Highly variable chloroplast genome from two endangered Papaveraceae lithophytes <i>Corydalis tomentella</i> and <i>Corydalis saxicola</i>

Ren, Fanggang; Wang, Liqiang; Li, Ying; Zhuo, Wei; Xu, Zhichao; Guo, Haojie; Liu, Yan; Gao, Ranran; Song, Jingyuan

doi:10.1002/ece3.7312

Cited by 25 publications

(27 citation statements)

References 67 publications

(88 reference statements)

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“…Mononucleotide SSRs which exist in a large numbers in cp genomes (George et al., 2015 ; Liang et al., 2019 ) are the most abundant (Table 3 ), and A/T motifs are the most common (Figure 3 ; Appendix Table S9 ). This finding is similar to previously reported patterns of land plants (George et al., 2015 ; Huang et al., 2021 ; Ren et al., 2021 ; Vieira et al., 2014 ; Wei et al., 2021 ). However, in Polypodiaceae plastomes, most repeats were C/G mononucleotides.…”

Section: Discussionsupporting

confidence: 92%

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Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae

Zhu

Feng

Ping

et al. 2021

Ecology and Evolution

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Simple sequence repeats (SSRs), also known as microsatellites, are short tandem repeat sequences with a motif length of 1-6 bp characterized by high variability and codominant inheritance and have been widely used in species identification, genetic diversity studies, and phylogenetic relationship determination (Chmielewski et al., 2015;Dashnow et al., 2015). SSRs are caused by slipped strand mispairing and subsequent errors during DNA replication, repair, and recombination (Levinson & Gutman, 1987). SSRs are mainly found in intergenic and noncoding regions, with a few present in introns (Li et al., 2004;Liu et al., 2021;Su et al., 2018). Previous studies have shown that the characteristics of genomic SSRs in different taxa (such as their distribution patterns) reflect their phylogenetic relationships (Manee et al., 2020;Srivastava et al., 2019).The distribution of SSRs in some chloroplast (cp) genomes is nonrandom and dominated by mononucleotides, where A/T bases account for the majority (Ellegren, 2004;George et al., 2015;

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Section: Discussionsupporting

confidence: 92%

“…The distribution of SSRs in some chloroplast (cp) genomes is nonrandom and dominated by mononucleotides, where A/T bases account for the majority (Ellegren, 2004 ; George et al., 2015 ; Ren et al., 2021 ). Some Polypodiaceae species show similar SSR distribution patterns in their cp genomes (Liu et al., 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae

Zhu

Feng

Ping

et al. 2021

Ecology and Evolution

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“…Previous studies reported a marked IR region expansion in some Corydalis cp-genomes; the IR region expanded into the simple sequence repeat (SSR) region and led to IR–SSC boundary variations 1 , 2 . In the present study, three newly sequenced Corydalis cp-genomes were compared with the C. edulis cp-genome, which exhibited a typical angiosperm quadripartite cp-genome structure (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…However, deep relationships remained poorly resolved by this phylogenetic approach applying a few plastid markers. Some studies reported that the protein-coding genes shared by all taxa could be used to reconstruct a phylogeny 2 , 34 . However, single-copy genes (SCGs) have subsequently emerged as candidates for phylogenetic analysis because paralogues are derived from duplication events other than speciation events and should therefore be discarded from phylogenetic analyses 69 , 70 .…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic analysis based on single-copy orthologous proteins in highly variable chloroplast genomes of Corydalis

Yin

Huang

Liu

et al. 2022

Sci Rep

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Corydalis is one of the few lineages that have been reported to have extensive large-scale chloroplast genome (cp-genome) rearrangements. In this study, novel cp-genome rearrangements of Corydalis pinnata, C. mucronate, and C. sheareri are described. C. pinnata is a narrow endemic species only distributed at Qingcheng Mountain in southwest China. Two independent relocations of the same four genes (trnM-CAU-rbcL) were found relocated from the typically posterior part of the large single-copy region to the front of it. A uniform inversion of an 11–14-kb segment (ndhB-trnR-ACG) was found in the inverted repeat region; and extensive losses of accD, clpP, and trnV-UAC genes were detected in all cp-genomes of all three species of Corydalis. In addition, a phylogenetic tree was reconstructed based on 31 single-copy orthologous proteins in 27 cp-genomes. This study provides insights into the evolution of cp-genomes throughout the genus Corydalis and also provides a reference for further studies on the taxonomy, identification, phylogeny, and genetic transformation of other lineages with extensive rearrangements in cp-genomes.

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“…Chloroplasts genomes regarding gene content and order are highly conserved, with the potential for the understanding of the taxonomy, phylogeny and evolution of plants (Ahlert et al 2003 ; Moore et al 2010 ). But less than ten species of Corydalis genomes are publicly available in NCBI to data (Wu et al 2020 ; Xu and Wang 2020 , 2021 ; Liu et al 2021 ; Ren et al 2021 ). Corydalis fangshanensis W.T.…”

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confidence: 99%

The complete chloroplast genome and phylogenetic analysis of Corydalis fangshanensis W.T. Wang ex S.Y. He (Papaveraceae)

Zhou

Li³

et al. 2021

Mitochondrial DNA Part B

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The complete chloroplast (cp) genome of Corydalis fangshanensis W.T. Wang ex S.Y. He, a Chinese endemic plant with limestone-specific distribution was first reported. The cp genome was circular in structure and 192,554 bp in length, consisting of a large single copy region (LSC, 98,393 bp), two inverted repeat regions (IRs, 42,263 bp), and a small single copy region (SSC, 9,635 bp). The overall GC content of the genome was 40.26%. It encoded 112 unique genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis resolved C. fangshanensis was closely related to C. saxicola G.S. Bunting within Corydalis sect. Thalictrifoliae (Fedde) Lid en, in line with morphological character-based taxonomy. Our result provides informative data for studying the taxonomy, phylogeny and ecology of Corydalis, especially species with specific-limestone distribution and also for studying the adaptive evolution in plants.

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Highly variable chloroplast genome from two endangered Papaveraceae lithophytes Corydalis tomentella and Corydalis saxicola

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 25 publications

References 67 publications

Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae

Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae

Phylogenetic analysis based on single-copy orthologous proteins in highly variable chloroplast genomes of Corydalis

The complete chloroplast genome and phylogenetic analysis of Corydalis fangshanensis W.T. Wang ex S.Y. He (Papaveraceae)

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