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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Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere

Journal of Integrative Plant Biology, Год журнала: 2022, Номер 64(5), С. 1020 - 1043

Опубликована: Март 11, 2022

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes 75 complete plastomes were used to infer the phylogenetic relationships estimate historical biogeography apple genus Malus sensu lato, economically important lineage disjunctly distributed in Northern Hemisphere involved known suspected hybridization allopolyploidy events. The phylogeny recovered monophyly s.l. (including Docynia); however, was be biphyletic plastid phylogeny. An ancient chloroplast capture event Eocene western North America best explains cytonuclear discordance. Our conflict analysis ILS, hybridization, could explain widespread gene tree One deep (Malus doumeri) one recent coronaria) detected Furthermore, our biogeographic integrating living fossil a East Asian-western American origin Eocene, followed by several extinction dispersal events Hemisphere. We also propose general workflow for assessing phylogenomic discordance using genome skimming sets.

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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Skimming genomes for systematics and DNA barcodes of corals

Ecology and Evolution, Год журнала: 2024, Номер 14(5)

Опубликована: Май 1, 2024

Numerous genomic methods developed over the past two decades have enabled discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa scales. Genome skimming (or low-coverage genome sequencing) is a promising method not only extract high-copy but also 100s 1000s phylogenetically informative nuclear (e.g., ultraconserved elements [UCEs] exons) from contemporary museum samples. The subphylum Anthozoa, including important ecosystem engineers stony corals, black anemones, octocorals) in marine environment, critical need resolution thus might benefit genome-skimming approach. We conducted on 242 anthozoan corals collected 1886 2022. Using existing target-capture baitsets, we bioinformatically obtained UCEs exons data incorporated them with previously published studies. mean number UCE exon extracted was 1837 ± 662 SD for octocorals 1379 476 hexacorals. Phylogenetic were well resolved within each class. A 1422 720 historical specimens, 1253 recovered oldest specimen 1886. partial whole mitogenomes rRNA genes >95% Bioinformatically pulling UCEs, exons, mitochondrial genomes, viable low-cost option This approach can be used review support taxonomic revisions reconstruct evolutionary histories, type specimens.

Язык: Английский

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GeneMiner: A tool for extracting phylogenetic markers from next‐generation sequencing data

Molecular Ecology Resources, Год журнала: 2024, Номер 24(3)

Опубликована: Янв. 10, 2024

Abstract The advancement of next‐generation sequencing (NGS) technologies has been revolutionary for the field evolutionary biology. This technology led to an abundance available genomes and transcriptomes researchers mine. Specifically, can mine various types molecular markers that are vital phylogenetic, ecological studies. Numerous tools have developed extract these from NGS data. However, due insufficient number well‐annotated reference non‐model organisms, it remains challenging obtain accurately efficiently. Here, we present GeneMiner, improved expanded version our previous tool, Easy353. GeneMiner combines reference‐guided de Bruijn graph assembly with seed self‐discovery greedy extension. Additionally, includes a verification step using parameter‐bootstrap method reduce pitfalls associated relatively distant reference. Our results, both experimental simulation data, showed acquire phylogenetic plants transcriptomic, genomic other is designed be user‐friendly, fast memory‐efficient. Further, compatible Linux, Windows macOS. All source codes publicly on GitHub ( https://github.com/sculab/GeneMine r) Gitee https://gitee.com/sculab/GeneMiner ) easy accessibility transparency.

Язык: Английский

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Nuclear phylogenomics of Asteraceae with increased sampling provides new insights into convergent morphological and molecular evolution

Plant Communications, Год журнала: 2024, Номер 5(6), С. 100851 - 100851

Опубликована: Фев. 25, 2024

Convergent morphological evolution is widespread in flowering plants, and understanding this phenomenon relies on well-resolved phylogenies. Nuclear phylogenetic reconstruction using transcriptome datasets has been successful various angiosperm groups, but it limited to taxa with available fresh materials. Asteraceae are one of the two largest families important for both ecosystems human livelihood, having multiple examples convergent evolution. phylogenies have resolved relationships among most subfamilies many tribes, evolutionary questions regarding subtribes genera remain due sampling. Here we increased sampling transcriptomes genome skimming produced nuclear trees 706 species representing thirds recognized subtribes. Ancestral character supports events Asteraceae, gains losses bilateral floral symmetry correlated diversification some smaller respectively. The presence calyx-related pappus might especially success genera. Molecular analyses supporting likely contribution duplications MADS-box TCP regulatory genes innovations, including capitulum inflorescence bilaterally symmetric flowers, potentially promoting Asteraceae. Subsequent divergences reductions CYC2 gene expression related gain loss zygomorphic flowers. phylogenomic work greater taxon by GS reveals feasibility expanded DNA samples

Язык: Английский

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An updated classification for the hyper‐diverse genusCorydalis(Papaveraceae: Fumarioideae) based on phylogenomic and morphological evidence

Journal of Integrative Plant Biology, Год журнала: 2023, Номер 65(9), С. 2138 - 2156

Опубликована: Апрель 29, 2023

Abstract The genus Corydalis , with ca. 530 species, has long been considered taxonomically challenging because of its great variability. Previous molecular analyses, based on a few markers and incomplete taxonomic sampling, were clearly inadequate to delimit sections subgenera. We have performed phylogenetic analyses related taxa, using 65 shared protein‐coding plastid genes from 313 accessions (including 280 samples 226 species ) 152 universal low‐copy nuclear 296 271 covering all 42 previously recognized five independent “series”. Phylogenetic trees inferred Bayesian Inference Maximum Likelihood. Eight selected morphological characters estimated ancestral state reconstructions. Results include: (i) the three subgenera two are fully supported by both data; third, subg. Cremnocapnos is weakly DNA only, whereas in data included form successive outgroups rest genus; (ii) among “series”, 25 one “series” resolved as monophyletic sets; (iii) common ancestor likely be perennial plant taproot, yellow flowers short saccate spur, linear fruits recurved fruiting pedicels, seeds elaiosomes; (iv) we provide new classification four (of which Bipapillatae here newly described), 39 sections, 16 consistent previous classification, recircumscribed, section reinstated six established. Characters associated lifespan, underground structures, floral fruit elaiosomes important for recognition sections. These combined character reconstructions uncovered unrecognized relationships, greatly improved our understanding evolution 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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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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Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses

Plant Diversity, Год журнала: 2023, Номер 45(4), С. 397 - 408

Опубликована: Апрель 6, 2023

is an economically important genus widely distributed in the temperate Northern Hemisphere. Previous studies on using a variety of loci yielded conflicting phylogenetic hypotheses. Here, we generated nuclear reduced representation sequencing data and plastid genomes for 36

Язык: Английский

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