Mordaciidae (about 132 MYA), followed by the monophyletic divergence of Geotriidae plus Petromyzontidae about 85 MYA. Taken together, the results in this study provide robust hypotheses regarding the interrelationship of lamprey families and the relationship between hagfish and lampreys, whilst providing an estimation of their divergence times.
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Rodovalho, Cynara de Melo [UNESP]. "Caracterização do transcriptoma e genoma mitocondrial da formiga cortadeira Atta laevigata (Formicidae : Attini)." Universidade Estadual Paulista (UNESP), 2011. http://hdl.handle.net/11449/100531.

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Formigas cortadeiras do gênero Atta, popularmente conhecidas como saúvas, são as mais derivadas dentro da tribo Attini. Apresentam grande importância ecológica, porém, pelo hábito de cortarem folhas para manutenção do fungo simbionte e pelo enorme tamanho das colônias, causam muitos prejuízos às lavouras, pastagens e plantações, sendo consideradas pragas agrícolas. Atta laevigata Smith, 1858 apresenta vasta distribuição pelo Brasil e é responsável pela herbivoria de inúmeras plantas dicotiledôneas, gramíneas e espécies nativas de diferentes biomas. O presente trabalho teve como objetivos a caracterização parcial do transcriptoma e do genoma mitocondrial de A. laevigata. Foram caracterizadas 2006 sequências únicas do transcriptoma, a partir de uma biblioteca de cDNA preparada com indivíduos inteiros da formiga. Entre essas sequências, 16 provavelmente representam genes com grande número de transcritos. Esses 16 genes estão relacionados a três funções celulares: (i) conservação de energia através de reações redox na mitocôndria; (ii) estrutural, pelo citoesqueleto e músculos; (iii) regulação da expressão gênica e metabolismo. Considerando o estilo de vida e processos biológicos chaves para essas formigas, 146 sequências foram identificadas com base na sua utilização para o controle de cortadeiras pragas. A partir de dados da biblioteca de cDNA e procedimentos envolvendo primer walking, o genoma mitocondrial de A. laevigata foi parcialmente caracterizado, apresentandose com 17920 pb, maior, portanto, do que outros já descritos em Hymenoptera, mesmo considerando-se a impossibilidade de determinação da sequência de uma pequena porção do mtDNA, envolvendo a região controle, uma parte do 12S e os tRNAs S1, V e M. Como já descrito para outros mitogenomas, o de A. laevigata apresentou alto conteúdo AT, os mesmos 13 genes codificadores...
Leafcutter ants from Atta genus, popularly known as “saúvas”, are the most derived of the tribe Attini. They have major ecological importance, but, because of their habit of cutting leaves for the maintenance of the symbiotic fungus and the huge colony size, they impose severe economic damages to plantations, pastures, and agriculture, being considered as agriculture pests. Atta laevigata shows wide distribution in Brazil and it is responsible for the herbivory of many dicots, grass, and native species from different biomes. The present work aimed to characterize the transcriptome and the mitochondrial genome of A. laevigata. 2,006 unique sequences of the transcriptome were characterized from a cDNA library constructed with whole individuals. Among those sequences, 16 are likely from genes with high number of transcripts. Those 16 genes are related with three cellular functions: (i) energy conservation through redox reactions in mitochondria; (ii) cytoskeleton and muscle structuring; (iii) regulation of gene expression and metabolism. Based on lifestyle and key biological processes of these ants, 146 sequences were identified with potential use for controlling pest leafcutters. Using data from cDNA library and primer walking proceedings, the mitochondrial genome of A. laevigata was partially characterized with 17,920 bp, being larger than the others already described for Hymenoptera. A small part of the mtDNA was not sequenced, including the control region, a portion of 12S and tRNAs S1, V, and M. As described before for other mitogenomes, A. laevigata mtDNA displayed high AT contain, the same 13 proteincoding genes and the two ribosomal subunits with length and location according to the hypothetic ancestral mitogenome. Rearrangements were found for the tRNAs, but the most remarkable difference were the high number and longer length of intergenic regions presented in the mtDNA... (Complete abstract click electronic access below)
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McCullagh, Bonnie. "Sequence evolution among divergent mitochondrial haplotypes within species of Junonia butterflies." Journal of Asia-Pacific Entomology, 2015. http://hdl.handle.net/1993/31105.

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The New World Junonia butterflies include well-studied model organisms yet their phylogeny remains unresolved by traditional cox1 DNA barcodes. Sixteen Junonia mitochondrial genomes were sequenced using next generation MiSeq technology. Junonia lemonias, an Old World species, has mitochondrial genome features typical of Ditrysian Lepidoptera, and synteny is maintained throughout Junonia. Analysis of Junonia mitogenomes produced a robust phylogeny that was used with biogeographic information to infer that Junonia crossed the Pacific Ocean to invade the New World on 3 separate occasions. Junonia vestina, a high elevation species from the Andes Mountains, shows high altitude adaptation in the mitochondrial protein coding loci atp6, atp8, cox1, cob, nad1, and nad2, with the strongest effects seen in cox1 and nad1. There is some overlap between these genes with human loci that have disease associations with the same amino acid positions which could help elucidate the function of high elevation mutations in J. vestina.
February 2016
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Finnegan, Kimberly A. "A Mitogenomics View of the Population Structure and Evolutionary History of the Basking Shark Cetorhinus maximum." NSUWorks, 2014. http://nsuworks.nova.edu/occ_stuetd/13.

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The basking shark, Cetorhinus maximus, has historically been a target of international fisheries, leading to well-documented declines in parts of its global distribution. Currently, the basking shark is listed as globally ‘Vulnerable’ and regionally ‘Endangered’ (North Pacific and Northeast Atlantic) on the IUCN Red List of Threatened Species, rendering the species an international conservation priority. Here, we assessed the global matrilineal genetic population structure and evolutionary history of the basking shark by completing the first whole mitochondrial genome sequence level survey of animals sampled from three globally widespread geographic regions: the western North Atlantic (n = 11), the eastern North Atlantic (n = 11), and within New Zealand territorial waters (n = 12). Despite the relatively large amount of sequence data assessed (~16,669 bp per individual), whole mitogenome analyses showed no evidence of population differentiation (ΦST = -0.047, P > 0.05) and very low nucleotide diversity (π = 0.0014 ± 0.000) across a global seascape. The absence of population structure across large distances and even between ocean basins is indicative of long-dispersal by this species, including an ability to cross known biogeographic barriers known to differentiate populations of other highly vagile pelagic fishes. Notably, evolutionary analyses of the mitogenome sequences revealed two globally sympatric but evolutionary divergent lineages, with a Bayesian framework estimated coalescence time of ~2.46 million years ago. Coalescent-based Bayesian skyline analysis uncovered subtle evidence of Pleistocene demographic flux for this species, including a potential decline in female effective population size. Thus, historical population changes may be responsible for the occurrence of the two highly divergent, yet sympatric lineages, as population declines may have resulted in the loss of intermediate haplotypes and resulted in an overall loss of genetic diversity. This work supports the recognition of basking sharks as a single matrilineal global population, and as such requires the application of a cooperative multiagency and international approach to fisheries management to conserve this highly vulnerable and ecologically unique species.
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Shen, Hong [Verfasser], Gerhard [Akademischer Betreuer] Scholtz, Thomas [Akademischer Betreuer] Stach, and Lars [Akademischer Betreuer] Podsiadlowski. "Mitogenomic analysis of decapod phylogeny : (Crustacea, Malacostraca) / Hong Shen. Gutachter: Gerhard Scholtz ; Thomas Stach ; Lars Podsiadlowski." Berlin : Humboldt Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2012. http://d-nb.info/1022837559/34.

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ROCHA, Patrícia Keytth Lins. "Qual região do DNA mitocondrial reflete a história evolutiva da ordem Lepidoptera?" Universidade Federal de Pernambuco, 2013. https://repositorio.ufpe.br/handle/123456789/13136.

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Submitted by Andre Moraes Queiroz (andre.moraesqueiroz@ufpe.br) on 2015-04-14T15:05:53Z No. of bitstreams: 2 Dissertação Patricia Rocha.pdf: 2020756 bytes, checksum: 96804531919a1d7e9cb5ab9787d73242 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5)
Made available in DSpace on 2015-04-14T15:05:53Z (GMT). No. of bitstreams: 2 Dissertação Patricia Rocha.pdf: 2020756 bytes, checksum: 96804531919a1d7e9cb5ab9787d73242 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Previous issue date: 2013
FACEPE
A ordem Lepidoptera apresenta uma gama de espécimes de importância econômica, algumas são agentes polinizadores e outras são pragas. Vários estudos têm sido realizados com base na morfologia com base em dados moleculares para elucidar a evolução da ordem. O DNA mitocondrial é muito utilizado por proporcionar boa resolução filogenética. Com base em genes mitocondriais informativos, nós propusemos um conjunto de dados que pode ser utilizado em análise filogenética de Lepidoptera obtendo a mesma robustez que a análise com mtDNAs completos. Para isso, as sequências dos mitogenomas de Lepidoptera foram recuperadas no banco de dados do NCBI. Foi identificada a ordem gênica das sequências utilizando o programa MAUVE. As regiões de interesse em D. flavipennella foram sequenciadas para testar a eficiência dos marcadores moleculares em sequência nova. Foi realizada análise de entropia, teste de sinal filogenético e de saturação para verificar características de bons marcadores moleculares e foram realizadas análises filogenéticas nos programas PhyML e MrBayes. Foram realizados também testes com e sem a terceira posição dos códons para verificar a influência da terceira posição nas análises filogenéticas de Lepidoptera. As regiões estudadas foram concatenadas para aumentar os valores de confiança das árvores. Verificamos que com a concatenação dos genes COI, ATP6, COIII, ND3, ND5, CYTB, ND1 e 16S foi possível obter resultados com robustez semelhante a dos mitogenomas completos.
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Books on the topic "Mitogenomes"

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Kulik, Tomasz, Anne D. Van Diepeningen, and Georg Hausner, eds. The Significance of Mitogenomics in Mycology. Frontiers Media SA, 2021. http://dx.doi.org/10.3389/978-2-88966-479-5.

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Book chapters on the topic "Mitogenomes"

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Fortes, Gloria Gonzales, and Johanna L. A. Paijmans. "Analysis of Whole Mitogenomes from Ancient Samples." In Whole Genome Amplification, 179–95. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2990-0_13.

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Alqahtani, Fahad, and Ion Măndoiu. "SMART2: Multi-library Statistical Mitogenome Assembly with Repeats." In Computational Advances in Bio and Medical Sciences, 184–98. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-46165-2_15.

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Bernt, Matthias, Daniel Merkle, and Martin Middendorf. "An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree." In Comparative Genomics, 143–57. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-87989-3_11.

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Lin, Runmao, Xinyue Cheng, and Bingyan Xie. "Comparative Analysis of Pochonia chlamydosporia Mitogenome Reveals Dynamic Mitochondrial Evolution of the Nematophagous Fungi in Hypocreales." In Perspectives in Sustainable Nematode Management Through Pochonia chlamydosporia Applications for Root and Rhizosphere Health, 183–95. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-59224-4_9.

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Pisani, Davide, Robert Carton, Lahcen I. Campbell, Wasiu A. Akanni, Eoin Mulville, and Omar Rota-Stabelli. "An Overview of Arthropod Genomics, Mitogenomics, and the Evolutionary Origins of the Arthropod Proteome." In Arthropod Biology and Evolution, 41–61. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-662-45798-6_3.

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Bentur, Jagadish S., R. M. Sundaram, Satendra Kumar Mangrauthia, and Suresh Nair. "Molecular Approaches for Insect Pest Management in Rice." In Rice Improvement, 379–423. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-66530-2_11.

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AbstractThis chapter focuses on the progress made in using molecular tools in understanding resistance in rice to insect pests and breeding rice for multiple and durable insect resistance. Currently, molecular markers are being extensively used to tag, map, introgress, and clone plant resistance genes against gall midge, planthoppers, and leafhoppers. Studies on cloned insect resistance genes are leading to a better understanding of plant defense against insect pests under different feeding guilds. While marker-assisted breeding is successfully tackling problems in durable and multiple pest resistance in rice, genomics of plants and insects has identified RNAi-based gene silencing as an alternative approach for conferring insect resistance. The use of these techniques in rice is in the developmental stage, with the main focus on brown planthopper and yellow stem borer. CRISPR-based genome editing techniques for pest control in plants has just begun. Insect susceptibility genes (negative regulators of resistance genes) in plants are apt targets for this approach while gene drive in insect populations, as a tool to study rice-pest interactions, is another concept being tested. Transformation of crop plants with diverse insecticidal genes is a proven technology with potential for commercial success. Despite advances in the development and testing of transgenic rice for insect resistance, no insect-resistant rice cultivar is now being commercially cultivated. An array of molecular tools is being used to study insect-rice interactions at transcriptome, proteome, metabolome, mitogenome, and metagenome levels, especially with reference to BPH and gall midge, and such studies are uncovering new approaches for insect pest management and for understanding population genetics and phylogeography of rice pests. Thus, it is evident that the new knowledge being gained through these studies has provided us with new tools and information for facing future challenges. However, what is also evident is that our attempts to manage rice pests cannot be a one-time effort but must be a continuing one.
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Ureña, Irene, Silvia Guimarães, Simon J. M. Davis, Cleia Detry, Gülşah Merve Kılınç, Rute Da Fonseca, Nicolas Dussex, et al. "An Archaeogenetics Study of Cattle Bones from Seventeenth Century Carnide, Lisbon, Portugal." In Cattle and People, 169–79. Lockwood Press, 2022. http://dx.doi.org/10.5913/archbio04.08.

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Inheritable traits of cattle were modified in various ways at different times by diverse cultures. A large collection of seventeenth century cattle remains excavated from 71 silos in the Largo do Coreto in Carnide, Lisbon, included 47 com- plete and 44 distal ends of metacarpals. These provide an opportunity to make a detailed osteometric and archaeogenetics study. While morphological changes such as size increase, as detected in bone measurements, indicate improvement for larger animals, ancient DNA is useful for studying evolutionary trajectories and modes of improvement of domestic animals. High-throughput sequencing can show evolutionary processes at unprecedented resolution. We generated whole-genome shotgun resequencing data for 6 Carnide specimens on the Illumina HiSeq X Ten platform. Mean en- dogenous DNA content for these samples varied between 1% (CAR008) and 4% (CAR014), and their mitogenomes were sequenced to between 3.56x and 33.44x mean depth of coverage, respectively. The Carnide cattle belong to the Europe- an-T3 (CAR002 and CAR021) and African-T1 haplogroups (CAR008, CAR009, CAR014, and CAR016). These haplogroups are also present in extant native breeds from the Iberian Peninsula, corroborating the hypothesis of a genetic continuity of maternal lineages over time. The admixture of African taurine cattle observed in these specimens from the Modern period supports the idea that current genetic diversity of Iberian cattle derives from the dispersal of a heterogeneous population since early times along the Mediterranean basin. In addition, the biological sex of the Carnide specimens was consistently determined by our genomic analysis and osteometric measurements. Further analyses of whole-genome nuclear data are needed to infer specific biological properties, for example, the coat color of these animals, as well as the variability of genes linked to body size, meat, and milk production traits.
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Cunha, Divino Bruno da, Luis Fernando da Silva Rodrigues‐Filho, and João Bráullio de Luna Sales. "A Review of the Mitogenomic Phylogeny of the Chondrichthyes." In Chondrichthyes - Multidisciplinary Approach. InTech, 2017. http://dx.doi.org/10.5772/intechopen.70028.

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Gáspárdy, András. "Reality of Mitogenome Investigation in Preservation of Native Domestic Sheep Breeds." In Landraces - Traditional Variety and Natural Breed. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.95768.

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This chapter deals with the study of extranuclear hereditary material and the possibilities of using it to maintain endangered animal breeds. The chapter characterizes mtDNA, presents its genes and their functions, while also emphasizing the hypervariable control region. It reports on the results of previous researches, referring to international publications. It sheds light on promising areas of mitogenomic research. It shows the maternal genetic background of local native varieties according to the results of the study of available country/geographical region. It deals with reasons for endangerment and the arguments for preservation of autochthonous breeds. In addition, it gives place to discuss some exciting professional concepts in rare breed preservation.
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Maár, Kitti, Gergely István Varga, Bence Kovács, Oszkár Schütz, Balázs Tihanyi, Emil Nyerki, István Raskó, et al. "A X-XI. századi Kárpát-medencei köznép anyai vonalainak jellemzése archeogenetikai módszerekkel." In A Magyarságkutató Intézet Évkönyve 2021, 281–309. Magyarságkutató Intézet, 2022. http://dx.doi.org/10.53644/mkie.2021.281.

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A honfoglaló magyarok nomád csoportjai meghatározó szerepet játszottak a magyar őstörténetben, de genetikai adatok csak a bevándorló elit rétegből állnak rendelkezésre. A X-XI. századi Kárpát-medencei maradványok nagy része a köznéphez tartozik, akiknek származása és a bevándorló elithez való viszonya széles körben vitatott. A mitogenom-szekvenciákat 202 egyedből nyertük ki újgenerációs szekvenálás és hibridizációs dúsítás kombinációjával. A filogenetikai vizsgálatokhoz Median-Joining Network-elemzést használtunk. A köznépi populációt 87 ősi eurázsiai populációval hasonlítottuk össze szekvenciaalapú (Fst) és haplocsoport-alapú populációgenetikai módszerekkel. A köznép haplocsoport-összetétele markánsan eltér az elitétől, és az elittel ellentétben a köznép európai populációkkal csoportosult. Emellett a megfigyelhető alhaplocsoport-megoszlás az elit és a köznép közötti keveredést jelzi. A X-XI. századi köznép többsége nagy valószínűséggel a Kárpát-medence ősi helyi lakosságát képviseli, amely keveredett a keleti eredetű bevándorló csoportokkal (akik között voltak honfoglaló magyarok is).
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Conference papers on the topic "Mitogenomes"

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Gillett, Conrad. "Weevil mitogenomics." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.94502.

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Alqahtani, Fahad, and Ion I. Mandoiu. "Statistical Mitogenome Assembly with Repeats." In 2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). IEEE, 2018. http://dx.doi.org/10.1109/iccabs.2018.8542062.

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Yan, Liping. "A mitogenomic perspective on calyptrate phylogeny." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.109353.

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Straeuli, Rieze, and Barbara van Asch. "Mitogenomics and Phylogeny of Seven African Saturniidae (Lepidoptera)." In The 1st International Electronic Conference on Entomology. Basel, Switzerland: MDPI, 2021. http://dx.doi.org/10.3390/iece-10372.

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"Mitogenomics and phylogenetics of vulnerable and endangered birds of genera Aratinga and Psittacus." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-148.

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"Assembling of the Siberian larch mitochondrial genome using long nucleotide sequence reads, the largest currently known mitogenome." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-145.

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