Articoli di riviste: "Organellar genomes"

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Hertle, Alexander P., Benedikt Haberl e Ralph Bock. "Horizontal genome transfer by cell-to-cell travel of whole organelles". Science Advances 7, n. 1 (gennaio 2021): eabd8215. http://dx.doi.org/10.1126/sciadv.abd8215.

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Recent work has revealed that both plants and animals transfer genomes between cells. In plants, horizontal transfer of entire plastid, mitochondrial, or nuclear genomes between species generates new combinations of nuclear and organellar genomes, or produces novel species that are allopolyploid. The mechanisms of genome transfer between cells are unknown. Here, we used grafting to identify the mechanisms involved in plastid genome transfer from plant to plant. We show that during proliferation of wound-induced callus, plastids dedifferentiate into small, highly motile, amoeboid organelles. Simultaneously, new intercellular connections emerge by localized cell wall disintegration, forming connective pores through which amoeboid plastids move into neighboring cells. Our work uncovers a pathway of organelle movement from cell to cell and provides a mechanistic framework for horizontal genome transfer.

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Greiner, Stephan, Pascal Lehwark e Ralph Bock. "OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes". Nucleic Acids Research 47, W1 (5 aprile 2019): W59—W64. http://dx.doi.org/10.1093/nar/gkz238.

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Abstract Organellar (plastid and mitochondrial) genomes play an important role in resolving phylogenetic relationships, and next-generation sequencing technologies have led to a burst in their availability. The ongoing massive sequencing efforts require software tools for routine assembly and annotation of organellar genomes as well as their display as physical maps. OrganellarGenomeDRAW (OGDRAW) has become the standard tool to draw graphical maps of plastid and mitochondrial genomes. Here, we present a new version of OGDRAW equipped with a new front end. Besides several new features, OGDRAW now has access to a local copy of the organelle genome database of the NCBI RefSeq project. Together with batch processing of (multi-)GenBank files, this enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades. The new OGDRAW server can be accessed at https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.

3

Ramsey, Adam J., David E. McCauley e Jennifer R. Mandel. "Heteroplasmy and Patterns of Cytonuclear Linkage Disequilibrium in Wild Carrot". Integrative and Comparative Biology 59, n. 4 (11 giugno 2019): 1005–15. http://dx.doi.org/10.1093/icb/icz102.

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Abstract Organellar genomes are considered to be strictly uniparentally-inherited. Uniparental inheritance allows for cytonuclear coevolution and the development of highly coordinated cytonuclear interactions. Yet, instances of biparental inheritance have been documented across eukaryotes. Biparental inheritance in otherwise uniparentally-inherited organelles is termed leakage (maternal or paternal) and allows for the presence of multiple variants of the same organellar genome within an individual, called heteroplasmy. It is unclear what, if any, evolutionary consequences are placed on nuclear and/or organellar genomes due to heteroplasmy. One way of accessing cytonuclear interactions and potential coevolution is through calculating cytonuclear linkage disequilibrium (cnLD), or the non-random association of alleles between nuclear and organellar genomes. Patterns of cnLD can indicate positive or negative cytonuclear selection, coevolution between the nuclear and organellar genomes, non-traditional organellar inheritance, or instances of ancestral heteroplasmy. In plants, cytonuclear interactions have been shown to play a role in cytoplasmic male sterility which occurs in gynodioecious species and is associated with leakage. We used the gynodioecious species, Daucus carota L. spp. carota, or wild carrot, to investigate cnLD. We genotyped a total of 265 individuals from two regions of the USA at 15 nuclear microsatellites, the mitochondrial genes cox1 and atp9, and an intergenic region between trnS and trnG (StoG) in the plastid genome to calculate nuclear–nuclear LD (nucLD), cnLD, and organellar LD (i.e., within the mtDNA and between mtDNA and ptDNA) within the two regions. We were further able to identify cox1 and StoG heteroplasmy and calculate some of the same LD measures within heteroplasmic and homoplasmic (non-heteroplasmic) datasets. We used a Z-transformation test to demonstrate that heteroplasmic individuals display significantly higher levels of cnLD within both regions. In spite of this, within and between organellar LD is low to moderate. Given these patterns of LD in two regions of the USA in which gene flow has been shown to occur between crop and wild carrot, we suggest that heteroplasmy is an evolutionary mechanism which permits the maintenance of cnLD while also acting to disrupt organellar LD.

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Wang, Haoqi, Xuezhu Liao, Luke R. Tembrock, Zuoren Yang e Zhiqiang Wu. "Evaluation of Intracellular Gene Transfers from Plastome to Nuclear Genome across Progressively Improved Assemblies for Arabidopsis thaliana and Oryza sativa". Genes 13, n. 9 (9 settembre 2022): 1620. http://dx.doi.org/10.3390/genes13091620.

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DNA originating from organellar genomes are regularly discovered in nuclear sequences during genome assembly. Nevertheless, such insertions are sometimes omitted during the process of nuclear genome assembly because the inserted DNA is assigned to organellar genomes, leading to a systematic underestimation of their frequency. With the rapid development of high-throughput sequencing technology, more inserted fragments from organelle genomes can now be detected. Therefore, it is necessary to be aware of the insertion events from organellar genomes during nuclear genome assembly to properly attribute the impact and rate of such insertions in the evolution of nuclear genomes. Here, we investigated the impact of intracellular gene transfer (IGT) from the plastome to the nuclear genome using genome assemblies that were refined through time with technological improvements from two model species, Arabidopsis thaliana and Oryza sativa. We found that IGT from the plastome to the nuclear genome is a dynamic and ongoing process in both A. thaliana and O. sativa, and mostly occurred recently, as the majority of transferred sequences showed over 95% sequence similarity with plastome sequences of origin. Differences in the plastome-to-nuclear genome IGT between A. thaliana and O. sativa varied among the different assembly versions and were associated with the quality of the nuclear genome assembly. IGTs from the plastome to nuclear genome occurred more frequently in intergenic regions, which were often associated with transposable elements (TEs). This study provides new insights into intracellular genome evolution and nuclear genome assembly by characterizing and comparing IGT from the plastome into the nuclear genome for two model plant species.

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Leister, Dario. "Towards understanding the evolution and functional diversification of DNA-containing plant organelles". F1000Research 5 (11 marzo 2016): 330. http://dx.doi.org/10.12688/f1000research.7915.1.

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Plastids and mitochondria derive from prokaryotic symbionts that lost most of their genes after the establishment of endosymbiosis. In consequence, relatively few of the thousands of different proteins in these organelles are actually encoded there. Most are now specified by nuclear genes. The most direct way to reconstruct the evolutionary history of plastids and mitochondria is to sequence and analyze their relatively small genomes. However, understanding the functional diversification of these organelles requires the identification of their complete protein repertoires – which is the ultimate goal of organellar proteomics. In the meantime, judicious combination of proteomics-based data with analyses of nuclear genes that include interspecies comparisons and/or predictions of subcellular location is the method of choice. Such genome-wide approaches can now make use of the entire sequences of plant nuclear genomes that have emerged since 2000. Here I review the results of these attempts to reconstruct the evolution and functions of plant DNA-containing organelles, focusing in particular on data from nuclear genomes. In addition, I discuss proteomic approaches to the direct identification of organellar proteins and briefly refer to ongoing research on non-coding nuclear DNAs of organellar origin (specifically, nuclear mitochondrial DNA and nuclear plastid DNA).

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Lyu, Jun. "Editing plant organellar genomes". Nature Plants 8, n. 1 (6 dicembre 2021): 4. http://dx.doi.org/10.1038/s41477-021-01059-w.

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Gray, Michael W. "Evolution of organellar genomes". Current Opinion in Genetics & Development 9, n. 6 (dicembre 1999): 678–87. http://dx.doi.org/10.1016/s0959-437x(99)00030-1.

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Havey, M. J., J. McCreight, W. Rhodes e G. Taurick. "Inheritance and Evolution of the Cucurbit Organellar Genomes". HortScience 31, n. 4 (agosto 1996): 601e—601. http://dx.doi.org/10.21273/hortsci.31.4.601e.

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The cucurbits have several-fold size differences in their mitochondrial genomes. Watermelon possesses a relatively small mitochondrial genome of 330 kb. Squash has a larger mitochondrial genome of 840 kb. Cucumber and melon possess huge mitochondrial genomes of 1500 and 2400 kb, respectively. We demonstrated predominately paternal transmission of the mitochondrial genome in cucumber. Squash shows maternal transmission of the chloroplast genome. We generated reciprocal crosses and identified restriction fragment length polymorphisms in the chloroplast and mitochondrial genomes of melon, squash, and watermelon to establish their transmission. Our analyses also revealed that intergenomic transfers contributed to the evolution of extremely large mitochondrial genomes.

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Barbrook, Adrian C., Christopher J. Howe, Davy P. Kurniawan e Sarah J. Tarr. "Organization and expression of organellar genomes". Philosophical Transactions of the Royal Society B: Biological Sciences 365, n. 1541 (12 marzo 2010): 785–97. http://dx.doi.org/10.1098/rstb.2009.0250.

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Protist mitochondrial genomes show a very wide range of gene content, ranging from three genes for respiratory chain components in Apicomplexa and dinoflagellates to nearly 100 genes in Reclinomonas americana . In many organisms the rRNA genes are fragmented, although still functional. Some protist mitochondria encode a full set of tRNAs, while others rely on imported molecules. There is similarly a wide variation in mitochondrial genome organization, even among closely related groups. Mitochondrial gene expression and control are generally poorly characterized. Transcription probably relies on a ‘viral-type’ RNA polymerase, although a ‘bacterial-type’ enzyme may be involved in some cases. Transcripts are heavily edited in many lineages. The chloroplast genome generally shows less variation in gene content and organization, although greatly reduced genomes are found in dinoflagellate algae and non-photosynthetic organisms. Genes in the former are located on small plasmids in contrast to the larger molecules found elsewhere. Control of gene expression in chloroplasts involves transcriptional and post-transcriptional regulation. Redox poise and the ATP/ADP ratio are likely to be important determinants. Some protists have an additional extranuclear genome, the nucleomorph, which is a remnant nucleus. Nucleomorphs of two separate lineages have a number of features in common.

10

Shatskaya, Natalia V., Vera S. Bogdanova, Oleg E. Kosterin e Gennadiy V. Vasiliev. "New Insights into Plastid and Mitochondria Evolution in Wild Peas (Pisum L.)". Diversity 15, n. 2 (2 febbraio 2023): 216. http://dx.doi.org/10.3390/d15020216.

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Plastids and mitochondria are organelles of plant cells with small genomes, which may exhibit discordant microevolution as we earlier revealed in pea crop wild relatives. We sequenced 22 plastid and mitochondrial genomes of Pisum sativum subsp. elatius and Pisum fulvum using Illumina platform, so that the updated sample comprised 64 accessions. Most wild peas from continental southern Europe and a single specimen from Morocco were found to share the same organellar genome constitution; four others, presumably hybrid constitutions, were revealed in Mediterranean islands and Athos Peninsula. A mitochondrial genome closely related to that of Pisum abyssinicum, from Yemen and Ethiopia, was unexpectedly found in an accession of P. sativum subsp. elatius from Israel, their plastid genomes being unrelated. Phylogenetic reconstructions based on plastid and mitochondrial genomes revealed different sets of wild peas to be most related to cultivated P. sativum subsp. sativum, making its wild progenitor and its origin area enigmatic. An accession of P. fulvum representing ‘fulvum-b’ branch, according to a nuclear marker, appeared in the same branch as other fulvum accessions in organellar trees. The results stress the complicated evolution and structure of genetic diversity of pea crop wild relatives.

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Morley, Stewart A., Niaz Ahmad e Brent L. Nielsen. "Plant Organelle Genome Replication". Plants 8, n. 10 (21 settembre 2019): 358. http://dx.doi.org/10.3390/plants8100358.

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Mitochondria and chloroplasts perform essential functions in respiration, ATP production, and photosynthesis, and both organelles contain genomes that encode only some of the proteins that are required for these functions. The proteins and mechanisms for organelle DNA replication are very similar to bacterial or phage systems. The minimal replisome may consist of DNA polymerase, a primase/helicase, and a single-stranded DNA binding protein (SSB), similar to that found in bacteriophage T7. In Arabidopsis, there are two genes for organellar DNA polymerases and multiple potential genes for SSB, but there is only one known primase/helicase protein to date. Genome copy number varies widely between type and age of plant tissues. Replication mechanisms are only poorly understood at present, and may involve multiple processes, including recombination-dependent replication (RDR) in plant mitochondria and perhaps also in chloroplasts. There are still important questions remaining as to how the genomes are maintained in new organelles, and how genome copy number is determined. This review summarizes our current understanding of these processes.

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Zhang, Guo-Jun, Ran Dong, Li-Na Lan, Shu-Fen Li, Wu-Jun Gao e Hong-Xing Niu. "Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants". International Journal of Molecular Sciences 21, n. 3 (21 gennaio 2020): 707. http://dx.doi.org/10.3390/ijms21030707.

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The transfer of genetic material from the mitochondria and plastid to the nucleus gives rise to nuclear integrants of mitochondrial DNA (NUMTs) and nuclear integrants of plastid DNA (NUPTs). This frequently occurring DNA transfer is ongoing and has important evolutionary implications. In this review, based on previous studies and the analysis of NUMT/NUPT insertions of more than 200 sequenced plant genomes, we analyzed and summarized the general features of NUMTs/NUPTs and highlighted the genetic consequence of organellar DNA insertions. The statistics of organellar DNA integrants among various plant genomes revealed that organellar DNA-derived sequence content is positively correlated with the nuclear genome size. After integration, the nuclear organellar DNA could undergo different fates, including elimination, mutation, rearrangement, fragmentation, and proliferation. The integrated organellar DNAs play important roles in increasing genetic diversity, promoting gene and genome evolution, and are involved in sex chromosome evolution in dioecious plants. The integrating mechanisms, involving non-homologous end joining at double-strand breaks were also discussed.

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Milner, David S., Jeremy G. Wideman, Courtney W. Stairs, Cory D. Dunn e Thomas A. Richards. "A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist". PLOS Biology 19, n. 4 (23 aprile 2021): e3001126. http://dx.doi.org/10.1371/journal.pbio.3001126.

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The overarching trend in mitochondrial genome evolution is functional streamlining coupled with gene loss. Therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occur in many organellar genomes, but the wider diversity of selfish elements, and how they persist in the DNA of organelles, has not been explored. In the mitochondrial genome of a marine heterotrophic katablepharid protist, we identify a functional type II restriction modification (RM) system originating from a horizontal gene transfer (HGT) event involving bacteria related to flavobacteria. This RM system consists of an HpaII-like endonuclease and a cognate cytosine methyltransferase (CM). We demonstrate that these proteins are functional by heterologous expression in both bacterial and eukaryotic cells. These results suggest that a mitochondrion-encoded RM system can function as a toxin–antitoxin selfish element, and that such elements could be co-opted by eukaryotic genomes to drive biased organellar inheritance.

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Mukhopadhyay, Jigeesha, e Georg Hausner. "Organellar Introns in Fungi, Algae, and Plants". Cells 10, n. 8 (6 agosto 2021): 2001. http://dx.doi.org/10.3390/cells10082001.

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Introns are ubiquitous in eukaryotic genomes and have long been considered as ‘junk RNA’ but the huge energy expenditure in their transcription, removal, and degradation indicate that they may have functional significance and can offer evolutionary advantages. In fungi, plants and algae introns make a significant contribution to the size of the organellar genomes. Organellar introns are classified as catalytic self-splicing introns that can be categorized as either Group I or Group II introns. There are some biases, with Group I introns being more frequently encountered in fungal mitochondrial genomes, whereas among plants Group II introns dominate within the mitochondrial and chloroplast genomes. Organellar introns can encode a variety of proteins, such as maturases, homing endonucleases, reverse transcriptases, and, in some cases, ribosomal proteins, along with other novel open reading frames. Although organellar introns are viewed to be ribozymes, they do interact with various intron- or nuclear genome-encoded protein factors that assist in the intron RNA to fold into competent splicing structures, or facilitate the turn-over of intron RNAs to prevent reverse splicing. Organellar introns are also known to be involved in non-canonical splicing, such as backsplicing and trans-splicing which can result in novel splicing products or, in some instances, compensate for the fragmentation of genes by recombination events. In organellar genomes, Group I and II introns may exist in nested intronic arrangements, such as introns within introns, referred to as twintrons, where splicing of the external intron may be dependent on splicing of the internal intron. These nested or complex introns, with two or three-component intron modules, are being explored as platforms for alternative splicing and their possible function as molecular switches for modulating gene expression which could be potentially applied towards heterologous gene expression. This review explores recent findings on organellar Group I and II introns, focusing on splicing and mobility mechanisms aided by associated intron/nuclear encoded proteins and their potential roles in organellar gene expression and cross talk between nuclear and organellar genomes. Potential application for these types of elements in biotechnology are also discussed.

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Leite, D. L., e M. J. Havey. "Restriction Enzyme Analyses of Cytoplasmic Diversity in Leek". HortScience 31, n. 4 (agosto 1996): 596e—596. http://dx.doi.org/10.21273/hortsci.31.4.596e.

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Hybrid leek (Allium ampeloprasum) is significantly more uniform and higher yielding than open-pollinated populations. Because leek has perfect flowers, a male-sterility system is required to produce hybrid seed economically. No cytoplasmic male sterility (CMS) has been described in leek. Restriction fragment length polymorphisms (RFLPs) in the chloroplast and mitochondrial genome have correlated with the expression of CMS in many crops. We undertook restriction-enzyme analyses of the chloroplast and mitochondrial DNAs to identify polymorphic organellar genomes among 65 accessions of cultivated leek. Polymorphisms were detected in the chloroplast and mitochondrial genomes. Reciprocal crosses were generated to establish the transmission of the organellar genomes of leek.

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STERN, D. B. "DNA Transposition Between Plant Organellar Genomes". Journal of Cell Science 1987, Supplement 7 (1 febbraio 1987): 145–54. http://dx.doi.org/10.1242/jcs.1987.supplement_7.11.

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Cheng, Lingling, Wenjie Wang, Yao Yao e Qianwen Sun. "Mitochondrial RNase H1 activity regulates R-loop homeostasis to maintain genome integrity and enable early embryogenesis in Arabidopsis". PLOS Biology 19, n. 8 (3 agosto 2021): e3001357. http://dx.doi.org/10.1371/journal.pbio.3001357.

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Plant mitochondrial genomes undergo frequent homologous recombination (HR). Ectopic HR activity is inhibited by the HR surveillance pathway, but the underlying regulatory mechanism is unclear. Here, we show that the mitochondrial RNase H1 AtRNH1B impairs the formation of RNA:DNA hybrids (R-loops) and participates in the HR surveillance pathway in Arabidopsis thaliana. AtRNH1B suppresses ectopic HR at intermediate-sized repeats (IRs) and thus maintains mitochondrial DNA (mtDNA) replication. The RNase H1 AtRNH1C is restricted to the chloroplast; however, when cells lack AtRNH1B, transport of chloroplast AtRNH1C into the mitochondria secures HR surveillance, thus ensuring the integrity of the mitochondrial genome and allowing embryogenesis to proceed. HR surveillance is further regulated by the single-stranded DNA-binding protein ORGANELLAR SINGLE-STRANDED DNA BINDING PROTEIN1 (OSB1), which decreases the formation of R-loops. This study uncovers a facultative dual targeting mechanism between organelles and sheds light on the roles of RNase H1 in organellar genome maintenance and embryogenesis.

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Havey, M. J., J. D. McCreight, B. Rhodes e G. Taurick. "Differential transmission of the Cucumis organellar genomes". Theoretical and Applied Genetics 97, n. 1-2 (luglio 1998): 122–28. http://dx.doi.org/10.1007/s001220050875.

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Wyman, S. K., R. K. Jansen e J. L. Boore. "Automatic annotation of organellar genomes with DOGMA". Bioinformatics 20, n. 17 (4 giugno 2004): 3252–55. http://dx.doi.org/10.1093/bioinformatics/bth352.

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Mandel, Jennifer R., Adam J. Ramsey, Jacob M. Holley, Victoria A. Scott, Dviti Mody e Patrick Abbot. "Disentangling Complex Inheritance Patterns of Plant Organellar Genomes: An Example From Carrot". Journal of Heredity 111, n. 6 (1 settembre 2020): 531–38. http://dx.doi.org/10.1093/jhered/esaa037.

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Abstract Plant mitochondria and plastids display an array of inheritance patterns and varying levels of heteroplasmy, where individuals harbor more than 1 version of a mitochondrial or plastid genome. Organelle inheritance in plants has the potential to be quite complex and can vary with plant growth, development, and reproduction. Few studies have sought to investigate these complicated patterns of within-individual variation and inheritance using experimental crosses in plants. We carried out crosses in carrot, Daucus carota L. (Apiaceae), which has previously been shown to exhibit organellar heteroplasmy. We used mitochondrial and plastid markers to begin to disentangle the patterns of organellar inheritance and the fate of heteroplasmic variation, with special focus on cases where the mother displayed heteroplasmy. We also investigated heteroplasmy across the plant, assaying leaf samples at different development stages and ages. Mitochondrial and plastid paternal leakage was rare and offspring received remarkably similar heteroplasmic mixtures to their heteroplasmic mothers, indicating that heteroplasmy is maintained over the course of maternal inheritance. When offspring did differ from their mother, they were likely to exhibit a loss of the genetic variation that was present in their mother. Finally, we found that mitochondrial variation did not vary significantly over plant development, indicating that substantial vegetative sorting did not occur. Our study is one of the first to quantitatively investigate inheritance patterns and heteroplasmy in plants using controlled crosses, and we look forward to future studies making use of whole genome information to study the complex evolutionary dynamics of plant organellar genomes.

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Gupta, Ankit, Priyanka Shah, Afreen Haider, Kirti Gupta, Mohammad Imran Siddiqi, Stuart A. Ralph e Saman Habib. "Reduced ribosomes of the apicoplast and mitochondrion of Plasmodium spp. and predicted interactions with antibiotics". Open Biology 4, n. 5 (maggio 2014): 140045. http://dx.doi.org/10.1098/rsob.140045.

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Apicomplexan protists such as Plasmodium and Toxoplasma contain a mitochondrion and a relic plastid (apicoplast) that are sites of protein translation. Although there is emerging interest in the partitioning and function of translation factors that participate in apicoplast and mitochondrial peptide synthesis, the composition of organellar ribosomes remains to be elucidated. We carried out an analysis of the complement of core ribosomal protein subunits that are encoded by either the parasite organellar or nuclear genomes, accompanied by a survey of ribosome assembly factors for the apicoplast and mitochondrion. A cross-species comparison with other apicomplexan, algal and diatom species revealed compositional differences in apicomplexan organelle ribosomes and identified considerable reduction and divergence with ribosomes of bacteria or characterized organelle ribosomes from other organisms. We assembled structural models of sections of Plasmodium falciparum organellar ribosomes and predicted interactions with translation inhibitory antibiotics. Differences in predicted drug–ribosome interactions with some of the modelled structures suggested specificity of inhibition between the apicoplast and mitochondrion. Our results indicate that Plasmodium and Toxoplasma organellar ribosomes have a unique composition, resulting from the loss of several large and small subunit proteins accompanied by significant sequence and size divergences in parasite orthologues of ribosomal proteins.

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Aunin, Eerik, Ulrike Böhme, Damer Blake, Alexander Dove, Michelle Smith, Craig Corton, Karen Oliver et al. "The complete genome sequence of Eimeria tenella (Tyzzer 1929), a common gut parasite of chickens". Wellcome Open Research 6 (9 settembre 2021): 225. http://dx.doi.org/10.12688/wellcomeopenres.17100.1.

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We present a genome assembly from a clonal population of Eimeria tenella Houghton parasites (Apicomplexa; Conoidasida; Eucoccidiorida; Eimeriidae). The genome sequence is 53.25 megabases in span. The entire assembly is scaffolded into 15 chromosomal pseudomolecules, with complete mitochondrion and apicoplast organellar genomes also present.

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Sawicki, Jakub, Katarzyna Krawczyk, Łukasz Paukszto, Mateusz Maździarz, Mateusz Kurzyński, Joanna Szablińska-Piernik e Monika Szczecińska. "Nanopore Sequencing Technology as an Emerging Tool for Diversity Studies of Plant Organellar Genomes". Diversity 16, n. 3 (7 marzo 2024): 173. http://dx.doi.org/10.3390/d16030173.

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In this comprehensive review, we explore the significant role that nanopore sequencing technology plays in the study of plant organellar genomes, particularly mitochondrial and chloroplast DNA. To date, the application of nanopore sequencing has led to the successful sequencing of over 100 plant mitochondrial genomes and around 80 chloroplast genomes. These figures not only demonstrate the technology’s robustness but also mark a substantial advancement in the field, highlighting its efficacy in decoding the complex and dynamic nature of these genomes. Nanopore sequencing, known for its long-read capabilities, significantly surpasses traditional sequencing techniques, especially in addressing challenges like structural complexity and sequence repetitiveness in organellar DNA. This review delves into the nuances of nanopore sequencing, elaborating on its benefits compared to conventional methods and the groundbreaking applications it has fostered in plant organellar genomics. While its transformative impact is clear, the technology’s limitations, including error rates and computational requirements, are discussed, alongside potential solutions and prospects for technological refinement.

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Liang, Yanshuo, Han-Gil Choi, Shuangshuang Zhang, Zi-Min Hu e Delin Duan. "The organellar genomes of Silvetia siliquosa (Fucales, Phaeophyceae) and comparative analyses of the brown algae". PLOS ONE 17, n. 6 (16 giugno 2022): e0269631. http://dx.doi.org/10.1371/journal.pone.0269631.

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The brown alga Silvetia siliquosa (Tseng et Chang) Serrão, Cho, Boo & Brawly is endemic to the Yellow-Bohai Sea and southwestern Korea. It is increasingly endangered due to habitat loss and excessive collection. Here, we sequenced the mitochondrial (mt) and chloroplast (cp) genomes of S. siliquosa. De novo assembly showed that the mt-genome was 36,036 bp in length, including 38 protein-coding genes (PCGs), 26 tRNAs, and 3 rRNAs, and the cp-genome was 124,991 bp in length, containing 139 PCGs, 28 tRNAs, and 6 rRNAs. Gene composition, gene number, and gene order of the mt-genome and cp-genome were very similar to those of other species in Fucales. Phylogenetic analysis revealed a close genetic relationship between S. siliquosa and F. vesiculosus, which diverged approximately 8 Mya (5.7–11.0 Mya), corresponding to the Late Miocene (5.3–11.6 Ma). The synonymous substitution rate of mitochondrial genes of phaeophycean species was 1.4 times higher than that of chloroplast genes, but the cp-genomes were more structurally variable than the mt-genomes, with numerous gene losses and rearrangements among the different orders in Phaeophyceae. This study reports the mt- and cp-genomes of the endangered S. siliquosa and improves our understanding of its phylogenetic position in Phaeophyceae and of organellar genomic evolution in brown algae.

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Robles, Pedro, e Víctor Quesada. "Transcriptional and Post-transcriptional Regulation of Organellar Gene Expression (OGE) and Its Roles in Plant Salt Tolerance". International Journal of Molecular Sciences 20, n. 5 (28 febbraio 2019): 1056. http://dx.doi.org/10.3390/ijms20051056.

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Given their endosymbiotic origin, chloroplasts and mitochondria genomes harbor only between 100 and 200 genes that encode the proteins involved in organellar gene expression (OGE), photosynthesis, and the electron transport chain. However, as the activity of these organelles also needs a few thousand proteins encoded by the nuclear genome, a close coordination of the gene expression between the nucleus and organelles must exist. In line with this, OGE regulation is crucial for plant growth and development, and is achieved mainly through post-transcriptional mechanisms performed by nuclear genes. In this way, the nucleus controls the activity of organelles and these, in turn, transmit information about their functional state to the nucleus by modulating nuclear expression according to the organelles’ physiological requirements. This adjusts organelle function to plant physiological, developmental, or growth demands. Therefore, OGE must appropriately respond to both the endogenous signals and exogenous environmental cues that can jeopardize plant survival. As sessile organisms, plants have to respond to adverse conditions to acclimate and adapt to them. Salinity is a major abiotic stress that negatively affects plant development and growth, disrupts chloroplast and mitochondria function, and leads to reduced yields. Information on the effects that the disturbance of the OGE function has on plant tolerance to salinity is still quite fragmented. Nonetheless, many plant mutants which display altered responses to salinity have been characterized in recent years, and interestingly, several are affected in nuclear genes encoding organelle-localized proteins that regulate the expression of organelle genes. These results strongly support a link between OGE and plant salt tolerance, likely through retrograde signaling. Our review analyzes recent findings on the OGE functions required by plants to respond and tolerate salinity, and highlights the fundamental role that chloroplast and mitochondrion homeostasis plays in plant adaptation to salt stress.

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Kamikawa, Ryoma, Tomonori Azuma, Ken-ichiro Ishii, Yusei Matsuno e Hideaki Miyashita. "Diversity of Organellar Genomes in Non-photosynthetic Diatoms". Protist 169, n. 3 (luglio 2018): 351–61. http://dx.doi.org/10.1016/j.protis.2018.04.009.

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Chardon, Fabien, Gwendal Cueff, Etienne Delannoy, Fabien Aubé, Aurélia Lornac, Magali Bedu, Françoise Gilard et al. "The Consequences of a Disruption in Cyto-Nuclear Coadaptation on the Molecular Response to a Nitrate Starvation in Arabidopsis". Plants 9, n. 5 (1 maggio 2020): 573. http://dx.doi.org/10.3390/plants9050573.

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Mitochondria and chloroplasts are important actors in the plant nutritional efficiency. So, it could be expected that a disruption of the coadaptation between nuclear and organellar genomes impact plant response to nutrient stresses. We addressed this issue using two Arabidopsis accessions, namely Ct-1 and Jea, and their reciprocal cytolines possessing the nuclear genome from one parent and the organellar genomes of the other one. We measured gene expression, and quantified proteins and metabolites under N starvation and non-limiting conditions. We observed a typical response to N starvation at the phenotype and molecular levels. The phenotypical response to N starvation was similar in the cytolines compared to the parents. However, we observed an effect of the disruption of genomic coadaptation at the molecular levels, distinct from the previously described responses to organellar stresses. Strikingly, genes differentially expressed in cytolines compared to parents were mainly repressed in the cytolines. These genes encoded more mitochondrial and nuclear proteins than randomly expected, while N starvation responsive ones were enriched in genes for chloroplast and nuclear proteins. In cytolines, the non-coadapted cytonuclear genomic combination tends to modulate the response to N starvation observed in the parental lines on various biological processes.

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Coate, Jeremy E., W. Max Schreyer, David Kum e Jeff J. Doyle. "Robust Cytonuclear Coordination of Transcription in Nascent Arabidopsis thaliana Autopolyploids". Genes 11, n. 2 (28 gennaio 2020): 134. http://dx.doi.org/10.3390/genes11020134.

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Polyploidy is hypothesized to cause dosage imbalances between the nucleus and the other genome-containing organelles (mitochondria and plastids), but the evidence for this is limited. We performed RNA-seq on Arabidopsis thaliana diploids and their derived autopolyploids to quantify the degree of inter-genome coordination of transcriptional responses to nuclear whole genome duplication in two different organs (sepals and rosette leaves). We show that nuclear and organellar genomes exhibit highly coordinated responses in both organs. First, organelle genome copy number increased in response to nuclear whole genome duplication (WGD), at least partially compensating for altered nuclear genome dosage. Second, transcriptional output of the different cellular compartments is tuned to maintain diploid-like levels of relative expression among interacting genes. In particular, plastid genes and nuclear genes whose products are plastid-targeted show coordinated down-regulation, such that their expression levels relative to each other remain constant across ploidy levels. Conversely, mitochondrial genes and nuclear genes with mitochondrial targeting show either constant or coordinated up-regulation of expression relative to other nuclear genes. Thus, cytonuclear coordination is robust to changes in nuclear ploidy level, with diploid-like balance in transcript abundances achieved within three generations after nuclear whole genome duplication.

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Bogdanova, Vera S., Natalia V. Shatskaya, Anatoliy V. Mglinets, Oleg E. Kosterin e Gennadiy V. Vasiliev. "Discordant evolution of organellar genomes in peas (Pisum L.)". Molecular Phylogenetics and Evolution 160 (luglio 2021): 107136. http://dx.doi.org/10.1016/j.ympev.2021.107136.

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Flood, Pádraic J., Tom P. J. M. Theeuwen, Korbinian Schneeberger, Paul Keizer, Willem Kruijer, Edouard Severing, Evangelos Kouklas et al. "Reciprocal cybrids reveal how organellar genomes affect plant phenotypes". Nature Plants 6, n. 1 (gennaio 2020): 13–21. http://dx.doi.org/10.1038/s41477-019-0575-9.

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Bell, Neil E., Jeffrey L. Boore, Brent D. Mishler e Jaakko Hyvönen. "Organellar genomes of the four-toothed moss, Tetraphis pellucida". BMC Genomics 15, n. 1 (2014): 383. http://dx.doi.org/10.1186/1471-2164-15-383.

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Ramakrishna, Ramaswamy, e Ramachandran Srinivasan. "Gene identification in bacterial and organellar genomes using GeneScan". Computers & Chemistry 23, n. 2 (marzo 1999): 165–74. http://dx.doi.org/10.1016/s0097-8485(98)00034-5.

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Woodson, Jesse D., e Joanne Chory. "Coordination of gene expression between organellar and nuclear genomes". Nature Reviews Genetics 9, n. 5 (maggio 2008): 383–95. http://dx.doi.org/10.1038/nrg2348.

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Iha, Cintia, Cayne Layton, Warren Flentje, Andrew Lenton, Craig Johnson, Ceridwen I. Fraser e Anusuya Willis. "Organellar genomes of giant kelp from the southern hemisphere". Applied Phycology 4, n. 1 (28 marzo 2023): 78–86. http://dx.doi.org/10.1080/26388081.2023.2193619.

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Nagano, Yukio, Kei Kimura, Genta Kobayashi e Yoshio Kawamura. "Genomic diversity of 39 samples of Pyropia species grown in Japan". PLOS ONE 16, n. 6 (9 giugno 2021): e0252207. http://dx.doi.org/10.1371/journal.pone.0252207.

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Abstract (sommario):

Some Pyropia species, such as nori (P. yezoensis), are important marine crops. We conducted a phylogenetic analysis of 39 samples of Pyropia species grown in Japan using organellar genome sequences. A comparison of the chloroplast DNA sequences with those from China showed a clear genetic separation between Japanese and Chinese P. yezoensis. Conversely, comparing the mitochondrial DNA sequences did not separate Japanese and Chinese P. yezoensis. Analysis of organellar genomes showed that the genetic diversity of Japanese P. yezoensis used in this study is lower than that of Chinese wild P. yezoensis. To analyze the genetic relationships between samples of Japanese Pyropia, we used whole-genome resequencing to analyze their nuclear genomes. In the offspring resulting from cross-breeding between P. yezoensis and P. tenera, nearly 90% of the genotypes analyzed by mapping were explained by the presence of different chromosomes originating from two different parental species. Although the genetic diversity of Japanese P. yezoensis is low, analysis of nuclear genomes genetically separated each sample. Samples isolated from the sea were often genetically similar to those being farmed. Study of genetic heterogeneity of samples within a single aquaculture strain of P. yezoensis showed that samples were divided into two groups and the samples with frequent abnormal budding formed a single, genetically similar group. The results of this study will be useful for breeding and the conservation of Pyropia species.

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Li, Changping, Xiaofei Wang, Yaxian Xiao, Xuhan Sun, Jinbin Wang, Xuan Yang, Yuchen Sun et al. "Coevolution in Hybrid Genomes: Nuclear-Encoded Rubisco Small Subunits and Their Plastid-Targeting Translocons Accompanying Sequential Allopolyploidy Events in Triticum". Molecular Biology and Evolution 37, n. 12 (30 giugno 2020): 3409–22. http://dx.doi.org/10.1093/molbev/msaa158.

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Abstract The Triticum/Aegilops complex includes hybrid species resulting from homoploid hybrid speciation and allopolyploid speciation. Sequential allotetra- and allohexaploidy events presumably result in two challenges for the hybrids, which involve 1) cytonuclear stoichiometric disruptions caused by combining two diverged nuclear genomes with the maternal inheritance of the cytoplasmic organellar donor; and 2) incompatibility of chimeric protein complexes with diverged subunits from nuclear and cytoplasmic genomes. Here, we describe coevolution of nuclear rbcS genes encoding the small subunits of Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) and nuclear genes encoding plastid translocons, which mediate recognition and translocation of nuclear-encoded proteins into plastids, in allopolyploid wheat species. We demonstrate that intergenomic paternal-to-maternal gene conversion specifically occurred in the genic region of the homoeologous rbcS3 gene from the D-genome progenitor of wheat (abbreviated as rbcS3D) such that it encodes a maternal-like or B-subgenome-like SSU3D transit peptide in allohexaploid wheat but not in allotetraploid wheat. Divergent and limited interaction between SSU3D and the D-subgenomic TOC90D translocon subunit is implicated to underpin SSU3D targeting into the chloroplast of hexaploid wheat. This implicates early selection favoring individuals harboring optimal maternal-like organellar SSU3D targeting in hexaploid wheat. These data represent a novel dimension of cytonuclear evolution mediated by organellar targeting and transportation of nuclear proteins.

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HUGHEY, JEFFERY R., VIVIANA PEÑA e PAUL W. GABRIELSON. "Deep sequencing of the epitype specimen of Synarthrophyton patena (Hooker f. & Harvey) R.A.Townsend (Hapalidiales, Rhodophyta) confirms the correct application of this name". Phytotaxa 558, n. 1 (11 agosto 2022): 81–92. http://dx.doi.org/10.11646/phytotaxa.558.1.5.

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Synarthrophyton patena (Hooker f. & Harvey) R.A.Townsend is a discoid marine coralline red alga distributed in the southwestern Pacific Ocean (type locality: southeast North Island, New Zealand). It is the generitype of Synarthrophyton R.A.Townsend, a genus of taxonomic debate. High-throughput sequencing was performed on the herein designated epitype specimen of S. patena to characterize its genetic markers and organellar genome structure. The complete plastid genome of S. patena is 181,685 bp in length and contains 232 genes. A partial mitogenome was assembled amounting to 25,779 bp and encodes 46 genes. Both genomes show a high level of gene synteny to the organellar genomes of S. chejuense. DNA markers rbcL, psbA, and cox1 are identical or very similar to sequences deposited in GenBank and analyzed here under the same name from Australia (including Tasmania) and New Zealand. A combined phylogenetic analysis of S. patena using rbcL and psbA gene sequences fully resolved it in a clade with other S. patena, Synarthrophyton spp., and unidentified Hapalidiales. These data confirm the accurate application of the binomial S. patena, stabilize the use of the generitype, and contribute to future congeneric evolutionary and taxonomic studies in the Hapalidiaceae.

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Wilson, R. J., e D. H. Williamson. "Extrachromosomal DNA in the Apicomplexa". Microbiology and Molecular Biology Reviews 61, n. 1 (marzo 1997): 1–16. http://dx.doi.org/10.1128/mmbr.61.1.1-16.1997.

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Malaria and related apicomplexan parasites have two highly conserved organellar genomes: one is of plastid (pl) origin, and the other is mitochondrial (mt). The organization of both organellar DNA molecules from the human malaria parasite Plasmodium falciparum has been determined, and they have been shown to be tightly packed with genes. The 35-kb circular DNA is the smallest known vestigial plastid genome and is presumed to be functional. All but two of its recognized genes are involved with genetic expression: one of the two encodes a member of the clp family of molecular chaperones, and the other encodes a conserved protein of unknown function found both in algal plastids and in eubacterial genomes. The possible evolutionary source and intracellular location of the plDNA are discussed. The 6-kb tandemly repeated mt genome is the smallest known and codes for only three proteins (cytochrome b and two subunits of cytochrome oxidase) as well as two bizarrely fragmented rRNAs. The organization of the mt genome differs somewhat among genera. The mtDNA sequence provides information not otherwise available about the structure of apicomplexan cytochrome b as well as the unusually fragmented rRNAs. The malarial mtDNA has a phage-like replication mechanism and undergoes extensive recombination like the mtDNA of some other lower eukaryotes.

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Orton, Lauren M., Elisabeth Fitzek, Xuehuan Feng, W. Scott Grayburn, Jeffrey P. Mower, Kan Liu, Chi Zhang, Melvin R. Duvall e Yanbin Yin. "Zygnema circumcarinatum UTEX 1559 chloroplast and mitochondrial genomes provide insight into land plant evolution". Journal of Experimental Botany 71, n. 11 (24 marzo 2020): 3361–73. http://dx.doi.org/10.1093/jxb/eraa149.

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Abstract The complete chloroplast and mitochondrial genomes of Charophyta have shed new light on land plant terrestrialization. Here, we report the organellar genomes of the Zygnema circumcarinatum strain UTEX 1559, and a comparative genomics investigation of 33 plastomes and 18 mitogenomes of Chlorophyta, Charophyta (including UTEX 1559 and its conspecific relative SAG 698-1a), and Embryophyta. Gene presence/absence was determined across these plastomes and mitogenomes. A comparison between the plastomes of UTEX 1559 (157 548 bp) and SAG 698-1a (165 372 bp) revealed very similar gene contents, but substantial genome rearrangements. Surprisingly, the two plastomes share only 85.69% nucleotide sequence identity. The UTEX 1559 mitogenome size is 215 954 bp, the largest among all sequenced Charophyta. Interestingly, this large mitogenome contains a 50 kb region without homology to any other organellar genomes, which is flanked by two 86 bp direct repeats and contains 15 ORFs. These ORFs have significant homology to proteins from bacteria and plants with functions such as primase, RNA polymerase, and DNA polymerase. We conclude that (i) the previously published SAG 698-1a plastome is probably from a different Zygnema species, and (ii) the 50 kb region in the UTEX 1559 mitogenome might be recently acquired as a mobile element.

40

Tian, Geng, Guoqing Li, Yanling Liu, Qinghua Liu, Yanxia Wang, Guangmin Xia e Mengcheng Wang. "Polyploidization is accompanied by synonymous codon usage bias in the chloroplast genomes of both cotton and wheat". PLOS ONE 15, n. 11 (19 novembre 2020): e0242624. http://dx.doi.org/10.1371/journal.pone.0242624.

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Synonymous codon usage bias (SCUB) of both nuclear and organellar genes can mirror the evolutionary specialization of plants. The polyploidization process exposes the nucleus to genomic shock, a syndrome which promotes, among other genetic variants, SCUB. Its effect on organellar genes has not, however, been widely addressed. The present analysis targeted the chloroplast genomes of two leading polyploid crop species, namely cotton and bread wheat. The frequency of codons in the chloroplast genomes ending in either adenosine (NNA) or thymine (NNT) proved to be higher than those ending in either guanidine or cytosine (NNG or NNC), and this difference was conserved when comparisons were made between polyploid and diploid forms in both the cotton and wheat taxa. Preference for NNA/T codons was heterogeneous among genes with various numbers of introns and was also differential among the exons. SCUB patterns distinguished tetraploid cotton from its diploid progenitor species, as well as bread wheat from its diploid/tetraploid progenitor species, indicating that SCUB in the chloroplast genome partially mirrors the formation of polyploidies.

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Shatskaya, N. V., V. S. Bogdanova, O. E. Kosterin, G. V. Vasiliev, A. K. Kimeklis, E. E. Andronov e N. A. Provorov. "The plastid and mitochondrial genomes of Vavilovia Formosa (Stev.) Fed. and the phylogeny of related legume genera". Vavilov Journal of Genetics and Breeding 23, n. 8 (10 gennaio 2020): 972–80. http://dx.doi.org/10.18699/vj19.574.

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The plastid and mitochondrial genomes of Vavilovia formosa (Stev.) Fed. were assembled on the base of the data of high-throughput sequencing of DNA isolated from a sample from North Osetia, Russia, using Illumina and PacBio platforms. The long PacBio reads were sufficient for reliable assembling organellar genomes while the short Illumina reads obtained from total DNA were unacceptable for this purpose because of substantial contamination by nuclear sequences. The organellar genomes were circular DNA molecules; the genome of mitochondria was represented by two circular chromosomes. A phylogenetic analysis on the basis of plastid genomes available in public databases was performed for some representatives of the tribes Fabeae, Trifolieae and Cicereae. As was expected, the V. formosa branch proved to be sister to the Pisum branch, and the tribe Fabeae was monophyletic. The position of Trifolium L. appeared sensitive to the phylogeny reconstruction method, either clustering with Fabeae or with the genera Medicago L., Trigonella L. and Melilotus Mill., but the internodes between successive divergences were short in all cases, suggesting that the radiation of Trifolium, other Trifolieae and Fabeae was fast, occurring within a small time interval as compared to further evolution of these lineages. The data on the relatedness of the plastid genomes of Trifolium and Fabeae correlate with the similarity of N2-fixing symbionts in these legumes represented by Rhizobium leguminosarum biovars trifolii and viciae, while the symbionts of Medicago, Melilotus and Trigonella belong to the Sinorhizobium meliloti and S. medicae species, which are distant from Rhizobium.

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Robles, Pedro, e Víctor Quesada. "Organelle Genetics in Plants". International Journal of Molecular Sciences 22, n. 4 (20 febbraio 2021): 2104. http://dx.doi.org/10.3390/ijms22042104.

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Eleven published articles (4 reviews, 7 research papers) are collected in the Special Issue entitled “Organelle Genetics in Plants.” This selection of papers covers a wide range of topics related to chloroplasts and plant mitochondria research: (i) organellar gene expression (OGE) and, more specifically, chloroplast RNA editing in soybean, mitochondria RNA editing, and intron splicing in soybean during nodulation, as well as the study of the roles of transcriptional and posttranscriptional regulation of OGE in plant adaptation to environmental stress; (ii) analysis of the nuclear integrants of mitochondrial DNA (NUMTs) or plastid DNA (NUPTs); (iii) sequencing and characterization of mitochondrial and chloroplast genomes; (iv) recent advances in plastid genome engineering. Here we summarize the main findings of these works, which represent the latest research on the genetics, genomics, and biotechnology of chloroplasts and mitochondria.

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Andersson, S. G. E., e C. G. Kurland. "Genomic evolution drives the evolution of the translation system". Biochemistry and Cell Biology 73, n. 11-12 (1 dicembre 1995): 775–87. http://dx.doi.org/10.1139/o95-086.

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Our thesis is that the characteristics of the translational machinery and its organization are selected in part by evolutionary pressure on genomic traits have nothing to do with translation per se. These genomic traits include size, composition, and architecture. To illustrate this point, we draw parallels between the structures of different genomes that have adapted to intracellular niches independently of each other. Our starting point is the general observation that the evolutionary history of organellar and parasitic bacteria have favored bantam genomes. Furthermore, we suggest that the constraints of the reductive mode of genomic evolution account for the divergence of the genetic code in mitochondria and the genetic organization of the translational system observed in parasitic bacteria. In particular, we associate codon reassignments in animal mitochondria with greatly simplified tRNA populations. Likewise, we relate the organization of translational genes in the obligate intracellular parasite Rickettsia prowazekii to the processes supporting the reductive mode of genomic evolution. Such findings provide strong support for the hypothesis that genomes of organelles and of parasitic bacteria have arisen from the much larger genomes of ancestral bacteria that have been reduced by intrachromosomal recombination and deletion events. A consequence of the reductive mode of genomic evolution is that the resulting translation systems may deviate markedly from conventional systems.Key words: translation, evolution, genome, reassignment, rearrangement.

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McNeal, Joel R., James H. Leebens-Mack, Kathiravetpillai Arumuganathan, Jennifer V. Kuehl, Jeffrey L. Boore e Claude W. dePamphilis. "Using partial genomic fosmid libraries for sequencing complete organellar genomes". BioTechniques 41, n. 1 (luglio 2006): 69–73. http://dx.doi.org/10.2144/000112202.

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Oborník, Miroslav, e Julius Lukeš. "The Organellar Genomes ofChromeraandVitrella, the Phototrophic Relatives of Apicomplexan Parasites". Annual Review of Microbiology 69, n. 1 (15 ottobre 2015): 129–44. http://dx.doi.org/10.1146/annurev-micro-091014-104449.

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Aguirre-Dugua, Xitlali, Gabriela Castellanos-Morales, Leslie M. Paredes-Torres, Helena S. Hernández-Rosales, Josué Barrera-Redondo, Guillermo Sánchez-de la Vega, Fernando Tapia-Aguirre et al. "Evolutionary Dynamics of Transferred Sequences Between Organellar Genomes in Cucurbita". Journal of Molecular Evolution 87, n. 9-10 (7 novembre 2019): 327–42. http://dx.doi.org/10.1007/s00239-019-09916-1.

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Jackman, Shaun D., René L. Warren, Ewan A. Gibb, Benjamin P. Vandervalk, Hamid Mohamadi, Justin Chu, Anthony Raymond et al. "Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation". Genome Biology and Evolution 8, n. 1 (8 dicembre 2015): 29–41. http://dx.doi.org/10.1093/gbe/evv244.

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Wright, Alan F., Michael P. Murphy e Douglass M. Turnbull. "Do organellar genomes function as long-term redox damage sensors?" Trends in Genetics 25, n. 6 (giugno 2009): 253–61. http://dx.doi.org/10.1016/j.tig.2009.04.006.

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Postel, Zoé, e Pascal Touzet. "Cytonuclear Genetic Incompatibilities in Plant Speciation". Plants 9, n. 4 (10 aprile 2020): 487. http://dx.doi.org/10.3390/plants9040487.

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Abstract (sommario):

Due to the endosymbiotic origin of organelles, a pattern of coevolution and coadaptation between organellar and nuclear genomes is required for proper cell function. In this review, we focus on the impact of cytonuclear interaction on the reproductive isolation of plant species. We give examples of cases where species exhibit barriers to reproduction which involve plastid-nuclear or mito-nuclear genetic incompatibilities, and describe the evolutionary processes at play. We also discuss potential mechanisms of hybrid fitness recovery such as paternal leakage. Finally, we point out the possible interplay between plant mating systems and cytonuclear coevolution, and its consequence on plant speciation.

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Petersen, G., H. Darby, V. K. Y. Lam, H. Æ. Pedersen, V. S. F. T. Merckx, A. Zervas, O. Seberg e S. W. Graham. "Mycoheterotrophic Epirixanthes (Polygalaceae) has a typical angiosperm mitogenome but unorthodox plastid genomes". Annals of Botany 124, n. 5 (26 luglio 2019): 791–807. http://dx.doi.org/10.1093/aob/mcz114.

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Abstract Background and Aims Fully mycoheterotrophic plants derive carbon and other nutrients from root-associated fungi and have lost the ability to photosynthesize. While mycoheterotroph plastomes are often degraded compared with green plants, the effect of this unusual symbiosis on mitochondrial genome evolution is unknown. By providing the first complete organelle genome data from Polygalaceae, one of only three eudicot families that developed mycoheterotrophy, we explore how both organellar genomes evolved after loss of photosynthesis. Methods We sequenced and assembled four complete plastid genomes and a mitochondrial genome from species of Polygalaceae, focusing on non-photosynthetic Epirixanthes. We compared these genomes with those of other mycoheterotroph and parasitic plant lineages, and assessed whether organelle genes in Epirixanthes experienced relaxed or intensified selection compared with autotrophic relatives. Key Results Plastomes of two species of Epirixanthes have become substantially degraded compared with that of autotrophic Polygala. Although the lack of photosynthesis is presumably homologous in the genus, the surveyed Epirixanthes species have marked differences in terms of plastome size, structural rearrangements, gene content and substitution rates. Remarkably, both apparently replaced a canonical plastid inverted repeat with large directly repeated sequences. The mitogenome of E. elongata incorporated a considerable number of fossilized plastid genes, by intracellular transfer from an ancestor with a less degraded plastome. Both plastid and mitochondrial genes in E. elongata have increased substitution rates, but the plastid genes of E. pallida do not. Despite this, both species have similar selection patterns operating on plastid housekeeping genes. Conclusions Plastome evolution largely fits with patterns of gene degradation seen in other heterotrophic plants, but includes highly unusual directly duplicated regions. The causes of rate elevation in the sequenced Epirixanthes mitogenome and of rate differences in plastomes of related mycoheterotrophic species are not currently understood.

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