Sliding‐window phylogenetic analyses uncover complex interplastomic recombination in the tropical Asian–American disjunct plant genus Hedyosmum (Chloranthaceae)

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

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Chromosome-level genome assembly of an important ethnic medicinal plant Callicarpa nudiflora

Scientific Data, Journal Year: 2025, Volume and Issue: 12(1)

Published: April 18, 2025

Callicarpa nudiflora is one of high medicinal and economic value plants in China, which was recorded Chinese pharmacopoeia (2020 edition) widely used to treat tropical bacterial infections, acute infectious hepatitis, internal external bleeding. In this study, we assembled the C. genome with a size approximately 597.82 Mb contig N50 length 34.14 Mb. A total 98.61% sequences were anchored 17 pseudo-chromosomes by using PacBio long reads Hi-C sequencing data. We totally predicted 31,266 protein-coding genes, 92.45% could be annotated databases such as NR, GO, KOG, KEGG. addition, identified 2,303 rRNAs, 884 MicroRNAs 531 tRNAs from genome. The chromosome-scale represents crucial resource for investigating molecular mechanisms underlying biosynthesis components facilitates exploration conservation nudiflora.

Language: Английский

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Plastome comparison and phylogenomics of Chinese endemic Schnabelia (Lamiaceae): insights into plastome evolution and species divergence

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: May 7, 2025

Schnabelia species, herbaceous perennial plants within the Lamiaceae family, possess medicinal value and are endemic to China. While previous studies have focused on morphological classification, molecular systematics, components, there has been limited research phylogenomics. To reveal their plastid genome characteristics phylogenetic relationships, we sequenced assembled plastomes of all five species (S. oligophylla, S. tetrodonta, nepetifolia, terniflora, aureoglandulosa), conducted comparative genomic analyses, constructed a tree incorporating closely related taxa in subfamily Ajugoideae, as well conducting divergence time estimation. Plastome size ranged from 155,733 bp 156,944 bp, encompassing 115 unique genes, with GC content 37.8% same for species. Five intergenic spacer regions (trnH-GUG-psbA, trnK-UUU-matK, petB-petD, ndhD-psaC, ndhA-ndhH) were identified hotspots. Gene selection pressure analysis demonstrated that genes under negative selection. Phylogenetic relationship Ajugoideae based confirmed monophyly Schnabelia. Two clades supported, one containing two original other comprising three transferred Caryopteris. The stem age is estimated be approximately 30.24 Ma, split Sections occurring around 12.60 Ma. We revealed evolutionary features genus highly variable can provide tool future identification these plants. diversification during middle Miocene Quaternary suggests historical geological climatic shifts facilitated differentiation. These findings enhance our understanding Schnabelia's evolution support chloroplast diversity, aiding conservation sustainable use.

Language: Английский

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New Insights Into the Phylogeny and Biogeography of Goji Berries (Lycium, Solanaceae) Inferred From Plastid Data

Journal of Biogeography, Journal Year: 2025, Volume and Issue: unknown

Published: May 28, 2025

ABSTRACT Aim Lycium L. (Solanaceae), which is known for producing goji berries, an important plant with both medicinal and edible uses. This genus globally distributed in temperate subtropical regions. However, a comprehensive phylogeny evolutionary history of this group lacking so far. study was executed to produce novel insights into the phylogenetic relationships small but economically genus. Location North America, South Hawaii, Africa Eurasia. Taxon (Solanaceae). Methods We established framework based on complete plastome sequences data from 80 protein‐coding genes across 43 species using maximum likelihood Bayesian inference methods. Furthermore, 14 Solanaceae family were used as outgroups. Additionally, two Solanoideae fossils one secondary calibration point estimate divergence times reveal biographical these plants through ancestral area reconstruction. Results Our analysis revealed that six American strongly supported monophyletic high support sister clades remainder The remaining America Hawaiian Islands shared common ancestor, whereas all Africa, Saharo‐Arabia Eurasia formed distinct clade. results indicated originated during Late Oligocene then dispersed Hawaii there further Saharo‐Arabia, more recent dispersal Main Conclusions plastid genome confirmed identified long‐distance key its global distribution. Genomic facilitate identification contribute conservation efforts.

Language: Английский

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Phylogenetic origin of dioecious Callicarpa (Lamiaceae) species endemic to the Ogasawara Islands revealed by chloroplast and nuclear whole genome analyses

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: unknown, P. 108234 - 108234

Published: Nov. 1, 2024

Language: Английский

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