The complete chloroplast genome sequence of <i>Saussurea polylepis</i> (Asteraceae), a vulnerable endemic species of Korea

Yun, Seon A; Gil, Hee-Young; Kim, Seung‐Chul

doi:10.1080/23802359.2017.1375881

Cited by 10 publications

(5 citation statements)

References 7 publications

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“…In this study, plastomes of five Korean endemic species, S. albifolia, S. calcicola, S. diamantica , S. grandicapitula, and S. seoulensis, were sequenced and comparative analyses were conducted, including two previously reported species S. chabyoungsanica [ 18 ] and S. polylepis [ 19 ]. Saussurea albifolia, described recently as a new species, has cordate or deltoid-cordate leaves with white or yellowish hair on the abaxial surface.…”

Section: Introductionmentioning

confidence: 99%

Comparative plastomes and phylogenetic analysis of seven Korean endemic Saussurea (Asteraceae)

Yun

Kim

2022

BMC Plant Biol

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Background Saussurea is one of the most species-rich genera in the Cardueae, Asteraceae. There are approximately 40 Saussurea species distributed in Korea, with nearly 40% of them endemics. Infrageneric relationships remain uncertain due to insufficient resolutions and low statistical support. In this study, we sequenced the plastid genomes of five Korean endemic Saussurea (S. albifolia, S. calcicola, S. diamantica, S. grandicapitula, and S. seoulensis), and comparative analyses including two other endemics (S. chabyoungsanica and S. polylepis) were conducted. Results The plastomes of Korean endemics were highly conserved in gene content, order, and numbers. Exceptionally, S. diamantica had mitochondrial DNA sequences including two tRNAs in SSC region. There were no significant differences of the type and numbers of SSRs among the seven Korean endemics except in S. seoulensis. Nine mutation hotspots with high nucleotide diversity value (Pi > 0.0033) were identified, and phylogenetic analysis suggested that those Korean endemic species most likely evolved several times from diverse lineages within the genus. Moreover, molecular dating estimated that the Korean endemic species diverged since the late Miocene. Conclusions This study provides insight into understanding the plastome evolution and evolutionary relationships of highly complex species of Saussurea in Korean peninsula.

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Section: Introductionmentioning

confidence: 99%

Comparative plastomes and phylogenetic analysis of seven Korean endemic Saussurea (Asteraceae)

Yun

Kim

2022

BMC Plant Biol

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“…A Gray ( Ishikawa, Sakaguchi & Ito, 2016 ; Luo et al, 2016 ; Zhang et al, 2017 ; Marochio et al, 2017 ; Han et al, 2018 ). In addition to the development of these molecular markers, complete cpDNA sequences have been reported for various Asteraceae species ( Kim, Choi & Jansen, 2005 ; Choi & Park, 2015 ; Wang et al, 2015a ; Wang et al, 2015b ; Yun, Gil & Kim, 2017 ; Liu et al, 2018 ; Ma, Sun & Zhao, 2018 ; Su et al, 2018 ). cpDNA sequences may be used to elucidate the phylogeny of angiosperms from the clade that is basal to monocots and eudicots ( Angiosperm Phylogeny Group, 2016 ).…”

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confidence: 99%

Comparative analysis and implications of the chloroplast genomes of three thistles (Carduus L., Asteraceae)

Jung

Khoa

Hyun

et al. 2021

PeerJ

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Background Carduus, commonly known as plumeless thistles, is a genus in the Asteraceae family that exhibits both medicinal value and invasive tendencies. However, the genomic data of Carduus (i.e., complete chloroplast genomes) have not been sequenced. Methods We sequenced and assembled the chloroplast genome (cpDNA) sequences of three Carduus species using the Illumina Miseq sequencing system and Geneious Prime. Phylogenetic relationships between Carduus and related taxa were reconstructed using Maximum Likelihood and Bayesian Inference analyses. In addition, we used a single nucleotide polymorphism (SNP) in the protein coding region of the matK gene to develop molecular markers to distinguish C. crispus from C. acanthoides and C. tenuiflorus. Results The cpDNA sequences of C. crispus, C. acanthoides, and C. tenuiflorus ranged from 152,342 bp to 152,617 bp in length. Comparative genomic analysis revealed high conservation in terms of gene content (including 80 protein-coding, 30 tRNA, and four rRNA genes) and gene order within the three focal species and members of subfamily Carduoideae. Despite their high similarity, the three species differed with respect to the number and content of repeats in the chloroplast genome. Additionally, eight hotspot regions, including psbI-trnS_GCU, trnE_UUC-rpoB, trnR_UCU-trnG_UCC, psbC-trnS_UGA, trnT_UGU-trnL_UAA, psbT-psbN, petD-rpoA, and rpl16-rps3, were identified in the study species. Phylogenetic analyses inferred from 78 protein-coding and non-coding regions indicated that Carduus is polyphyletic, suggesting the need for additional studies to reconstruct relationships between thistles and related taxa. Based on a SNP in matK, we successfully developed a molecular marker and protocol for distinguishing C. crispus from the other two focal species. Our study provides preliminary chloroplast genome data for further studies on plastid genome evolution, phylogeny, and development of species-level markers in Carduus.

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“…To date, only three Saussurea plastomes have been reported: S. involucrata [36], S. chabyoungsanica [37] and S. polylepis [38]. Here, we sequenced 17 species representing all four subgenera of Saussurea in order to (1) elucidate plastome evolution, including structural variation and molecular signals of selection, (2) estimate the effectiveness of different plastome data sets in resolving relationships within this radiating lineage, and (3) investigate the backbone relationships within Saussurea.…”

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Plastome phylogenomics of Saussurea (Asteraceae: Cardueae)

et al. 2019

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Background: Saussurea DC. is one of the largest and most morphologically heterogeneous genera in Asteraceae. The relationships within Saussurea have been poorly resolved, probably due an early, rapid radiation. To examine plastome evolution and resolve backbone relationships within Saussurea, we sequenced the complete plastomes of 17 species representing all four subgenera. Results: All Saussurea plastomes shared the gene content and structure of most Asteraceae plastomes. Molecular evolutionary analysis showed most of the plastid protein-coding genes have been under purifying selection. Phylogenomic analyses of 20 Saussurea plastomes that alternatively included nucleotide or amino acid sequences of all protein-coding genes, vs. the nucleotide sequence of the entire plastome, supported the monophyly of Saussurea and identified three clades within it. Three of the four traditional subgenera were recovered as paraphyletic. Seven plastome regions were identified as containing the highest nucleotide variability. Conclusions: Our analyses reveal both the structural conservatism and power of the plastome for resolving relationships in congeneric taxa. It is very likely that differences in topology among data sets is due primarily to differences in numbers of parsimony-informative characters. Our study demonstrates that the current taxonomy of Saussurea is likely based at least partly on convergent morphological character states. Greater taxon sampling will be necessary to explore character evolution and biogeography in the genus. Our results here provide helpful insight into which loci will provide the most phylogenetic signal in Saussurea and Cardueae.

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The complete chloroplast genome sequence of Saussurea polylepis (Asteraceae), a vulnerable endemic species of Korea

Cited by 10 publications

References 7 publications

Comparative plastomes and phylogenetic analysis of seven Korean endemic Saussurea (Asteraceae)

Comparative plastomes and phylogenetic analysis of seven Korean endemic Saussurea (Asteraceae)

Comparative analysis and implications of the chloroplast genomes of three thistles (Carduus L., Asteraceae)

Plastome phylogenomics of Saussurea (Asteraceae: Cardueae)

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