Phylogenomics and the flowering plant tree of life

Journal of Integrative Plant Biology, Год журнала: 2022, Номер 65(2), С. 299 - 323

Опубликована: Ноя. 23, 2022

Abstract The advances accelerated by next‐generation sequencing and long‐read technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of studies adopting hundreds thousands genes across wealth clades have emerged ushered phylogenetics evolution into new era. meantime, roadmap researchers when making decisions different approaches their phylogenomic research design is imminent. This review focuses on utility genomic data (from organelle genomes, both reduced representation whole‐genome sequencing) in evolutionary investigations, describes baseline methodology experimental analytical procedures, summarizes recent progress flowering phylogenomics at ordinal, familial, tribal, lower levels. We also discuss challenges, such as adverse impact orthology inference reconstruction raised from systematic errors, underlying biological factors, duplication, hybridization/introgression, incomplete lineage sorting, together suggesting that bifurcating tree may not be best model life. Finally, we promising avenues future studies.

Язык: Английский

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Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants

American Journal of Botany, Год журнала: 2021, Номер 108(7), С. 1059 - 1065

Опубликована: Июль 1, 2021

Язык: Английский

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A holocentric twist to chromosomal speciation?

Trends in Ecology & Evolution, Год журнала: 2022, Номер 37(8), С. 655 - 662

Опубликована: Апрель 26, 2022

Язык: Английский

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A Bird’s Eye View of the Systematics of Convolvulaceae: Novel Insights From Nuclear Genomic Data

Frontiers in Plant Science, Год журнала: 2022, Номер 13

Опубликована: Июль 14, 2022

Convolvulaceae is a family of c. 2,000 species, distributed across 60 currently recognized genera. It includes species high economic importance, such as the crop sweet potato (Ipomoea batatas L.), ornamental morning glories bindweeds (Convolvulus and dodders, parasitic vines (Cuscuta L.). Earlier phylogenetic studies, based predominantly on chloroplast markers or single nuclear region, have provided framework for systematic studies family, but uncertainty remains at level relationships among subfamilies, tribes, genera, hindering evolutionary inferences taxonomic advances. One enduring enigmas has been relationship Cuscuta to rest Convolvulaceae. Other examples unresolved issues include monophyly within Merremieae, "bifid-style" clade (Dicranostyloideae), well relative positions Erycibe Roxb. Cardiochlamyeae. In this study, we explore large dataset genes generated using Angiosperms353 kit, contribution resolving some these remaining uncertainties For first time, strongly supported backbone provided. confirmed belong "Merremieae," in their former tribal circumscription, are recovered non-monophyletic, with unexpected placement Distimake Raf. sister that contains Ipomoeeae Decalobanthus Ooststr., Convolvuleae nested "Merremieae." The Dicranostyloideae, including Jacquemontia Choisy, supported, albeit novel between genera hypothesized, challenging current delimitation. exact placements remain uncertain, requiring further investigation. Our study explores benefits limitations increasing sequence data higher-level Convolvulaceae, highlights need expanded sampling, facilitate much-needed revised classification family.

Язык: Английский

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Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure

Frontiers in Plant Science, Год журнала: 2023, Номер 14

Опубликована: Янв. 26, 2023

The chloroplast genomes of angiosperms usually have a stable circular quadripartite structure that exhibits high consistency in genome size and gene order. As one the most diverse genera angiosperms, Carex is great value for study evolutionary relationships speciation within its genus, but limited due to highly expanded restructured with large number repeats. In this study, we provided more detailed account using hybrid assembly second- third-generation sequencing examined structural variation genus. revealed four species are significantly longer than characterized by sequence rearrangement rates, low GC content density, increased repetitive sequences. location studied closely related positions long repeat sequences; genus provides typical example expansion caused Phylogenetic constructed based on protein-coding genes support latest taxonomic system Carex, while revealing may some phylogenetic significance. Moreover, demonstrated approach short reads analyze complex also an important reference analysis rearrangements other taxa.

Язык: Английский

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Global analysis of Poales diversification – parallel evolution in space and time into open and closed habitats

New Phytologist, Год журнала: 2023, Номер 242(2), С. 727 - 743

Опубликована: Ноя. 27, 2023

Poales are one of the most species-rich, ecologically and economically important orders plants often characterise open habitats, enabled by unique suites traits. We test six hypotheses regarding evolution assembly in closed habitats throughout world, examine whether diversification patterns demonstrate parallel evolution. sampled 42% species obtained taxonomic biogeographic data from World Checklist Vascular Plants database, which was combined with open/closed habitat scored experts. A dated supertree constructed. integrated spatial phylogenetics regionalisation analyses, historical biogeography ancestral state estimations. Diversification result dynamic evolutionary processes that vary across lineages, time space, prominently tropical southern latitudes. Our results reveal recurrent trait transitions species-rich families Poaceae Cyperaceae. Smaller display divergent trajectories. The have achieved global dominance via notable, spatially phylogenetically restricted divergences into strictly habitats.

Язык: Английский

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Genome size variation and whole-genome duplications in the monocot order Poales

Plant Systematics and Evolution, Год журнала: 2025, Номер 311(1)

Опубликована: Янв. 22, 2025

Язык: Английский

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A linear classification of Cyperaceae

Kew Bulletin, Год журнала: 2022, Номер 77(1), С. 309 - 315

Опубликована: Март 1, 2022

Summary This paper provides a linear classification of two subfamilies, 24 tribes, 10 subtribes and 95 genera the monocot family Cyperaceae (Poales), based on stable phylogenetic framework resulting from years morphological, molecular phylogenomic studies. The includes c. 5687 species. most species-rich tribes are monogeneric tribe Cariceae with 2003 species, Cypereae 1131 highest generic diversity is found in Schoeneae (25 genera), which resulted recognition eight to facilitate studying this group. will help organisation specimens herbaria according systematic order an easy-to-use summary current family.

Язык: Английский

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The genome of Eleocharis vivipara elucidates the genetics of C₃–C₄ photosynthetic plasticity and karyotype evolution in the Cyperaceae

Journal of Integrative Plant Biology, Год журнала: 2024, Номер 66(11), С. 2505 - 2527

Опубликована: Авг. 23, 2024

ABSTRACT Eleocharis vivipara , an amphibious sedge in the Cyperaceae family, has several remarkable properties, most notably its alternate use of C 3 photosynthesis underwater and 4 on land. However, absence genomic data hindered utility for evolutionary genetic research. Here, we present a high‐quality genome E. representing first chromosome‐level genus, with approximate size 965.22 Mb mainly distributed across 10 chromosomes. Its Hi–C pattern, chromosome clustering results, one‐to‐one synteny two subgroups indicates tetraploid structure count 2 n = x 20. Phylogenetic analysis suggests that diverged from Cyperus esculentus approximately 32.96 million years ago (Mya), underwent whole‐genome duplication (WGD) about 3.5 Mya. Numerous fusion fission events were identified between chromosomes close relatives. We demonstrate holocentromeres, chromosomal feature which can maintain stability such rearrangements. Experimental transplantation cross‐section studies showed terrestrial culms developed Kranz anatomy increased number chloroplasts bundle sheath (BS) cells. Gene expression weighted gene co‐expression network (WGCNA) overall elevated core genes associated pathway, significant enrichment related to modified culm efficiency. found evidence mixed nicotinamide adenine dinucleotide ‐ malic enzyme phosphoenolpyruvate carboxykinase type hypothesize evolution predates WGD event. The is dominated by subgenome A supplemented B. Collectively, our findings not only shed light karyotype within but also provide valuable insights into transition photosynthesis, offering promising avenues crop improvement breeding.

Язык: Английский

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Chromosome size matters: genome evolution in the cyperid clade

Annals of Botany, Год журнала: 2022, Номер 130(7), С. 999 - 1014

Опубликована: Ноя. 7, 2022

Abstract Background and Aims While variation in genome size chromosome numbers their consequences are often investigated plants, the biological relevance of remains poorly known. Here, we examine mean cyperid clade (families Cyperaceae, Juncaceae Thurniaceae), which is largest vascular plant lineage with predominantly holocentric chromosomes. Methods We measured 436 species cyperids using flow cytometry, augment these data previously published datasets. then separately compared sizes (2C/2n) amongst major lineages analysed how two genomic traits associated various environmental factors phylogenetically informed methods. Key Results show that have smallest recorded seed a large divergence between values. found smaller chromosomes larger geographical distributions there strong inverse association number across this lineage. Conclusions The distinct patterns might be explained by holokinetic drive. numerous small function to increase genetic diversity where crossovers limited during meiosis.

Язык: Английский

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