Comparison of <i>Oryza sativa</i> and <i>Oryza brachyantha</i> Genomes Reveals Selection-Driven Gene Escape from the Centromeric Regions

Liao, Yi; Zhang, Xuemei; Li, Bo; Liu, Tie-Yan; Chen, Jinfeng; Bai, Zetao; Wang, Meijiao; Shi, Jinfeng; Walling, Jason G.; Wing, Rod A.; Jiang, Jiming; Chen, Mingsheng

doi:10.1105/tpc.18.00163

Cited by 22 publications

(19 citation statements)

References 83 publications

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“…1c). This inversion has been reported previously to contain 404 genes (69), and it was also identified in O. brachyantha compared to indica assemblies (70). Another SV feature is genic hemizygosity, which can be estimated reasonably from SMRT reads (35).…”

Section: Svs Across Datasetssupporting

confidence: 62%

Evolutionary genomics of structural variation in Asian rice (Oryza sativa) and its wild progenitor (O. rufipogon)

Kou

Liao

Toivainen

et al. 2019

Preprint

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Structural variants (SVs) are a largely unstudied feature of plant genome evolution, despite the fact that SVs contribute substantially to phenotypes. In this study, we discovered structural variants (SVs) across a population sample of 358 high-coverage, resequenced genomes of Asian rice (Oryza sativa) and its wild ancestor (O. rufipogon). In addition to this short-read dataset, we also inferred SVs from whole-genome assemblies and long-read data. Comparisons among datasets revealed different features of genome variability. For example, genome alignment identified a large (~4.3 Mb) inversion in indica rice varieties relative to an outgroup, and longread analyses suggest that ~9% of genes from this outgroup are hemizygous. We focused, however, on the resequencing sample to investigate the population genomics of SVs. Clustering analyses with SVs recapitulated the rice cultivar groups that were also inferred from SNPs.However, the site-frequency spectrum of each SV type --which included inversions, duplications, deletions, translocations and mobile element insertions --was skewed toward lower frequency variants than synonymous SNPs, suggesting that SVs are predominantly deleterious. The strength of these deleterious effects varied among SV types, with inversions especially deleterious, and across transposable element (TE) families. Among TEs SINE and mariner insertions were especially deleterious, due to stronger selection against their insertions. We also used SVs to study domestication by contrasting between rice and O. rufipogon. Cultivated genomes contained ~25% more derived SVs than O. rufipogon, suggesting these deleterious SVs contribute to the cost of domestication. We also used SVs to study the effects of positive selection on the rice genome. Generally, the search for domestication genes were enriched for known candidates, suggesting some utility for SVs towards this purpose. More importantly, we detected hundreds to thousands of genes gained and lost during domestication, many of which are predicted to contribute to traits of agronomic interest.

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Section: Svs Across Datasetssupporting

confidence: 62%

Evolutionary genomics of structural variation in Asian rice (Oryza sativa) and its wild progenitor (O. rufipogon)

Kou

Liao

Toivainen

et al. 2019

Preprint

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“…These findings suggested that NUPTs likely more accumulated in centromeric or pericentromeric regions in A. officinalis . Centromeric and pericentromeric regions are hotspots of organelle–nucleus DNA transfer [15, 39], because of the low gene density and high heterochromatin content of these regions [43–46], which may provide a stable genomic environment for the integration of the organelle-derived DNA [6, 15]. However, Yoshida et al showed that NUPTs also accumulate in the distal regions of chromosomes [38].…”

Section: Discussionmentioning

confidence: 99%

Cytogenetic and genomic organization analyses of chloroplast DNA invasions in the nuclear genome of Asparagus officinalis L. provides signatures of evolutionary complexity and informativity in sex chromosome evolution

Wang

et al. 2019

BMC Plant Biol

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Background The transfer of chloroplast DNA into nuclear genome is a common process in plants. These transfers form nuclear integrants of plastid DNAs (NUPTs), which are thought to be driving forces in genome evolution, including sex chromosome evolution. In this study, NUPTs in the genome of a dioecious plant Asparagus officinalis L. were systematically analyzed, in order to investigate the characteristics of NUPTs in the nuclear genome and the relationship between NUPTs and sex chromosome evolution in this species. Results A total of 3155 NUPT insertions were detected, and they represented approximated 0.06% of the nuclear genome. About 45% of the NUPTs were organized in clusters. These clusters were derived from various evolutionary events. The Y chromosome contained the highest number and largest proportion of NUPTs, suggesting more accumulation of NUPTs on sex chromosomes. NUPTs were distributed widely in all of the chromosomes, and some regions preferred these insertions. The highest density of NUPTs was found in a 47 kb region in the Y chromosome; more than 75% of this region was occupied by NUPTs. Further cytogenetic and sequence alignment analysis revealed that this region was likely the centromeric region of the sex chromosomes. On the other hand, the male-specific region of the Y chromosome (MSY) and the adjacent regions did not have NUPT insertions. Conclusions These results indicated that NUPTs were involved in shaping the genome of A. officinalis through complicated process. NUPTs may play important roles in the centromere shaping of the sex chromosomes of A. officinalis , but were not implicated in MSY formation. Electronic supplementary material The online version of this article (10.1186/s12870-019-1975-8) contains supplementary material, which is available to authorized users.

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“…NUPTs/NUMTs are usually distributed unevenly in the analyzed plant genomes [20,21,39]. NUPTs and NUMTs are more preferred to distribute in centromeric and pericentromeric regions [36,39], which have few genes and a high level of heterochromatin content [42][43][44]. Such regions may offer a stable genomic environment for the maintenance of the alien organelle-originated DNA [16,36].…”

Section: Organization and Distribution Patternsmentioning

confidence: 99%

Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants

Zhang

Dong

Lan

et al. 2020

IJMS

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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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Comparison of Oryza sativa and Oryza brachyantha Genomes Reveals Selection-Driven Gene Escape from the Centromeric Regions

Cited by 22 publications

References 83 publications

Evolutionary genomics of structural variation in Asian rice (Oryza sativa) and its wild progenitor (O. rufipogon)

Evolutionary genomics of structural variation in Asian rice (Oryza sativa) and its wild progenitor (O. rufipogon)

Cytogenetic and genomic organization analyses of chloroplast DNA invasions in the nuclear genome of Asparagus officinalis L. provides signatures of evolutionary complexity and informativity in sex chromosome evolution

Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants

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