The Amount of RNA Editing Sites in Liverwort Organellar Genes Is Correlated with GC Content and Nuclear PPR Protein Diversity

Dong, Shanshan; Zhao, Chaoxian; Zhang, Shouzhou; Wu, Hong; Mu, Weixue; Wei, Tong; Li, Na; Wan, Tao; Liu, Huan; Cui, Jie; Zhu, Rui‐Liang; Goffinet, Bernard; Liu, Yang

doi:10.1093/gbe/evz232

Cited by 31 publications

(41 citation statements)

References 56 publications

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“…Due to the very large difference between the numbers of predicted and empirically measured RNA editing sites in Taxus (this study) and Welwitschia [81], we did not compare the variation in RNA editing sites among the five focal species in detail. Generally, the number of mitochondrial RNA editing sites is not correlated with mitogenome size or GC content but is significantly correlated with the GC content of genes [53,82]. However, this correlation is not supported in this study.…”

Section: Separate Losses Of Multiple Mitochondrial Trna Genes In Pinacontrasting

confidence: 87%

The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome

et al. 2020

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Background: Gymnosperms represent five of the six lineages of seed plants. However, most sequenced plant mitochondrial genomes (mitogenomes) have been generated for angiosperms, whereas mitogenomic sequences have been generated for only six gymnosperms. In particular, complete mitogenomes are available for all major seed plant lineages except Conifer II (non-Pinaceae conifers or Cupressophyta), an important lineage including six families, which impedes a comprehensive understanding of the mitogenomic diversity and evolution in gymnosperms. Results: Here, we report the complete mitogenome of Taxus cuspidata in Conifer II. In comparison with previously released gymnosperm mitogenomes, we found that the mitogenomes of Taxus and Welwitschia have lost many genes individually, whereas all genes were identified in the mitogenomes of Cycas, Ginkgo and Pinaceae. Multiple tRNA genes and introns also have been lost in some lineages of gymnosperms, similar to the pattern observed in angiosperms. In general, gene clusters could be less conserved in gymnosperms than in angiosperms. Moreover, fewer RNA editing sites were identified in the Taxus and Welwitschia mitogenomes than in other mitogenomes, which could be correlated with fewer introns and frequent gene losses in these two species. Conclusions: We have sequenced the Taxus cuspidata mitogenome, and compared it with mitogenomes from the other four gymnosperm lineages. The results revealed the diversity in size, structure, gene and intron contents, foreign sequences, and mutation rates of gymnosperm mitogenomes, which are different from angiosperm mitogenomes.

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Section: Separate Losses Of Multiple Mitochondrial Trna Genes In Pinacontrasting

confidence: 87%

The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome

et al. 2020

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“…The tRNA genes were annotated using tRNAscan-SE v2.0 [47]. Mitochondrial RNA editing sites were obtained from our previous study on liverwort organellar RNA editing [48]. We summarized and compared the structural evolution of all the formally published (as by June 2019) liverwort mt genomes (Additional file 2: Table S2) from the gff3 annotation files.…”

Section: Methodsmentioning

confidence: 99%

Mitochondrial genomes of the early land plant lineage liverworts (Marchantiophyta): conserved genome structure, and ongoing low frequency recombination

et al. 2019

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Background: In contrast to the highly labile mitochondrial (mt) genomes of vascular plants, the architecture and composition of mt genomes within the main lineages of bryophytes appear stable and invariant. The available mt genomes of 18 liverwort accessions representing nine genera and five orders are syntenous except for Gymnomitrion concinnatum whose genome is characterized by two rearrangements. Here, we expanded the number of assembled liverwort mt genomes to 47, broadening the sampling to 31 genera and 10 orders spanning much of the phylogenetic breadth of liverworts to further test whether the evolution of the liverwort mitogenome is overall static. Results: Liverwort mt genomes range in size from 147 Kb in Jungermanniales (clade B) to 185 Kb in Marchantiopsida, mainly due to the size variation of intergenic spacers and number of introns. All newly assembled liverwort mt genomes hold a conserved set of genes, but vary considerably in their intron content. The loss of introns in liverwort mt genomes might be explained by localized retroprocessing events. Liverwort mt genomes are strictly syntenous in genome structure with no structural variant detected in our newly assembled mt genomes. However, by screening the paired-end reads, we do find rare cases of recombination, which means multiple concurrent genome structures may exist in the vegetative tissues of liverworts. Our phylogenetic analyses of the nuclear encoded double stand break repair protein families revealed liverwort-specific subfamilies expansions. Conclusions: The low repeat recombination level, selection, along with the intensified nuclear surveillance, might together shape the structural evolution of liverwort mt genomes.

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“…Mosses seem to hold the least amount of RNa editing sites, e.g., Physcomitrium holds 11 C-to-u RNa editing events in its mt transcripts (Rüdinger et al 2009). using genomic and transcriptomic data, our previous study (Dong et al 2019b) has identified 4,694 RNa editing sites in the mitogenomes of 33 liverwort species, 91% of these occurring as nonsynonymous editing. The abundance of RNa editing site varies greatly among different liverwort lineages, species, and genes.…”

Section: Bryophyte Mitochondrial Rna Editingmentioning

confidence: 98%

“…Bryophyte mitogenomes demonstrate much smaller sizes (100-242 Kb) with narrow size fluctuations compared with that of the large and variable mitogenomes of vascular plants. each bryophyte lineage holds a constant protein-coding gene (PCg) set with very small variations (Liu et al 2014b;Dong et al 2018a;Dong et al 2019b). Liverworts and mosses hold the most complete mt gene repertoire of 40-42 PCgs among land plants, whereas hornwort mitogenomes show distinctly reduced numbers of functional genes, with most ribosomal protein genes lost or pseudogenized (Dong et al 2018a).…”

Section: Introductionmentioning

confidence: 99%

The mitochondrial genomes of bryophytes

Dong

Liu

2021

BDE

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In contrast to the highly variable mitogenomes of vascular plants, the composition and architecture of mitogenomes within the three bryophyte lineages appear stable and invariant. Currently, complete mitogenomes are available from 113 bryophyte accessions of 71 genera and 28 orders. Liverworts and mosses hold a rich mitochondrial (mt) gene repertoire among land plants with 40–42 protein-coding genes, whereas hornworts maintain the smallest functional gene set among land plants, of only around two dozen protein-coding genes, with the majority of ribosomal genes pseudogenized and all cytochrome c maturase genes lost. The rRNA and tRNA genes are also conserved and rich in mosses and liverworts, whereas subject to patchy losses in hornworts. In contrast to the conserved gene set, intron content varies significantly with only one intron shared among the three bryophyte lineages. Bryophytes hold relatively compact mitogenomes with narrow size fluctuations. Among the three bryophyte lineages, intergenic spacers and repeat content are smallest in mosses, largest in hornworts, and intermediate in liverworts, mirroring their size differences and levels of structural dynamics among the three lineages. Mosses, with the least repeated sequences, show the most static genome structure; whereas hornworts, with a relatively large set of repeated sequences, experience 1–4 rearrangements; liverworts, with intermediate repeat levels, see only one structural variant that requires two inversions to gain collinearity with the mitogenome of other liverworts. Repeat sequences were evoked to explain the mt gene order rearrangements in hornwort and liverwort mitogenomes; with the latter also supported by sequencing read evidence, which suggests that the conserved mitogenome structure observed in bryophyte lineages might be shaped by low repeat recombination level, and/or along with the intensified nucleus’ surveillance. Mitochondrial RNA editing is abundant in hornworts, with medium frequency and high variation in liverwort species, and generally limited in mosses, reflecting the diversity of nuclear encoded PPR proteins that are functionally related to RNA editing processes.

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The Amount of RNA Editing Sites in Liverwort Organellar Genes Is Correlated with GC Content and Nuclear PPR Protein Diversity

Cited by 31 publications

References 56 publications

The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome

The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome

Mitochondrial genomes of the early land plant lineage liverworts (Marchantiophyta): conserved genome structure, and ongoing low frequency recombination

The mitochondrial genomes of bryophytes

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