Complete chloroplast genome of novel Adrinandra megaphylla Hu species: molecular structure, comparative and phylogenetic analysis DOI Creative Commons
Quan Huu Nguyen, Nguyễn Thị Ngọc Lan,

Thi Nhung Doan

и другие.

Scientific Reports, Год журнала: 2021, Номер 11(1)

Опубликована: Июнь 3, 2021

Abstract Adrinandra megaphylla Hu is a medicinal plant belonging to the genus, which well-known for its potential health benefits due bioactive compounds. This study aimed assemble and annotate chloroplast genome of A. as well compare it with previously published cp genomes within genus. The was reconstructed using de novo reference-based assembly paired-end reads generated by long-read sequencing total genomic DNA. size 156,298 bp, comprised large single-copy (LSC) region 85,688 small (SSC) 18,424 pair inverted repeats (IRa IRb) 26,093 bp each; 51 SSRs 48 repeat structures were detected. includes 131 functional genes, containing 86 protein-coding 37 transfer RNA 8 ribosomal genes. indicated that gene content structure are highly conserved. phylogenetic reconstruction complete sequences, matK trnL genes from Pentaphylacaceae species exhibited genetic relationship. Among them, sequence better candidate resolution. first report .

Язык: Английский

Deep soil moisture has limited impact on mitigating drought stress effects on plant transpiration in a subtropical secondary forest DOI

Ji Zhang,

Na Liu,

Cicheng Zhang

и другие.

Plant and Soil, Год журнала: 2025, Номер unknown

Опубликована: Март 26, 2025

Язык: Английский

Процитировано

1

Rapid diversification of alpine bamboos associated with the uplift of the Hengduan Mountains DOI

Xia‐Ying Ye,

Pengfei Ma, Guoqian Yang

и другие.

Journal of Biogeography, Год журнала: 2019, Номер 46(12), С. 2678 - 2689

Опубликована: Сен. 30, 2019

Abstract Aim The Hengduan Mountains (HDM) of southwest China is a biodiversity hotspot and harbours one the world's richest temperate floras. However, origin evolution its biota remain largely unresolved. Here we explore impact mountain uplift on diversification process in this using alpine bamboos. Location HDM region, China. Taxon Alpine Methods We used ddRAD‐seq data from most complete sampling bamboos undertaken to date (79% species diversity), investigate their evolutionary history. ancestral area these was reconstructed time‐calibrated phylogeny BioGeoBEARS rates were inferred BAMM analyses. In addition, divergence evaluated trait‐dependent models diversification. Results strongly supported as monophyletic, relationships within them robustly resolved. Fargesia found be polyphyletic Yushania resolved monophyletic. originated outside region during late Miocene, spread Pliocene, undergoing significant acceleration net diversification, which temporally congruent with orogeny. speciation rate increased altitude high rate, estimated 0.75 per million years, detected for distributed elevations. Main Conclusions Our study demonstrates that heterogeneous habitats geographical isolation bamboos, have limited dispersal ability, are important drivers rapid This also highlights power complementary analyses revealing link between past geological changes.

Язык: Английский

Процитировано

68

Phylogenomic conflict resulting from ancient introgression following species diversification in Stewartia s.l. (Theaceae) DOI
Hanyang Lin,

Ya-Jun Hao,

Jianhua Li

и другие.

Molecular Phylogenetics and Evolution, Год журнала: 2019, Номер 135, С. 1 - 11

Опубликована: Фев. 23, 2019

Язык: Английский

Процитировано

59

Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos DOI Creative Commons
Cen Guo, Pengfei Ma, Guoqian Yang

и другие.

Systematic Biology, Год журнала: 2020, Номер 70(4), С. 756 - 773

Опубликована: Сен. 25, 2020

Rapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g., morphology and molecular) or genetic markers nuclear organelle) often yield inconsistent results. The tribe Arundinarieae, that is, temperate bamboos, is a clade tetraploid originated 22 Ma subsequently radiated in East Asia. Previous studies Arundinarieae have found conflicting relationships and/or low support. Here, we obtain from ddRAD for 213 taxa parallel sampling chloroplast genomes genome skimming 147 taxa. We first assess feasibility using ddRAD-seq estimates paleopolyploid rapidly lineages, optimize clustering thresholds, analysis workflow orthology identification. Reference-based assembly approaches perform well strongly supported generally concordant with morphology-based taxonomy. recover five major two which notable (the pachymorph leptomorph lineages), they correspond distinct rhizome morphologies. By contrast, phylogeny differed significantly. Based on multiple lines evidence, tree favored as best species estimation bamboos. Using time-calibrated tree, find diversified around mid-Miocene corresponding intensification Asian monsoon evolution key innovations including rhizomes. Our results provide highly resolved shed new light radiation reticulate history this tribe, an empirical example study recalcitrant plant radiations. [Arundinarieae; ddRAD; paleopolyploid; skimming; rapid diversification; incongruence.].

Язык: Английский

Процитировано

59

Phylogenomic analyses based on genome-skimming data reveal cyto-nuclear discordance in the evolutionary history of Cotoneaster (Rosaceae) DOI

Kaikai Meng,

Sufang Chen, Ke‐Wang Xu

и другие.

Molecular Phylogenetics and Evolution, Год журнала: 2021, Номер 158, С. 107083 - 107083

Опубликована: Янв. 28, 2021

Язык: Английский

Процитировано

49

Phylotranscriptomics of Theaceae: generic-level relationships, reticulation and whole-genome duplication DOI Open Access
Qiong Zhang, Lei Zhao, Ryan A. Folk

и другие.

Annals of Botany, Год журнала: 2022, Номер 129(4), С. 457 - 471

Опубликована: Янв. 16, 2022

Theaceae, with three tribes, nine genera and more than 200 species, are of great economic ecological importance. Recent phylogenetic analyses based on plastomic data resolved the relationships among tribes intergeneric within two those tribes. However, generic-level largest tribe, Theeae, were not fully resolved. The role putative whole-genome duplication (WGD) events in family possible hybridization Theeae also remain to be tested further.Transcriptomes or low-depth sequencing 57 species as well additional plastome sequence data, generated. Using a dataset low-copy nuclear genes, we reconstructed using concatenated, tree network approaches. We further conducted molecular dating inferred WGD by examining distribution number synonymous substitutions per site (Ks) for paralogues each species. For plastid protein-coding sequences , phylogenies comparison results obtained from analysis dataset.Based 610 genes (858 606 bp length) investigated, Stewartieae was sister other Within Apterosperma-Laplacea clade grouped Pyrenaria, leaving Camellia Polyspora sister. estimated ages Theaceae largely consistent previous studies mainly data. Two reticulation one between common ancestor Gordonia Schima found. All members tea shared events, an older At-γ recent Ad-β; both outgroups (Diapensiaceae, Pentaphylacaceae, Styracaceae Symplocaceae).Our improved understanding at tribal generic levels previously proposed but position needs attention. There is no evidence extensive Theaceae-specific event. Land bridges (e.g. Bering land bridge) during Late Oligocene may have permitted intercontinental plant movements that facilitated ancient introgression Schima.

Язык: Английский

Процитировано

39

The early Oligocene establishment of modern topography and plant diversity on the southeastern margin of the Tibetan Plateau DOI

Mengxiao Wu,

Jian Huang, Robert A. Spicer

и другие.

Global and Planetary Change, Год журнала: 2022, Номер 214, С. 103856 - 103856

Опубликована: Май 29, 2022

Язык: Английский

Процитировано

39

Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea DOI
Zaibao Zhang, Tao Xiong, Jiahui Chen

и другие.

Journal of Molecular Evolution, Год журнала: 2023, Номер 91(2), С. 156 - 168

Опубликована: Март 1, 2023

Язык: Английский

Процитировано

19

Phylogenomic insights into the origin and evolutionary history of evergreen broadleaved forests in East Asia under Cenozoic climate change DOI

Sheng‐Yuan Qin,

Zheng‐Yu Zuo, Cen Guo

и другие.

Molecular Ecology, Год журнала: 2023, Номер 32(11), С. 2850 - 2868

Опубликована: Фев. 27, 2023

The evergreen versus deciduous leaf habit is an important functional trait for adaptation of forest trees and has been hypothesized to be related the evolutionary processes component species under paleoclimatic change, potentially reflected in dynamic history broadleaved forests (EBLFs) East Asia. However, knowledge about shift with impact change using genomic data remains rare. Here, we focus on Litsea complex (Lauraceae), a key lineage dominant EBLFs, gain insights into how shifted, providing origin historical dynamics EBLFs Asia Cenozoic climate change. We reconstructed robust phylogeny genome-wide single-nucleotide variants (SNVs) eight clades resolved. Fossil-calibrated analyses, diversification rate shifts, ancestral habit, ecological niche modelling reconstruction were employed estimate its pattern. Taking account studies other plant lineages dominating Asia, it was revealed that prototype probably emerged Early Eocene (55-50 million years ago [Ma]), facilitated by greenhouse warming. As response cooling drying Middle Late (48-38 Ma), habits evolved Up Miocene (23 prevailing Asian monsoon increased extreme seasonal precipitation accelerated emergence lineages, ultimately shaped vegetation resembling today.

Язык: Английский

Процитировано

18

Genome assembly of Stewartia sinensis reveals origin and evolution of orphan genes in Theaceae DOI Creative Commons
Lin Cheng,

Qunwei Han,

Yanlin Hao

и другие.

Communications Biology, Год журнала: 2025, Номер 8(1)

Опубликована: Март 3, 2025

Orphan genes play crucial roles in diverse biological processes, but the evolutionary trajectories and functional divergence remain largely unexplored. The Theaceae family, including economically culturally important tea plant, offers a distinctive model to examine these aspects. Here, we integrated Nanopore long-read sequencing, Illumina short-read Hi-C methods decode pseudo-chromosomal genome assembly of Stewartia sinensis, from earliest-diverging tribe Theaceae, spanning 2.95 Gb. Comparative genomic analysis revealed absence recent whole-genome duplication events ancestor, highlighting tandem duplications as predominant mechanism gene expansion. We identified 31,331 orphan genes, some which appear have ancient origins, suggesting early emergence with frequent gains losses, while others seem more specific recent. Notably, are distinguished by shorter lengths, fewer exons domains compared that originate much earlier, like transcription factors. Moreover, contributes significantly adaptive evolution characteristic diversity it is also major driving origination genes. This study illuminates dynamics providing valuable resource for understanding origin plant flavor enhancing genetic breeding efforts. nearly complete an early-diverging species, phylogenomic studies provide insights into Theaceae.

Язык: Английский

Процитировано

1