Chloroplast genome characteristics and phylogenetic analysis of the medicinal plant Blumea balsamifera (L.) DC

Zhao, Chao; Xu, Wen-Fen; Huang, Yuan; Sun, Qingwen; Wang, Bo; Chen, Chunlin; Chen, Qiyu

doi:10.1590/1678-4685-gmb-2021-0095

Cited by 5 publications

(2 citation statements)

References 30 publications

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“…The lack of genomic information on the original herbal species used in TCMs has marginalized their use in modern medicine and seriously restricted their further development (Gan et al, 2021;Sun et al, 2020;Zhao et al, 2021). Herb genomics can help to bridge the gap between traditional herbal medicine and cutting-edge omics research (Hu et al, 2019;Li & Chen, 2020).…”

Section: Introductionmentioning

confidence: 99%

IGTCM: An integrative genome database of traditional Chinese medicine plants

Liang

et al. 2023

The Plant Genome

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Fully understanding traditional Chinese medicines (TCMs) is still challenging because of the extreme complexity of their chemical components and mechanisms of action. The TCM Plant Genome Project aimed to obtain genetic information, determine gene functions, discover regulatory networks of herbal species, and elucidate the molecular mechanisms involved in the disease prevention and treatment, thereby accelerating the modernization of TCMs. A comprehensive database that contains TCM‐related information will provide a vital resource. Here, we present an integrative genome database of TCM plants (IGTCM) that contains 14,711,220 records of 83 annotated TCM‐related herb genomes, including 3,610,350 genes, 3,534,314 proteins and corresponding coding sequences, and 4,032,242 RNAs, as well as 1033 non‐redundant component records for 68 herbs, downloaded and integrated from the GenBank and RefSeq databases. For minimal interconnectivity, each gene, protein, and component was annotated using the eggNOG‐mapper tool and Kyoto Encyclopedia of Genes and Genomes database to acquire pathway information and enzyme classifications. These features can be linked across several species and different components. The IGTCM database also provides visualization and sequence similarity search tools for data analyses. These annotated herb genome sequences in IGTCM database are a necessary resource for systematically exploring genes related to the biosynthesis of compounds that have significant medicinal activities and excellent agronomic traits that can be used to improve TCM‐related varieties through molecular breeding. It also provides valuable data and tools for future research on drug discovery and the protection and rational use of TCM plant resources. The IGTCM database is freely available at http://yeyn.group:96/.

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Section: Introductionmentioning

confidence: 99%

IGTCM: An integrative genome database of traditional Chinese medicine plants

Liang

et al. 2023

The Plant Genome

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“…The family Asteraceae is the most differentiated dicotyledons with about 1,479 genera and 21,105 species distributed worldwide, except for the Antarctic region [1]. Carpesium is a genus of the Asteraceae family with beneficial medicinal value.…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of chloroplast genomes of three medicinal Carpesium species: Genome structures and phylogenetic relationships

Shi

Wan

et al. 2022

PLoS ONE

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Carpesium (Asteraceae) is a genus that contains many plant species with important medicinal values. However, the lack of chloroplast genome research of this genus has greatly hindered the study of its molecular evolution and phylogenetic relationship. This study used the Illumina sequencing platform to sequence three medicinal plants of the Carpesium genus: Carpesium abrotanoides, Carpesium cernuum, and Carpesium faberi, obtaining three complete chloroplast genome sequences after assembly and annotation. It was revealed that the three chloroplast genomes were typical quadripartite structures with lengths of 151,389 bp (C. abrotanoides), 151,278 bp (C. cernuum), and 151,250 bp (C. faberi), respectively. A total of 114 different genes were annotated, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Abundant SSR loci were detected in all three chloroplast genomes, with most composed of A/T. The expansion and contraction of the IR region indicate that the boundary regions of IR/SC are relatively conserved for the three species. Using C. abrotanoides as a reference, most of the non-coding regions of the chloroplast genomes were significantly different among the three species. Five different mutation hot spots (trnC-GCA-petN, psaI, petA-psbJ, ndhF, ycf1) with high nucleotide variability (Pi) can serve as potential DNA barcodes of Carpesium species. Additionally, phylogenetic evolution analysis of the three species suggests that C. cernuum has a closer genetic relationship to C. faberi than C. abrotanoides. Simultaneously, Carpesium is a monophyletic group closely related to the genus Inula. Complete chloroplast genomes of Carpesium species can help study the evolutionary and phylogenetic relationships and are expected to provide genetic marker assistance to identify Carpesium species.

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