The Antarctic sea ice alga Chlamydomonas sp. ICE-L provides insights into adaptive patterns of chloroplast evolution

Zhang, Zhenhua; An, Meiling; Miao, Jun; Gu, Zhiqiang; Liu, Chang; Zhong, Bojian

doi:10.1186/s12870-018-1273-x

Cited by 24 publications

(13 citation statements)

References 75 publications

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“…Understanding the patterns of divergence and adaptation among the members of a specific phylogenetic clade can offer important clues about the forces driving its evolution [12, 57–59]. In this study, we detected some positive selective signals in the tropical clade, but sites under positive selection are quite rare and mainly detected in the ycf1 and ycf2 genes.…”

Section: Discussionmentioning

confidence: 57%

Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation

Zhang-hai

Wang

et al. 2019

BMC Evol Biol

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Background The plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparisons of plastid genome evolution at high taxonomic levels, and comparative studies of the process of plastome evolution at the infrageneric or intraspecific level remain elusive. Holcoglossum is a small genus of Orchidaceae, consisting of approximately 20 species of recent radiation . This made it an ideal group to explore the plastome mutation mode at the infrageneric or intraspecific level. Results In this paper, we reported 15 complete plastid genomes from 12 species of Holcoglossum and 1 species of Vanda. The plastid genomes of Holcoglossum have a total length range between 145 kb and 148 kb, encoding a set of 102 genes. The whole set of ndh -gene families in Holcoglossum have been truncated or pseudogenized. Hairpin inversion in the coding region of the plastid gene ycf2 has been found. Conclusions Using a comprehensive comparative plastome analysis, we found that all the indels between different individuals of the same species resulted from the copy number variation of the short repeat sequence, which may be caused by replication slippage. Annotation of tandem repeats shows that the variation introduced by tandem repeats is widespread in plastid genomes. The hairpin inversion found in the plastid gene ycf2 occurred randomly in the Orchidaceae. Electronic supplementary material The online version of this article (10.1186/s12862-019-1384-5) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 57%

Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation

Zhang-hai

Wang

et al. 2019

BMC Evol Biol

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“…To support this analysis, the 2∆LnL value of rpl20 is zero and the p-value of LRT is greater than 0.05 (Tables 2 and 3). All these highly positive selection genes are involved in the functions of the plant genetic system or photosynthesis process [27][28][29][30][31]. Besides, these seven genes have undergone positive selection, which might be the result of adaptation to their diverse habitats.…”

Section: Discussionmentioning

confidence: 99%

The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

Raman¹,

Park²

2020

Agronomy

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The plant “False Lily of the Valley”, Speirantha gardenii is restricted to south-east China and considered as an endemic plant. Due to its limited availability, this plant was less studied. Hence, this study is focused on its molecular studies, where we have sequenced the complete chloroplast genome of S. gardenii and this is the first report on the chloroplast genome sequence of Speirantha. The complete S. gardenii chloroplast genome is of 156,869 bp in length with 37.6% GC, which included a pair of inverted repeats (IRs) each of 26,437 bp that separated a large single-copy (LSC) region of 85,368 bp and a small single-copy (SSC) region of 18,627 bp. The chloroplast genome comprises 81 protein-coding genes, 30 tRNA and four rRNA unique genes. Furthermore, a total of 699 repeats and 805 simple-sequence repeats (SSRs) markers are identified in the genome. Additionally, KA/KS nucleotide substitution analysis showed that seven protein-coding genes have highly diverged and identified nine amino acid sites under potentially positive selection in these genes. Phylogenetic analyses suggest that S. gardenii species has a closer genetic relationship to the Reineckea, Rohdea and Convallaria genera. The present study will provide insights into developing a lineage-specific marker for genetic diversity and gene evolution studies in the Nolinoideae taxa.

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“…For example, Guisinger et al (2008) calculated the nucleotide substitution rates of chloroplast protein-coding genes of angiosperm, and found unprecedented accumulation of nucleotide substitutions in Geraniaceae, then a model was proposed to illustrate this phenomenon. Zhang et al (2018) studied the molecular evolution of chloroplast protein-coding genes of an Antarctic sea ice alga Chlamydomonas sp. and revealed the adaptive mechanism of sed-ice environment.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary Analysis of Unicellular Species in Chlamydomonadales Through Chloroplast Genome Comparison With the Colonial Volvocine Algae

Xing

Huang

et al. 2019

Front. Microbiol.

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This study is the first determination of six chloroplast genomes of colonial volvocine algae, Colemanosphaera charkowiensis, Volvulina compacta, Pandorina colemaniae, Pandorina morum, Colemanosphaera angeleri, and Yamagishiella unicocca. Based on 55 chloroplast protein-coding genes, we compared the nonsynonymous (dN) and synonymous (dS) substitution rates between colonial volvocine algae and the other unicellular Chlamydomonadales species. When refer to the dN, we found 27 genes were significantly different, among them, 19 genes were significant higher in unicellular species (FDR-adjusted P < 0.05). When refer to the dS, we found 10 genes were significantly different, among them, 6 genes were significant higher in unicellular species (FDR-adjusted P < 0.05). Then we identified 14 putative fast-evolving genes and 11 putative positively selected genes of unicellular species, we analyzed the function of positively selected sites of the overlap genes of putative fast-evolving and positively selected genes, and found some sites were close to the important functional region of the proteins. Photosynthesis is the process to transform and store solar energy by chloroplast, it plays a vital role in the survival of algae, this study is the first to use the chloroplast genomes to analysis the evolutionary relationship between colonial and unicellular species in Chlamydomonadales. We found more genes have higher substitution rates in unicellular species and proposed that the fast-evolving and positively selected two genes, psbA and psbC, may help to improve the photosynthetic efficiency of unicellular species in Chlamydomonadales.

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The Antarctic sea ice alga Chlamydomonas sp. ICE-L provides insights into adaptive patterns of chloroplast evolution

Cited by 24 publications

References 75 publications

Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation

Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation

The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

Evolutionary Analysis of Unicellular Species in Chlamydomonadales Through Chloroplast Genome Comparison With the Colonial Volvocine Algae

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