Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes

BMC Plant Biology, Год журнала: 2024, Номер 24(1)

Опубликована: Март 11, 2024

Abstract Background The era of high throughput sequencing offers new paths to identifying species boundaries that are complementary traditional morphology-based delimitations. De novo delimitation using or DNA super-barcodes serve as efficient approaches recognizing putative (molecular operational taxonomic units, MOTUs). Tea plants ( Camellia sect. Thea ) form a group morphologically similar with significant economic value, providing the raw material for tea, which is most popular nonalcoholic caffeine-containing beverage in world. Taxonomic challenges have arisen from vague this group. Results Based on comprehensive sampling C. by far (165 individuals 39 morphospecies), we applied three de methods (ASAP, PTP, and mPTP) plastome data provide an independent evaluation tea plants. Comparing MOTU partitions morphospecies, particularly tested congruence MOTUs resulting different methods. We recognized 28 consensus within , while tentatively suggesting 11 morphospecies be discarded. Ten were uncovered complexes need further study integrating other evidence. Our results also showed strong imbalance among analyzed terms number molecular diagnostic characters. Conclusion This serves solid step forward underlying plants, needed evidence-based framework utilization conservation economically important plant

Язык: Английский

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

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

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

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

Опубликована: Фев. 23, 2019

Язык: Английский

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Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos

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

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

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

Опубликована: Янв. 28, 2021

Язык: Английский

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Phylotranscriptomics of Theaceae: generic-level relationships, reticulation and whole-genome duplication

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

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Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea

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

Опубликована: Март 1, 2023

Язык: Английский

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

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

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Genome assembly of Stewartia sinensis reveals origin and evolution of orphan genes in Theaceae

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

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Comparative chloroplast genomes and phylogenetic analyses shed new insights on the phyloevolution of different ploidy in Camellia reticulata

BMC Plant Biology, Год журнала: 2025, Номер 25(1)

Опубликована: Март 12, 2025

Camellia reticulata Lindl. (C. reticulata) is the tallest ornamental camellia globally, with wild populations comprising a polyploid complex of diploids (2×), tetraploids (4×), and hexaploids (6×). The type specimen C. heteroploid hexaploid derived from 2 × ancestors, including pitardii, saluenensis, reticulata. Currently, limited information exists regarding evolutionary characteristics chloroplast genomes at different ploidy levels, phylogenetic position 4 remains unclear. This study sequenced, assembled, annotated reticulata, comparing them those 6 other closely related species. results indicated that genome sizes ranged 156,519 to 156,927 bp, gene counts, distributions, GC content, codon usage being similar across levels. ycf1 exhibited significant differentiation among species, was identified as candidate for adaptive evolution in Additionally, 11 highly differentiated intergenic regions were identified, six hotspots variation can serve molecular markers genetic studies populations. Analysis selection pressure four genes under positive selection. Phylogenetic analysis revealed along mairei, formed well-supported clade. distances between its three ancestors relatively small. mairei may have participated allopolyploidization both potential independent classification. These findings provide valuable insights into alterations following allopolyploidization, establishing crucial foundation understanding systematic history various levels

Язык: Английский

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