Phylogeny, Genetic Diversity and Population Structure of Fritillaria cirrhosa and Its Relatives Based on Chloroplast Genome Data

Genes, Journal Year: 2024, Volume and Issue: 15(6), P. 730 - 730

Published: June 2, 2024

Fritillaria cirrhosa and its relatives have been utilized in traditional Chinese medicine for many years are under priority protection China. Despite their medicinal protective value, research on phylogeny, genetic diversity, divergence remains limited. Here, we investigate the chloroplast genome variation architecture of 46 samples F. collected from various regions, encompassing majority wild populations across diverse geographical areas. The results indicate abundant variations accessions including 1659 single-nucleotide polymorphisms 440 indels. Six variable markers (psbJ, ndhD, ycf1, ndhG, trnT-trnL, rpl32-trnL) were identified. Phylogenetic network analysis, population structure principal component analysis showed that formed five clades with significant divergence, which related to distribution. regions spanning southern Hengduan Mountains Qinghai–Tibet Plateau exhibited highest levels diversity. may suffered a bottleneck relatively low diversity level. Moreover, barriers discrete patches accelerated divergence. study offers novel perspectives relatives, information can inform conservation utilization strategies future.

Language: Английский

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A Comparative Phylogenetic Analysis on the Chloroplast Genome in Different Reynoutria japonica Populations

Genes, Journal Year: 2022, Volume and Issue: 13(11), P. 1979 - 1979

Published: Oct. 30, 2022

Reynoutria japonica Houtt., a traditional medicine herb of the Polygonaceae family, has been used since ancient times in China due to its various pharmacological effects. Chloroplast genomes are conservative and play an essential role population diversity analysis. However, there few studies on chloroplast genome R. japonica. In this study, complete three from different regions were performed by next-generation sequencing technology. The results revealed that lengths between 163,371~163,372 bp, they have highly conserved structure with pair inverted repeat (IR) (31,121 bp), large single-copy (LSC) region (87,571~87,572 small (SSC) (13,558 bp). total, 132 genes annotated, including 8 rRNA genes, 37 tRNA 87 protein-coding genes. phylogenetic analysis strongly 13 populations form monophyly, Fallopia multiflora (Polygonaceae) is closest species. two species diverged at ~20.47 million years ago, could be further divided into major groups based genetic addition, several potential loci suitable polymorphism identified as molecular markers. Our study provides important resources for development utilization germplasm, well some new insights evolutionary characteristics medicinal plant.

Language: Английский

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The discovery and characterization of AeHGO in the branching route from shikonin biosynthesis to shikonofuran in Arnebia euchroma

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: April 25, 2023

Shikonin derivatives are natural naphthoquinone compounds and the main bioactive components produced by several boraginaceous plants, such as Lithospermum erythrorhizon Arnebia euchroma. Phytochemical studies utilizing both L. A. euchroma cultured cells indicate existence of a competing route branching out from shikonin biosynthetic pathway to shikonofuran. A previous study has shown that branch point is transformation (Z)-3''-hydroxy-geranylhydroquinone an aldehyde intermediate (E)-3''-oxo-geranylhydroquinone. However, gene encoding oxidoreductase catalyzes reaction remains unidentified. In this study, we discovered candidate belonging cinnamyl alcohol dehydrogenase family, AeHGO, through coexpression analysis transcriptome data sets shikonin-proficient shikonin-deficient cell lines biochemical assays, purified AeHGO protein reversibly oxidized produce (E)-3''-oxo-geranylhydroquinone followed reducing (E)-3''-hydroxy-geranylhydroquinone, resulting in equilibrium mixture three compounds. Time course kinetic parameters showed reduction was stereoselective efficient presence NADPH, which determined overall proceeded (E)-3''-hydroxy-geranylhydroquinone. Considering there competition between accumulation shikonofuran plant cells, supposed play important role metabolic regulation pathway. Characterization should help expedite development engineering synthetic biology toward production derivatives.

Language: Английский

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Complete chloroplast genomes of Microula sikkimensis and comparative analyses with related species from Boraginaceae

Published: Dec. 28, 2023

The present study provides a detailed analysis of the chloroplast genome Microula sikkimensis. was consisted altogether 149,428bp and distinct regions, including large single-copy (81329bp), small (17261bp), inverted repeat (25419bp). contained 112 genes, 78 protein-coding 30 tRNA 4 rRNA some exhibited duplication in IR region. displayed different GC content across with region exhibiting highest. Codon usage identification simple sequence repeats (SSRs) offer valuable genetic markers. Comparative other Boraginaceae species highlighted conservation diversity coding noncoding regions. Phylogenetic placed M. sikkimensis within family, revealing its relationship specific species.

Language: Английский

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Phylogenomics and plastome evolution of Lithospermeae (Boraginaceae)

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Oct. 14, 2024

Lithospermeae is the largest tribe within Boraginaceae. The has been focus of multiple phylogenetic studies over last 15 years, with most focused on one genus or a few genera. In present study, we newly sequenced 69 species and relatives to analyze phylogenomic relationships among its members as well evolution plastid genome.

Language: Английский

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Variations in genetic diversity in cultivated Pistacia chinensis

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Nov. 10, 2022

Identification of the evolution history and genetic diversity a species is important in utilization novel variation this species, as well for its conservation. Pistacia chinensis an biodiesel tree crop China, due to high oil content fruit. The aim study was uncover structure P. investigate influence intraspecific gene flow on process domestication diversification varieties. We investigated chinensis, introgression subpopulations, through analysis plastid nuclear genomes 39 individuals from across China. High levels were detected plastome, 460 polymorphic sites, 104 indels three small inversions identified. Phylogenetic population using plastome dataset supported five clades chinensis. Population based SNPs showed two groups, clearly clustered together, more than third total classified hybrids. Discordance between suggested that hybridization events may have occurred highly divergent samples subclades. Most subclade diverged late Miocene mid-Pliocene. processes cultivation decreased extensive variability structuring together with genomic suggests much unexploited available improvement recently domesticated species.

Language: Английский

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The complete chloroplast genome of Cynoglossum amabile Stapf & J. R. Drumm., 1906 (Boraginaceae), a traditional Chinese herbal medicine

Mitochondrial DNA Part B, Journal Year: 2023, Volume and Issue: 8(1), P. 52 - 56

Published: Jan. 2, 2023

Cynoglossum amabile Stapf & J. R. Drumm., 1906 is a traditional Chinese herbal medicine from southwest China. To better determine its phylogenetic relatedness to other Boraginaceae species, the chloroplast (cp) genome of C. was sequenced. The complete cp 151,532 bp in length, containing small single-copy (SSC) region with length 17,366 bp, large (LSC) 82,902 and pair inverted repeats (IRs) regions each 25,632 bp. overall GC content 37.4%. maximum-likelihood tree showed that Bothriospermum zeylanicum (J. Jacq.) Druce, 1917 closely related amabile.

Language: Английский

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A cinnamyl alcohol dehydrogenase (CAD) like enzyme leads to a branch in the shikonin biosynthetic pathway inArnebia euchroma

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 9, 2023

Summary Shikonin derivatives are natural naphthoquinone compounds and the main bioactive components produced by several boraginaceous plants, such as Lithospermum erythrorhizon Arnebia euchroma . Phytochemical researches utilizing L. A. cultured cells both indicate existence of a competing route branching out from shikonin biosynthetic pathway toward benzo/hydroquinones. A previous study has shown that branch point is putative alcohol dehydrogenase converting ( Z )-3’’-hydroxygeranylhydroquinone [( )-3’’-OH-GHQ] to an aldehyde intermediate E )-3’’-oxo-GHQ. However, enzyme involved in reaction not characterized at molecular level yet. In this study, we clone candidate gene belonging cinnamyl (CAD) family, AeHGO , through coexpression analysis transcriptome data sets shikonin-proficient shikonin-deficient cell lines biochemical assays, purified protein reversibly oxidizes )-3’’-OH-GHQ produce )-3’’-oxo-GHQ followed reducing )-3’’-OH-GHQ, resulting equilibrium mixture three compounds. Time course kinetic parameters show with about twice efficient which leads predominance mixture. According report, can be converted deoxyshikonofuran, hydroquinone metabolite plants. Considering there competition for accumulation between benzo/hydroquinones cells, supposed play important role metabolic regulation pathway.

Language: Английский

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