Characterization of the complete chloroplast genome of Arabis stellari and comparisons with related species

Raman, Gurusamy; Park, Veronica; Kwak, Myounghai; Lee, Byoung-Yoon; Park, Seon Joo

doi:10.1371/journal.pone.0183197

Cited by 33 publications

(31 citation statements)

References 53 publications

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“…For the location of FP, 240, 38, and 137 microsatellite loci were detected in the LSC, SSC, and IR regions, respectively. Similar patterns were also reported in other species, such as Cerasus humilis [ 36 ], Arabis stellari [ 40 ], and Paeonia ostii [ 41 ]. However, though the total number of microsatellites was highly conserved, polymorphisms might still be observed in certain loci, which could be helpful in population and evolutionary studies [ 42 , 43 , 44 ].…”

Section: Resultssupporting

confidence: 85%

Characterization of the Chloroplast Genome Sequence of Acer miaotaiense: Comparative and Phylogenetic Analyses

Zhao

et al. 2018

Molecules

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Acer miaotaiense is an endangered species within the Aceraceae family, and has only a few small natural distributions in China’s Qingling Mountains and Bashan Mountains. Comparative analyses of the complete chloroplast genome could provide useful knowledge on the diversity and evolution of this species in different environments. In this study, we sequenced and compared the chloroplast genome of Acer miaotaiense from five ecological regions in the Qingling and Mashan Regions of China. The size of the chloroplast genome ranged from 156,260 bp to 156,204 bp, including two inverted repeat regions, a small single-copy region, and a large single-copy region. Across the whole chloroplast genome, there were 130 genes in total, and 92 of them were protein-coding genes. We observed four genes with non-synonymous mutations involving post-transcriptional modification (matK), photosynthesis (atpI), and self-replication (rps4 and rpl20). A total of 415 microsatellite loci were identified, and the dominant microsatellite types were composed of dinucleotide and trinucleotide motifs. The dominant repeat units were AT and AG, accounting for 37.92% and 31.16% of the total microsatellite loci, respectively. A phylogenetic analysis showed that samples with the same altitude (Xunyangba, Ningshan country, and Zhangliangmiao, Liuba country) had a strong bootstrap value (88%), while the remaining ones shared a similar longitude. These results provided clues about the importance of longitude/altitude for the genetic diversity of Acer miaotaiense. This information will be useful for the conservation and improved management of this endangered species.

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Section: Resultssupporting

confidence: 85%

Characterization of the Chloroplast Genome Sequence of Acer miaotaiense: Comparative and Phylogenetic Analyses

Zhao

et al. 2018

Molecules

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“…The rps16 sequence of A. alpina also lacked part of the second exon and had mutations in the start and stop codons. Therefore, different patterns of rps16 pseudogenization were observed in A. alpina and the other Arabis species, as was previously suggested [ 23 ]. The A. alpina lineage had acquired independent dysfunctional mutation(s).…”

Section: Resultsmentioning

confidence: 63%

“…Of these, seven protein-coding genes, seven tRNA genes, and four rRNA genes were located in the IR regions, and were therefore duplicated. The rps16 gene became a pseudogene in A. flagellosa , A. hirsuta , and A. nipponica strain Midori, which was previously reported as a related species [ 23 ]. In addition, the rps16 sequences of D. nemorosa , A. stelleri , A. flagellosa , A. hirsuta , and A. nipponica shared a 10 base pair deletion in the first exon, while A. stelleri , A. flagellosa , A. hirsuta , and A. nipponica shared a 1 base pair deletion in the second exon and D. nemorosa lacked the second exon entirely.…”

Section: Resultsmentioning

confidence: 99%

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Exploring the History of Chloroplast Capture in Arabis Using Whole Chloroplast Genome Sequencing

Kawabe

Nukii

Furihata

2018

IJMS

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Chloroplast capture occurs when the chloroplast of one plant species is introgressed into another plant species. The phylogenies of nuclear and chloroplast markers from East Asian Arabis species are incongruent, which indicates hybrid origin and shows chloroplast capture. In the present study, the complete chloroplast genomes of A. hirsuta, A. nipponica, and A. flagellosa were sequenced in order to analyze their divergence and their relationships. The chloroplast genomes of A. nipponica and A. flagellosa were similar, which indicates chloroplast replacement. If hybridization causing chloroplast capture occurred once, divergence between recipient species would be lower than between donor species. However, the chloroplast genomes of species with possible hybrid origins, A. nipponica and A. stelleri, differ at similar levels to possible maternal donor species A. flagellosa, which suggests that multiple hybridization events have occurred in their respective histories. The mitochondrial genomes exhibited similar patterns, while A. nipponica and A. flagellosa were more similar to each other than to A. hirsuta. This suggests that the two organellar genomes were co-transferred during the hybridization history of the East Asian Arabis species.

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“…Pseudogenes are frequently identified in cp genomes [ 38 , 39 ]. Four pseudogenes were identified in the current study, i.e., Ψrps19 , Ψycf1 , ΨinfA and ΨaccD ( Table 2 ).…”

Section: Resultsmentioning

confidence: 99%

Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae

Liu

Kong

Zhou

et al. 2018

IJMS

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The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana, endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole chloroplast (cp) genome of C. chuniana and compare it to six other species from the Caesalpinioideae. Comparative analyses of gene synteny and simple sequence repeats (SSRs), as well as estimation of nucleotide diversity, the relative ratios of synonymous and nonsynonymous substitutions (dn/ds), and Kimura 2-parameter (K2P) interspecific genetic distances, were all conducted. The whole cp genome of C. chuniana was found to be 158,433 bp long with a total of 114 genes, 81 of which code for proteins. Nucleotide substitutions and length variation are present, particularly at the boundaries among large single copy (LSC), inverted repeat (IR) and small single copy (SSC) regions. Nucleotide diversity among all species was estimated to be 0.03, the average dn/ds ratio 0.3177, and the average K2P value 0.0372. Ninety-one SSRs were identified in C. chuniana, with the highest proportion in the LSC region. Ninety-seven species from the old Caesalpinioideae were selected for phylogenetic reconstruction, the analysis of which strongly supports the monophyly of Cercidoideae based on the new classification of the Fabaceae. Our study provides genomic information for further phylogenetic reconstruction and biogeographic inference of Cercis and other legume species.

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Characterization of the complete chloroplast genome of Arabis stellari and comparisons with related species

Cited by 33 publications

References 53 publications

Characterization of the Chloroplast Genome Sequence of Acer miaotaiense: Comparative and Phylogenetic Analyses

Characterization of the Chloroplast Genome Sequence of Acer miaotaiense: Comparative and Phylogenetic Analyses

Exploring the History of Chloroplast Capture in Arabis Using Whole Chloroplast Genome Sequencing

Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae

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