The complete chloroplast genome sequence of <i>Crepidiastrum lanceolatum</i> (<i>Asteraceae</i>)

Kim, Hyoung Tae; Pak, Jae‐Hong; Kim, Jung Sung

doi:10.1080/23802359.2019.1598799

Cited by 4 publications

(5 citation statements)

References 5 publications

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“…This shows that the reported genomes have certain errors in annotations as stated previously in a detailed study of the family Solanaceae (Amiryousefi et al, 2018a) and the comparative genomics of the two species of Malvaceae . The gene content was found to be the same in all the species of Asteroideae after correction of annotations, which is also in agreement with gene features in the previously reported plastome of other subfamilies such as Cichorioideae, Pertyoideae, and Carduoideae (Jung et al, 2021;Kim et al, 2019;Lin et al, 2019).…”

Section: Plastome Comparison Of Blumea and Asteroideaesupporting

confidence: 89%

“…Hence, the plastomes of Asteroideae avoid the rearrangements by a certain mechanism. The GC content of the plastomes was also similar to previous Asteraceae genomes and of other plant lineages, and high GC content was observed in IRs, which might be due to the presence of rRNAs, as they have a GC content of up to 55% (Amiryousefi et al, 2018a;Jung et al, 2021;Kim et al, 2019;Lin et al, 2019;Poczai & Hyvönen, 2017).…”

Section: Plastome Comparison Of Blumea and Asteroideaesupporting

confidence: 78%

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Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae

Abdullah

Mehmood

Rahim

et al. 2021

Ecology and Evolution

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Section: Plastome Comparison Of Blumea and Asteroideaesupporting

confidence: 89%

Section: Plastome Comparison Of Blumea and Asteroideaesupporting

confidence: 78%

Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae

Abdullah

Mehmood

Rahim

et al. 2021

Ecology and Evolution

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“…While the protein-coding regions were relatively conserved, variations were also observed in the atpA-atpF , atpB , and psaI-ycf4 genes. The high GC content observed in the genome may contribute to the lower variation in tRNA sequences and IR regions, underscoring the significance of GC content in maintaining sequence stability, as previously reported ( Necsulea and Lobry, 2007 ; Kim et al., 2019 ).…”

Section: Discussionsupporting

confidence: 68%

Comparative and phylogenetic analyses based on the complete chloroplast genome of Cornus subg. Syncarpea (Cornaceae) species

Guan,

Wen,

Guo

et al. 2024

Front. Plant Sci.

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This study presents a comprehensive analysis of the chloroplast (cp) genomes of Cornus species, including comparative and phylogenetic evaluations, as well as examinations of their genomic structure and composition. The cp genomes exhibit a typical circular quadripartite structure and demonstrate highly similar gene order and genomic structure. The complete cp genome size of the 10 taxa in this study is 156,965 bp to 157,383 bp, where the length of the large single-copy (LSC) region is 86,296 bp to 86,691 bp, small single-copy (SSC) region is 18,386 bp to 18,454 bp, and inverted repeat (IR) region is 23,143 bp to 26,112 bp. A total of 131 genes were found, including 86 protein-coding genes (PCGs), eight rRNA genes, and 37 tRNA genes. The mean GC content of the 10 taxa is 38.145%, where the LSC region is 36.396%, the SSC region is 32.372%, and the IR region is 43.076%. Despite the relatively conserved nature of the cp genome within the species of Cornus, 25–31 simple sequence repeats (SSRs) were identified in the 10 taxa in our study. The SSRs were found to be distributed in the LSC, SSC, and IR regions in Cornus hongkongensis subsp. hongkongensis, C. hongkongensis subsp. elegans, C. hongkongensis subsp. gigantea, and C. hongkongensis subsp. tonkinensis, while the SSR was not found in the IR region of the other six taxa. Thus, whole cp genomics is a valuable tool for species identification, taxonomic clarification, and genomic evolutionary analysis. Furthermore, our findings reveal that C. hongkongensis and C. hongkongensis subsp. gigantea, along with Cornus kousa and Cornus elliptica, form sister groups. Notably, C. hongkongensis subsp. ferruginea and C. hongkongensis subsp. melanotricha did not exhibit affinity with C. hongkongensis subsp. hongkongensis. Our study furnishes essential data for further research on their classification and provides novel insights into the relationship within Cornus subg. Syncarpea.

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“…The highly variable regions detected in this study were promising to be developed as specific DNA barcodes for the subfamily Pooideae, which has positive implications for the identification of species. In addition, the high GC content might be one of the reasons for less variation in tRNA sequences and IR regions, which further demonstrates the significance of GC content in maintaining sequence stability (Necsulea and Lobry, 2007;Kim et al, 2019).…”

Section: Discussion Plastome Comparison Of Coleanthus Subtilis and Ot...mentioning

confidence: 96%

Comparative and Phylogenetic Analysis Based on the Chloroplast Genome of Coleanthus subtilis (Tratt.) Seidel, a Protected Rare Species of Monotypic Genus

et al. 2022

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Coleanthus subtilis (Tratt.) Seidel (Poaceae) is an ephemeral grass from the monotypic genus Coleanthus Seidl, which grows on wet muddy areas such as fishponds or reservoirs. As a rare species with strict habitat requirements, it is protected at international and national levels. In this study, we sequenced its whole chloroplast genome for the first time using the next-generation sequencing (NGS) technology on the Illumina platform, and performed a comparative and phylogenetic analysis with the related species in Poaceae. The complete chloroplast genome of C. subtilis is 135,915 bp in length, with a quadripartite structure having two 21,529 bp inverted repeat regions (IRs) dividing the entire circular genome into a large single copy region (LSC) of 80,100 bp and a small single copy region (SSC) of 12,757 bp. The overall GC content is 38.3%, while the GC contents in LSC, SSC, and IR regions are 36.3%, 32.4%, and 43.9%, respectively. A total of 129 genes were annotated in the chloroplast genome, including 83 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The accD gene and the introns of both clpP and rpoC1 genes were missing. In addition, the ycf1, ycf2, ycf15, and ycf68 were pseudogenes. Although the chloroplast genome structure of C. subtilis was found to be conserved and stable in general, 26 SSRs and 13 highly variable loci were detected, these regions have the potential to be developed as important molecular markers for the subfamily Pooideae. Phylogenetic analysis with species in Poaceae indicated that Coleanthus and Phippsia were sister groups, and provided new insights into the relationship between Coleanthus, Zingeria, and Colpodium. This study presents the initial chloroplast genome report of C. subtilis, which provides an essential data reference for further research on its origin.

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The complete chloroplast genome sequence of Crepidiastrum lanceolatum (Asteraceae)

Cited by 4 publications

References 5 publications

Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae

Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae

Comparative and phylogenetic analyses based on the complete chloroplast genome of Cornus subg. Syncarpea (Cornaceae) species

Comparative and Phylogenetic Analysis Based on the Chloroplast Genome of Coleanthus subtilis (Tratt.) Seidel, a Protected Rare Species of Monotypic Genus

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