Subfamily evolution analysis using nuclear and chloroplast data from the same reads

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 3, 2025

The chloroplast (cp) genome is a widely used tool for exploring plant evolutionary relationships, yet its effectiveness in fully resolving these relationships remains uncertain. Integrating cp data with nuclear DNA information offers more comprehensive view but often requires separate datasets. In response, we employed the same raw read sequencing to construct genome-based trees and phylogenetic using Read2Tree, cost-efficient method extracting conserved gene sequences from data, focusing on Aurantioideae subfamily, which includes Citrus relatives. resulting were consistent existing derived high-throughput sequencing, diverged trees. To elucidate underlying complex processes causing discordances, implemented an integrative workflow that utilized multiple alignments of each generated by conjunction other phylogenomic methods. Our analysis revealed incomplete lineage sorting predominantly drives while introgression ancient also contribute topological discrepancies within certain clades. This study underscores cost-effectiveness both analyses understanding relationships.

Language: Английский

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Phylogeography and genetic diversity of Ulmus elongata (Ulmaceae), a Tertiary relict tree with extremely small populations (PSESP)

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

Published: Jan. 16, 2025

Assessing the current status and identifying mechanisms threatening endangered plants are significant challenges fundamental to biodiversity conservation, particularly for protecting Tertiary relict trees plant species with extremely small populations (PSESP). Ulmus elongata (Ulmus, Ulmaceae) high values ornamental application, is a tree one of members from PSESP in China. Currently, wild U. have been threatened by excessive deforestation urbanization, but limited knowledges its genetic diversity seriously hinder conservation efforts. Therefore, further study on drivers pattern crucial preserving resources can serve as reference other under climate change. Here, total 12 70 individuals were collected covering geographical distribution Utilizing chloroplast genome datasets, we found that exhibited remarkably low nucleotide gene flow (π = 0.00013, Nm 0.03). Analysis molecular variance (AMOVA) showed variation occurs mainly between eight clades (60.95%). The Mantel tests indicated correlation differentiation distances (r 0.3777, p < 0.05) populations. A notable phylogeographic structure was identified elongata, comprising distinct haplogroups (NST 0.917, GST 0.876, 0.05), which attributed global cooling East Asia Quaternary oscillations. Overall, our using representative supported hypothesis belonging simultaneously exhibits significantly lower compared those either or individually. Furthermore, be primarily ascribed combination factors, including habitat fragmentation resulting human activities, contraction during LGM population sizes. This provides foundation guiding efforts implementing management strategies PSESP. Our findings also provide evidence important roles Asian monsoon system oscillations shaping subtropical broad-leaved forests.

Language: Английский

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Phylogenomic analyses revealed widely occurring hybridization events across Elsholtzieae (Lamiaceae)

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 198, P. 108112 - 108112

Published: May 26, 2024

Language: Английский

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Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae)

Plant Diversity, Journal Year: 2023, Volume and Issue: 46(3), P. 344 - 352

Published: June 7, 2023

(Poaceae: Bambusoideae) is a temperate woody bamboo species endemic to South-central China with narrow distribution. Previous phylogenetic studies revealed an unexpected, isolated position of

Language: Английский

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Transcriptome data reveals the conservation genetics of Cypripedium forrestii, a plant species with extremely small populations endemic to Yunnan, China

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Jan. 31, 2024

The Cypripedium forrestii is an orchid species with extremely small populations (PSESP) in Yunnan, China. C. range-restricted and less-studied than many species, it exposed to various threats its survival. We investigated potential habitats collected 52 samples from eight locations, as well two outgroup for reference. developed genetic markers (SNPs) based on transcriptome sequencing (RNA-seq) data, analyzed the diversity, population structure, gene flow demographic history of detail. a taxonomically independent protect. found that diversity was very low (1.7e -4 ) compared other endangered species. identified three clusters, several distinct backgrounds. Most within sampling sites (87.87%) clusters (91.39%). Gene has been greatly limited over most recent generations, probably due geographical distance, historical climate change habitat fragmentation. also detected severe bottleneck event brought about by constraints. These factors, together reproductive characteristics, contribute fragmentation . Based our findings, we suggest integrative conservation strategy protect recover further comprehensive study ecological traits future.

Language: Английский

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The medicinal plant Buddleja asiatica and its relation to the welfare of local people in the Pan‐Himalayan region: Past, present, and future perspectives

Plants People Planet, Journal Year: 2024, Volume and Issue: 6(6), P. 1231 - 1248

Published: Aug. 27, 2024

Societal Impact Statement Globalization and rapid shifts in culture economy threaten indigenous local knowledge (ILK) systems, large intergenerational gaps this already exist. Buddleja asiatica is a deciduous shrub or small tree with traditional medicinal applications but currently largely overlooked as resource. This study investigates the uses of B. communities Pan‐Himalayan region through ethnobotanical field surveys, view to preserving cultural heritage strengthening economic resilience these communities, well developing Prioritizing well‐being mountain aims bridge community development nature. Summary Lour. (Scrophulariaceae) widely distributed across region. It has value, ecological significance. We conducted an combining surveys from Nepal Xizang, China literature review using Web Science (WoS) ethnobotanical, phytochemical, pharmacological aspects species. Our highlights significance within and, particular, use leaves make starter for preparation wine. However, evident gap transfer exists. The phytochemical investigation revealed presence various chemical classes (carbohydrates, terpenoids, flavonoids, saponins, esters, steroids, glycosides, fatty acids), which 15 phytoconstituents were first reported parts . potential properties chemicals include anti‐inflammatory, antioxidant, cytotoxic, antihepatotoxic, antimicrobial, cholinesterase activities. combine lines evidence show prospects livelihoods people propose future research directions.

Language: Английский

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Analysis of chloroplast genomes of ten central Asian Fritillaria species and their phylogenetic relationships

Nordic Journal of Botany, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 26, 2024

Fritillaria is a taxonomically complex genus of Liliaceae that contains many important ornamental and medicinal species. In this study, we sequenced the chloroplast genomes ten species distributed in central Asia compared them to previously cp genomes. Comparison 36 species' identified as useful potential molecular markers due their high level divergence three coding regions 11 intergenic spacers. Effective single sequence repeats (SSRs) for population genetic studies were also identified. Phylogenetic analysis showed two recently described species, F. baisunensis rugillosa belong F . subg. Rhinopetalum , belonging ussuriensis meleagroides should be revised. These camschatsencese currently assigned Liliorhiza members same taxonomic unit. although small group, more complicated than it was thought, apparently comprises too distant one subgenus. maximowischii treated new

Language: Английский

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Phylogenomic insights into species relationships, reticulate evolution, and biogeographic diversification of the ginseng genus Panax (Araliaceae), with an emphasis on the diversification in the Himalayan‐Hengduan Mountains

Journal of Systematics and Evolution, Journal Year: 2024, Volume and Issue: 63(1), P. 99 - 114

Published: Nov. 11, 2024

Abstract Panax (Araliaceae) is a small genus containing several well known medicinally important species. It has disjunct distribution between Eastern Asia and North America, with most species from eastern Asia, especially the Himalayan‐Hengduan Mountains (HHM). This study used genomic target enrichment method to obtain 358 nuclear ortholog loci complete plastome sequences 59 accessions representing all 18 of genus. Divergence time estimation biogeographic analyses suggest that was probably widely distributed America during middle Eocene. During late Eocene Oligocene may have experienced extensive extinctions global climate cooling. survived diverged early in mountains Southwest China tropical Indochina, where some taxa migrated northwestward HHM, eastward central China, then onward toward Japan America. Gene flow identified as main contributor phylogenetic discordance (33.46%) within . We hypothesize common ancestors P. ginseng + japonicus quinquefolius clade had allopolyploidization, which increased adaptability cooler drier environments. Miocene, dispersals occurred region HHM contiguous areas, suggesting acted refugium also served secondary diversification center for Our findings highlight interplay orographic uplift climatic changes greatly contributed diversity

Language: Английский

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Hybridization and polyploidization generate evolutionary diversification of the genus Buddleja in the Sino-Himalayan region. A commentary on ‘Deciphering complex reticulate evolution of Asian Buddleja (Scrophulariaceae): insights into the taxonomy and speciation of polyploid taxa in the Sino-Himalayan region’

Annals of Botany, Journal Year: 2023, Volume and Issue: 132(1), P. v - vii

Published: July 1, 2023

This article comments on: Fengmao Yang, Jia Ge, Yongjie Guo, Richard Olmstead and Weibang Sun. Deciphering complex reticulate evolution of Asian Buddleja (Scrophulariaceae): insights into the taxonomy speciation polyploid taxa in Sino-Himalayan region, Annals Botany, Volume 132, Issue 1, 01 July 2023, Pages 15–28, https://doi.org/10.1093/aob/mcad022

Language: Английский

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Comparing traditional and automated conservation assessments for Himalayan species of Buddleja

Oryx, Journal Year: 2024, Volume and Issue: 58(5), P. 618 - 626

Published: Sept. 1, 2024

Abstract To compare the benefits and drawbacks of traditional automated conservation assessments, we used a field-based study assessments using GeoCAT , red ConR to assess four species Buddleja (Scrophulariaceae), cosmopolitan genus flowering plants. colvilei sessilifolia delavayi yunnanensis are endemic Himalayan region. They have not yet been assessed for IUCN Red List Threatened Species but facing elevated risks extinction because various anthropogenic environmental pressures. B. listed as Plant with Extremely Small Populations in Yunnan, China, where they known be threatened. Although evaluated Endangered Vulnerable, our field studies indicated different categorization three species: Critically Endangered. Our findings indicate that accuracy reliability assessment methods can differ surveys remain important assessments. We recommend an integrated approach addressing these limitations, safeguard future other

Language: Английский

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