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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DNA barcoding of Cymbidium by genome skimming: Call for next‐generation nuclear barcodes

Molecular Ecology Resources, Год журнала: 2022, Номер 23(2), С. 424 - 439

Опубликована: Окт. 11, 2022

Cymbidium is an orchid genus that has undergone rapid radiation and high ornamental, economic, ecological cultural importance, but its classification based on morphology controversial. The plastid genome (plastome), as extension of plant standard DNA barcodes, been widely used a potential molecular marker for identifying recently diverged species or complicated groups. In this study, we newly generated 237 plastomes 50 (at least two individuals per species) by skimming, covering 71.4% members the Cymbidium. Sequence-based analyses (barcoding gaps automatic barcode gap discovery) tree-based (maximum likelihood, Bayesian inference multirate Poisson tree processes model) were conducted identification Our work provides comprehensive reference library identification. results show compared with barcodes (rbcL + matK) well trnH-psbA, rate plastome increased moderately from 58% to 68%. At same time, propose optimized strategy species. cannot completely resolve Cymbidium, main reasons being incomplete lineage sorting, artificial cultivation, natural hybridization chloroplast capture. To further explore use nuclear data in species, Skmer method was adopted 72%. It appears have vital role are expected be next-generation barcodes.

Язык: Английский

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A plastid phylogenomic framework for the palm family (Arecaceae)

BMC Biology, Год журнала: 2023, Номер 21(1)

Опубликована: Март 8, 2023

Abstract Background Over the past decade, phylogenomics has greatly advanced our knowledge of angiosperm evolution. However, phylogenomic studies large families with complete species or genus-level sampling are still lacking. The palms, Arecaceae, a family ca. 181 genera and 2600 important components tropical rainforests bearing great cultural economic significance. Taxonomy phylogeny have been extensively investigated by series molecular phylogenetic in last two decades. Nevertheless, some relationships within not yet well-resolved, especially at tribal generic levels, consequent impacts for downstream research. Results Plastomes 182 palm representing 111 were newly sequenced. Combining these previously published plastid DNA data, we able to sample 98% conduct investigation family. Maximum likelihood analyses yielded robustly supported hypothesis. Phylogenetic among all five subfamilies 28 tribes most inter-generic also resolved strong support. Conclusions inclusion nearly generic-level coupled genomes strengthened understanding plastid-based palms. This comprehensive genome dataset complements growing body nuclear genomic data. Together, datasets form novel baseline palms an increasingly robust framework future comparative biological this exceptionally plant

Язык: Английский

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Advancing Pyrus phylogeny: Deep genome skimming‐based inference coupled with paralogy analysis yields a robust phylogenetic backbone and an updated infrageneric classification of the pear genus (Maleae, Rosaceae)

Taxon, Год журнала: 2024, Номер 73(3), С. 784 - 799

Опубликована: Март 28, 2024

Abstract The lack of a robust phylogenetic backbone has posed significant challenges to proposing an infrageneric taxonomic classification the pear genus, Pyrus , widely distributed Eurasian lineage Rosaceae. This issue been exacerbated by limited informative loci and inaccessible taxon sampling. To address these limitations, we conducted extensive sampling, encompassing 78 ingroup individuals representing 32 species, along with 4 outgroup species. comprehensive sampling strategy covers wide range morphological geographical variations. enable accurate phylogenomic inference, assembled 801 single‐copy nuclear genes 72 plastid coding sequences from deep genome skimming (DGS) data. Additionally, employed tree‐based method for orthology which led generation three orthologous datasets: one‐to‐one orthologs (1to1), monophyletic outgroups (MO), rooted ingroups (RT). results yielded both analyses consistently support monophyly two well‐supported clades, Occidental Oriental were recovered in nine trees. Integrating evidence morphology phylogenomics, propose updated consists subgenera: P. subg. Pashia stat. nov. revised provides more framework understanding evolutionary relationships within genus.

Язык: Английский

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Phylogenomic conflict analyses of the plastid and mitochondrial genomes via deep genome skimming highlight their independent evolutionary histories: A case study in the cinquefoil genus Potentilla sensu lato (Potentilleae, Rosaceae)

Molecular Phylogenetics and Evolution, Год журнала: 2023, Номер 190, С. 107956 - 107956

Опубликована: Окт. 27, 2023

Язык: Английский

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Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Journal of Integrative Plant Biology, Год журнала: 2024, Номер 66(3), С. 546 - 578

Опубликована: Янв. 30, 2024

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of angiosperms in fossil record was referred to Darwin as "abominable mystery," hence contributing heightened interest angiosperm evolution. display wide ranges morphological, physiological, and ecological characters, some which have probably influenced their species richness. evolutionary analyses these characteristics help address questions diversification require well resolved phylogeny. Following great successes phylogenetic using plastid sequences, dozens thousands nuclear genes from next-generation sequencing been used phylogenomic analyses, providing phylogenies new insights into evolution angiosperms. In this review we focus on recent large clades, orders, families, subdivisions families provide a summarized Nuclear Phylogenetic Tree Angiosperm Families. newly established relationships highlighted compared previous results. sequenced genomes Amborella, Nymphaea, Chloranthus, Ceratophyllum, monocots, Magnoliids, basal eudicots, facilitated phylogenomics among five major clades. All but one 64 orders were included except placements several orders. Most robust highly supported placements, especially for within important families. Additionally, examine divergence time estimation biogeographic basis frameworks discuss differences analyses. Furthermore, implications ancestral reconstruction characters groups, limitations current studies, taxa that future attention.

Язык: Английский

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Assembly and comparative analysis of the initial complete mitochondrial genome of Primulina hunanensis (Gesneriaceae): a cave-dwelling endangered plant

BMC Genomics, Год журнала: 2024, Номер 25(1)

Опубликована: Апрель 1, 2024

Abstract Background Primulina hunanensis , a troglobitic plant within the genus of Gesneriaceae family, exhibits robust resilience to arid conditions and holds great horticultural potential as an ornamental plant. The work chloroplast genome (cpDNA) has been recently accomplished, however, mitochondrial (mtDNA) that is crucial for evolution not reported. Results In this study, we sequenced assembled P. complete mtDNA, elucidated its evolutionary phylogenetic relationships. mtDNA spans 575,242 bp with 43.54% GC content, encompassing 60 genes, including 37 protein-coding genes (PCGs), 20 tRNA 3 rRNA genes. Notably, high number repetitive sequences in substantial sequence translocation from chloroplasts mitochondria were observed. To determine taxonomic positioning tree was constructed using PCGs 32 other taxa. Furthermore, exploration relative synonymous codon usage, identification RNA editing events, investigation collinearity closely related species conducted. Conclusions This study reports initial assembly annotation contributing limited repository plants advancing our understanding their improved utilization conservation.

Язык: Английский

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Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of Photinia and its allies in the Old World

PhytoKeys, Год журнала: 2024, Номер 242, С. 161 - 227

Опубликована: Май 31, 2024

This study addresses the longstanding absence of a comprehensive phylogenetic backbone for apple tribe Maleae, deficiency attributed to limited taxon and marker sampling. We conducted an extensive sampling, incorporating 563 plastomes from diverse range 370 species encompassing 26 presently recognized genera. Employing inference methods, including RAxML IQ-TREE2 Maximum Likelihood (ML) analyses, we established robust framework Maleae tribe. Our phylogenomic investigations provided compelling support three major clades within Maleae. By integrating nuclear data with morphological chromosomal evidence, propose updated infra-tribal taxonomic system, comprising subtribe Malinae Reveal, Lindleyinae Vauqueliniinae B.B.Liu (

Язык: Английский

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Pan-genome analysis reveals the evolution and diversity of Malus

Nature Genetics, Год журнала: 2025, Номер unknown

Опубликована: Апрель 16, 2025

Язык: Английский

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Synthesis of Nuclear and Chloroplast Data Combined With Network Analyses Supports the Polyploid Origin of the Apple Tribe and the Hybrid Origin of the Maleae—Gillenieae Clade

Frontiers in Plant Science, Год журнала: 2022, Номер 12

Опубликована: Янв. 25, 2022

Plant biologists have debated the evolutionary origin of apple tribe (Maleae; Rosaceae) for over a century. The "wide-hybridization hypothesis" posits that pome-bearing members Maleae (base chromosome number x = 17) resulted from hybridization and/or allopolyploid event between progenitors other tribes in subfamily Amygdaloideae with 8 and 9, respectively. An alternative "spiraeoid proposed 17 arose via genome doubling 9 ancestors to 18, subsequent aneuploidy resulting 17. We use publicly available genomic data-448 nuclear genes complete plastomes-from 27 species representing all major within investigate relationships containing tribe. Specifically, we network analyses multi-labeled trees test competing wide-hybridization spiraeoid hypotheses. Hybridization occurred an ancestor Spiraeeae (x 9) clade Sorbarieae + Exochordeae 8) Kerrieae 9), giving rise Gillenieae 17). distantly related (i.e., supporting wide hypothesis). However, some evidence supports aspect hypothesis-the involved were likely both so was followed by result observed Maleae. By synthesizing existing data novel analyses, resolve nearly century-old mystery regarding Our results also indicate gene tree-species tree conflict cytonuclear are pervasive at several nodes Rosaceae.

Язык: Английский

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