The complete chloroplast genome of <i>Caryopteris incana</i> (Lamiaceae) and phylogenetic analysis

Zhao, Fei; Peng, Hua

doi:10.1080/23802359.2020.1736963

Cited by 3 publications

(4 citation statements)

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“…The analysis demonstrated that the M. sikkimensis chloroplast genome spanned a length of 149,428 bp, and it featured the circular quadripartite typical of chloroplast genomes, consisting of the LSC, SSC, and a pair of IR regions. Gene annotation indicated that the genome contains 112 genes, which include 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, which is consistent with the genomic structure and gene quantity observed in the chloroplasts of other species within the Boraginaceae family [47][48][49][50][51]. Introns were crucial for the regulatory mechanisms that control gene expression.…”

Section: Discussionsupporting

confidence: 68%

Comparative Analyses of Complete Chloroplast Genomes of Microula sikkimensis and Related Species of Boraginaceae

Gao,

Chen,

et al. 2024

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The present study provides a detailed analysis of the chloroplast genome of Microula sikkimensis. The genome consisted of a total of 149,428 bp and four distinct regions, including a large single-copy region (81,329 bp), a small single-copy region (17,261 bp), and an inverted repeat region (25,419 bp). The genome contained 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, and some exhibited duplication in the inverted repeat region. The chloroplast genome displayed different GC content across regions, with the inverted repeat region exhibiting the highest. Codon usage analysis and the identification of simple sequence repeats (SSRs) offer valuable genetic markers. Comparative analysis with other Boraginaceae species highlighted conservation and diversity in coding and noncoding regions. Phylogenetic analysis placed M. sikkimensis within the Boraginaceae family, revealing its distinct relationship with specific species.

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Section: Discussionsupporting

confidence: 68%

Comparative Analyses of Complete Chloroplast Genomes of Microula sikkimensis and Related Species of Boraginaceae

Gao,

Chen,

et al. 2024

Genes

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“…In this study, plastomes of 50 taxa were newly sequenced and 61 taxa were reassembled from the sequence read archive (SRA) database; others were acquired from previous studies [ 66 , 67 , 206 , 207 ] or downloaded from NCBI ( https://www.ncbi.nlm.nih.gov ; Additional file 8 : Table S3). In total, the ingroup sampling included 170 taxa (175 accessions), 79 genera, and represented all 15 currently recognized tribes and all 12 subfamilies within Lamiaceae [ 19 , 51 ].…”

Section: Methodsmentioning

confidence: 99%

“…All the newly sequenced and annotated plastomes in the present study were submitted to the National Center for Biotechnology Information (NCBI) database with accession numbers MT473738-MT473786 (Table 1). Other plastomes analyzed were acquired from previous studies [66,67,206,207] or downloaded from NCBI (https://www.ncbi.nlm.nih.gov; Additional file 8; Table S3). The alignments and ML tree are deposited at TreeBase with study #S26639 (http://treebase.org/treebase-web/phylows/ study/TB2:S26639?x-access-code=bb02a4c5bc226f4604690ea0f21ccd41 &format=html) [226].…”

Section: Supplementary Informationmentioning

confidence: 99%

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An updated tribal classification of Lamiaceae based on plastome phylogenomics

et al. 2021

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Background A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, the resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data. Results We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updated phylogenetically informed tribal classification for Lamiaceae that is supplemented with a detailed summary of taxonomic history, generic and species diversity, morphology, synapomorphies, and distribution for each subfamily and tribe. Conclusions Increased taxon sampling conjoined with phylogenetic analyses based on plastome sequences has provided robust support at both deep and shallow nodes and offers new insights into the phylogenetic relationships among tribes and subfamilies of Lamiaceae. This robust phylogenetic backbone of Lamiaceae will serve as a framework for future studies on mint classification, biogeography, character evolution, and diversification. Graphical abstract

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Unprecedented diterpene skeletons isolated from vascular plants in the last twenty years (2001–2021)

Chacón-Morales

2022

Phytochemistry

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The complete chloroplast genome of Caryopteris incana (Lamiaceae) and phylogenetic analysis

Cited by 3 publications

References 8 publications

Comparative Analyses of Complete Chloroplast Genomes of Microula sikkimensis and Related Species of Boraginaceae

Comparative Analyses of Complete Chloroplast Genomes of Microula sikkimensis and Related Species of Boraginaceae

An updated tribal classification of Lamiaceae based on plastome phylogenomics

Unprecedented diterpene skeletons isolated from vascular plants in the last twenty years (2001–2021)

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