Phylogenomics and the flowering plant tree of life

Journal of Integrative Plant Biology, Journal Year: 2022, Volume and Issue: 65(2), P. 299 - 323

Published: Nov. 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.

Language: Английский

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Deep reticulation: the long legacy of hybridization in vascular plant evolution

The Plant Journal, Journal Year: 2023, Volume and Issue: 114(4), P. 743 - 766

Published: Feb. 13, 2023

Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep scales largely obscure. Over the past decade, genomic phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, common throughout history plants, particularly various lineages flowering plants. However, studies also highlighted challenges disentangling signals ancient hybridization from other sources conflict (in particular, incomplete lineage sorting). Here, we provide critical review vascular outlining well-documented cases plant phylogeny, well unique to documenting versus recent hybridization. We definition for which, knowledge, explicitly attempted before. Further extent reticulation should remain an important research focus, especially because published examples likely represent tip iceberg terms total future increasingly explore macroevolutionary this process, impact on trajectories (e.g. how does influence trait evolution or generation biodiversity over time scales?), life ecological factors shape, shaped, frequency geologic phylogeny. Finally, consider implications ubiquitous conceptualize, analyze, classify Networks, opposed bifurcating trees, more accurate representations many cases, although ability infer, visualize, use networks comparative analyses is highly limited. Developing improved methods generation, visualization, represents direction biology. Current classification systems do generally allow recognition reticulate lineages, classifications themselves are based evidence chloroplast genome. Updating better reflect nuclear phylogenies, considering whether recognize systems, will challenge systematics community.

Language: Английский

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A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

American Journal of Botany, Journal Year: 2021, Volume and Issue: 108(7), P. 1087 - 1111

Published: July 1, 2021

Premise To further advance the understanding of species‐rich, economically and ecologically important angiosperm order Myrtales in rosid clade, comprising nine families, approximately 400 genera almost 14,000 species occurring on all continents (except Antarctica), we tested Angiosperms353 probe kit. Methods We combined high‐throughput sequencing target enrichment with kit to evaluate a sample 485 across 305 (76% order). Results provide most comprehensive phylogenetic hypothesis for date. Relationships at ranks, such as relationship early‐diverging often reflect previous studies, but gene conflict is evident, relationships previously found be uncertain remain so. Technical considerations processing HTS data are also discussed. Conclusions High‐throughput powerful tools phylogenomic analysis, better genetic available required identify genes trees that account likely incomplete lineage sorting and/or hybridization events.

Language: Английский

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

American Journal of Botany, Journal Year: 2021, Volume and Issue: 108(7), P. 1059 - 1065

Published: July 1, 2021

Language: Английский

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Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Feb. 23, 2022

Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one most extraordinarily diverse clades among angiosperms. Papilionoids are a major source food forage, ecologically successful in all biomes, display dramatic variation both floral architecture plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding relationships groups Papilionoideae, yet backbone phylogeny remains unresolved. In this study, we sequenced assembled 39 new plastomes that covering key representing morphological diversity subfamily. From 244 total taxa, produced eight datasets for maximum likelihood (ML) based on entire and/or concatenated sequences 77 protein-coding (CDS) two multispecies coalescent (MSC) individual gene trees. We additionally combined nucleotide dataset comprising CDS plus matK only, which papilionoid were sampled. A ML tree plastome maximally supported deep recent divergences papilionoids (223 out 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, Amburaneae), Cladrastis, Andira, Exostyleae formed grade to remainder concordant with nine MSC Phylogenetic remaining five lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because insufficient support conflicting Our study fully resolved nodes however, some require further exploration. More genome-scale data rigorous needed disentangle lineages.

Language: Английский

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Phylogeny and classification of the coffee family (Rubiaceae, Gentianales): Overview and outlook

Taxon, Journal Year: 2024, Volume and Issue: 73(3), P. 673 - 717

Published: April 5, 2024

Abstract The use of molecular data in phylogenetic reconstruction during more than three decades has greatly improved our understanding the macroevolutionary history coffee family (Rubiaceae) and provided a solid basis for improvement its classification. Based on results 130 studies, among them most recent phylogenomic works, we present consensus phylogeny robust classification Rubiaceae that shed light evolutionary success this highly diverse angiosperm can serve as framework ecological studies. There are 14,000 species about 580 accepted genera assigned to 71 tribes, which 68 classified two subfamilies (Dialypetalanthoideae with 38 tribes Rubioideae 30 tribes). Three (Acranthereae, Coptosapelteae, Luculieae) remain unclassified subfamily. Sixty‐three these nine informal alliances (four five Dialypetalanthoideae). These listed alphabetical order within their respective alliances. Five one (Coussareeae) four (Airospermeae, Jackieae, Retiniphylleae, Steenisieae) Dialypetalanthoideae, excluded from due unclear or conflicting positions. Thirty‐six retain tribal status but receive new generic limits remedy previous para‐ polyphyletic nature. Twenty‐nine not implemented classifications have been added, (Chioneae, Glionnetieae, Temnopterygeae) newly described here. Basic information phylogenies, distributions, former classifications, useful references works all future perspectives discussed.

Language: Английский

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Evolution and diversification of carboxylesterase-like [4+2] cyclases in aspidosperma and iboga alkaloid biosynthesis

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(7)

Published: Feb. 6, 2024

Monoterpene indole alkaloids (MIAs) are a large and diverse class of plant natural products, their biosynthetic construction has been subject intensive study for many years. The enzymatic basis the production aspidosperma iboga alkaloids, which produced exclusively by members Apocynaceae family, recently discovered. Three carboxylesterase (CXE)-like enzymes from Catharanthus roseus Tabernanthe catalyze regio- enantiodivergent [4+2] cycloaddition reactions to generate (tabersonine synthase, TS) (coronaridine CorS; catharanthine CS) scaffolds common intermediate. Here, we use combined phylogenetic biochemical approach investigate evolution functional diversification these cyclase enzymes. Through ancestral sequence reconstruction, provide evidence initial TS an CXE followed emergence CorS in two separate lineages, leading turn CS genus. This progression alkaloid biosynthesis is consistent with chemotaxonomic distribution MIAs. We subsequently test panel chimeras based on cyclases probe molecular differential cyclization activity. Finally, show through partial heterologous reconstitution tabersonine using non-pathway how could have first appeared as “underground metabolites” via recruitment promiscuous protein families. Our results insight into new secondary metabolic pathways can emerge small but important changes following co-option preexisting functions.

Language: Английский

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Phylogenomics Of Boraginaceae and Boraginales Using Lineage-Specific and Angiosperms353 Loci

Systematic Botany, Journal Year: 2025, Volume and Issue: 49(4), P. 749 - 767

Published: Jan. 6, 2025

Abstract— During the past 20 yr, phylogenetics of Boraginaceae has taken shape using plastid DNA regions and nuclear ribosomal internal transcribed spacer (ITS), but these only reflect a limited understanding evolutionary history family. Using hybridization-enrichment sequencing, 531 from lineage-specific Angiosperms353 loci were sequenced aligned for 49 species across Boraginaceae. Additionally, incorporated with broader dataset same 115 accessions Boraginales relatives. Based on multiple phylogenetic approaches datasets, resolved phylogenies quite similar to our current understanding, yet taxa recognized in different positions. These included: 1) Echiochiloideae as sister Cynoglossoideae instead rest entire family, 2) Moritzinae nested within Boragininae, 3) Lasiocaryeae Trichodesmeae not sisters. positions recovered, via methods, hundreds suggest that incomplete lineage sorting, hybridization, shifts substitution rates may have occurred during early origin In analyses Boraginales, Namaceae was non-monophyletic, providing evidence Hydrophyllaceae again be appropriate, Lennoaceae Ehretiaceae. While both sets allowed well-resolved well-supported phylogeny reconstructed, recovered some more intriguing relationships part because appear less conserved than those Angiosperms353. The two provide an interesting complement patterns evolution family order.

Language: Английский

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On the potential of Angiosperms353 for population genomic studies

Applications in Plant Sciences, Journal Year: 2021, Volume and Issue: 9(7)

Published: May 18, 2021

PREMISE The successful application of universal targeted sequencing markers, such as those developed for the Angiosperms353 probe set, within populations could reduce or eliminate need specific marker development, while retaining benefits full‐gene sequences in population‐level analyses. However, whether markers provide sufficient variation species to calculate demographic parameters is untested. METHODS Using herbarium specimens from a 50‐year‐old floristic survey Texas, we sequenced 95 samples 24 using set. Our data workflow calls variants and prepares population genetic analysis standard metrics. In our case study, gene recovery was affected by genomic library concentration only at low concentrations displayed limited phylogenetic bias. RESULTS We identified over 1000 segregating with zero missing 92% demonstrate that contain estimate pairwise nucleotide diversity (π)—typically between 0.002 0.010, most found flanking non‐coding regions. subset were filtered linkage, uncovered high heterozygosity many species, suggesting denser sampling should permit estimation flow dynamics. DISCUSSION benefit conservation studies providing repeatable data, haplotype information, permitting inclusion decades‐old specimens.

Language: Английский

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Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(12)

Published: Dec. 1, 2022

Abstract The Angiosperms353 gene set (AGS) consists of a 353 universal low-copy nuclear genes that were selected by examining more than 600 angiosperm species. These can be used for phylogenetic studies and population genetics at multiple taxonomic scales. However, current pipelines are not able to recover efficiently accurately from high-throughput sequences. Here, we developed Easy353, reference-guided assembly tool the AGS sequencing (HTS) data (including genome skimming, RNA-seq, target enrichment). Easy353 is an open-source user-friendly assembler diverse types data. It has graphical user interface command-line compatible with all widely-used computer systems. Evaluations, based on both simulated empirical data, suggest yields low rates errors.

Language: Английский

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