Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Sept. 1, 2022

Abstract The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana numerous crop species that feed billions worldwide. Despite its relevance, most published phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies between datasets. Here, we present complete Brassicaceae genus-level to date (Brassicaceae Tree of Life, or BrassiToL) based on nuclear (>1,000 genes, almost all 349 genera 53 tribes) plastome (60 79% genera, data. We found cytonuclear discordance plastome-derived phylogenies, which likely result rampant hybridisation among closely more distantly related species, highlight rogue taxa. To evaluate impact this phylogeny reconstruction, performed four different sampling routines increasingly removed variable data paralogs. Our resulting cleaned subset 297 genes revealed high support for tribes, while main lineages remained relatively low. Calibration 20 clock-like suggests late Eocene Oligocene ‘icehouse origin’ family. Finally, propose five new re-established including recognition Arabidopsideae, monotypic tribe accommodate . With worldwide community thousands researchers working our new, densely sampled will be an indispensable tool further as excellent studies biodiversity biology.

Language: Английский

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Complementing model species with model clades

The Plant Cell, Journal Year: 2023, Volume and Issue: 36(5), P. 1205 - 1226

Published: Oct. 12, 2023

Abstract Model species continue to underpin groundbreaking plant science research. At the same time, phylogenetic resolution of land tree life continues improve. The intersection these 2 research paths creates a unique opportunity further extend usefulness model across larger taxonomic groups. Here we promote utility Arabidopsis thaliana species, especially ability connect its genetic and functional resources, entire Brassicales order. We focus on using genomics phylogenomics bridge evolution diversification several traits resources in Arabidopsis, thereby extending scope from by establishing “model clade.” These Brassicales-wide are discussed context both family Brassicaceae. such clade” make suggestions for building global networks support future studies order Brassicales.

Language: Английский

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Towards a phylogenomic classification of Magnoliidae

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 10, 2024

Premise: Magnoliidae are a strongly supported clade of angiosperms. Previous phylogenetic studies based primarily on analyses limited number mostly plastid markers have led to the current classification magnoliids into four orders and 18 families. However, uncertainty remains regarding placement several Methods: Here we present first comprehensive phylogenomic analysis as whole, sampling 235 species from 199 (74%) genera representing all families most previously accepted subfamilies tribes. We analyze newly generated data Angiosperms353 probe set using both coalescent concatenation testing impact multiple filtering alignment strategies. Results: While our results generally provide further support for established relationships in whole large including Annonaceae Lauraceae, they also new evidence ambiguous relationships. In particular, find position Hydnoraceae sister remainder Piperales and, time, resolve backbone among Myristicaceae. Conclusions: Although some by low gene recovery taxa significant tree conflict relationships, this study represents step towards reconstructing evolutionary history major lineage Based these results, an updated Magnoliidae, recognizing 21 families, summarizing tribes, describing tribes

Language: Английский

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Integrating genomic sequencing resources: an innovative perspective on recycling with universal Angiosperms353 probe sets

Horticulture Advances, Journal Year: 2024, Volume and Issue: 2(1)

Published: Jan. 29, 2024

Abstract Sequencing strategies have continually advanced, with high-throughput sequencing (HTS) technologies emerging as pivotal tools in plant phylogenomics. As a standard form of target capture sequencing, hybridization enrichment (Hyb-seq) is innovative and flexible, then HTS strategy widely adopted The universal Angiosperms353 probe sets (Angiosperms353) are instrumental Hyb-seq been witnessed increased application recent years. This review integrates numerous publications empirical datasets to comprehensively assess the potential applications Angiosperms353. Through evaluations using 18-taxa 343-taxa genomic datasets, this explores factors influencing gene capture. RNA-seq yielded highest number genes, followed by whole-genome genome skimming. Increased depth enhanced yields, no evident bias was observed across all tested angiosperm groups. In genomics era extensive data, provides comprehensive guidelines for practical Angiosperms353, promoting resource recycling maximizing data sharing utilization.

Language: Английский

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Development of a Target Enrichment Probe Set for Conifer (REMcon)

Biology, Journal Year: 2024, Volume and Issue: 13(6), P. 361 - 361

Published: May 22, 2024

Conifers are an ecologically and economically important seed plant group that can provide significant insights into the evolution of land plants. Molecular phylogenetics has developed as approach in evolutionary studies, although there have been relatively few studies conifers employ large-scale data sourced from multiple nuclear genes. Target enrichment sequencing (target capture, exon or Hyb-Seq) a key modern phylogenomic studies. However, until now, no bait set specifically targets entire conifer clade. REMcon is target sequence capture probe intended for family- species-level phylogenetic c. 100 single-copy loci. We tested using 69 species, including 44 genera across six families four other gymnosperm taxa, to evaluate efficiency efficiently generate comparable DNA conifers. The recovery loci was high, with, on average, 94% targeted regions recovered samples with high read coverage. A analysis these produced well-supported topology consistent current understanding relationships among will be useful generating sets consistently any lineage.

Language: Английский

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