Phylogenomics and the rise of the angiosperms

Nature, Journal Year: 2024, Volume and Issue: 629(8013), P. 843 - 850

Published: April 24, 2024

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods

Language: Английский

---

Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding

Cell, Journal Year: 2023, Volume and Issue: 186(11), P. 2313 - 2328.e15

Published: May 1, 2023

Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to seed-reproducing diploid. Historical accumulation of deleterious mutations in genomes has hindered development elite inbred lines and hybrids. Utilizing whole-genome phylogeny 92 Solanaceae its sister clade species, we employ an evolutionary strategy identify mutations. The deep reveals genome-wide landscape highly constrained sites, comprising ∼2.4% genome. Based on diploid diversity panel, infer 367,499 variants, which 50% occur at non-coding 15% synonymous sites. Counterintuitively, with relatively high homozygous burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion inferred increases genomic-prediction accuracy yield by 24.7%. Our study generates insights into incidence properties their far-reaching consequences breeding.

Language: Английский

---

Convergent evolution of plant prickles by repeated gene co-option over deep time

Science, Journal Year: 2024, Volume and Issue: 385(6708)

Published: Aug. 1, 2024

An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on same genetic programs, particularly over long timescales. In this work, we genetically dissected repeated origins and losses prickles-sharp epidermal projections-that convergently evolved numerous plant lineages. Mutations a cytokinin hormone biosynthetic gene caused at least 16 independent prickles eggplants wild relatives genus

Language: Английский

---

Solanum pan-genetics reveals paralogues as contingencies in crop engineering

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: March 5, 2025

Language: Английский

---

Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum

American Journal of Botany, Journal Year: 2022, Volume and Issue: 109(4), P. 580 - 601

Published: Feb. 16, 2022

Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree gene-tree discordance Solanum, one largest flowering plant genera includes cultivated potato, tomato, eggplant, as well 24 minor crop plants.A densely sampled species-level phylogeny Solanum is built using unpublished publicly available Sanger sequences comprising 60% all accepted species (742 spp.) nine regions (ITS, waxy, seven plastid markers). The robustness this topology tested by examining a full plastome dataset with 140 nuclear target-capture 39 (Angiosperms353 probe set).While taxonomic framework remained stable, tree conflicts generated from datasets were observed. latter correspond short internodal branches, network analysis polytomy tests suggest backbone composed three found at different evolutionary depths. strongest area discordance, near crown node could potentially represent hard polytomy.We argue incomplete lineage sorting due rapid diversification most likely cause for polytomies, embracing uncertainty underlies them crucial understand evolution large rapidly radiating lineages.

Language: Английский

---

Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants

Plant Communications, Journal Year: 2023, Volume and Issue: 4(4), P. 100595 - 100595

Published: March 25, 2023

Solanaceae, the nightshade family, have ∼2700 species, including important crops potato and tomato, ornamentals, medicinal plants. Several sequenced Solanaceae genomes show evidence for whole-genome duplication (WGD), providing an excellent opportunity to investigate WGD its impacts. Here, we generated 93 transcriptomes/genomes combined them with 87 public datasets, a total of 180 species representing all four subfamilies 14 15 tribes. Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used reconstruct highly resolved phylogenetic tree six major clades. The supports previously recognized (Goetzeioideae, Cestroideae, Nicotianoideae, Solanoideae) designation three other (Schizanthoideae, Schwenckioideae, Petunioideae), placement several unassigned genera. We placed Solanaceae-specific triplication (WGT1) at ∼81 million years ago (mya), before divergence Schizanthoideae ∼73 mya. In addition, detected two gene bursts (GDBs) supporting proposed events GDBs. An investigation evolutionary histories homologs carpel fruit developmental in (sub)families revealed that 21 clades retained duplicates. These likely by WGT1 may promoted fleshy development. This study presents well-resolved phylogeny new perspective on duplicates carpel/fruit development, improved understanding evolution.

Language: Английский

---

Exploring biodiversity and ethnobotanical significance of Solanum species in Uzbekistan: unveiling the cultural wealth and ethnopharmacological uses

Frontiers in Pharmacology, Journal Year: 2024, Volume and Issue: 14

Published: Jan. 24, 2024

Despite its millennial existence and empirical documentation, the ethnological knowledge of herbs is a more recent phenomenon. The their historical uses as food, medicine, source income small-scale businesses, sociological impacts are threatened due to slow ethnobotanical research drive. Species genus Solanum have long been extensively used in folk medicine treat various illnesses humans since dawn civilization. All data were systematically obtained from papers, monographs, books written Uzbek, Russian, English through scientific online databases, including Google, Google Scholar, PubMed, Scopus, Semantic Science Direct, Web using specific keywords focused on eight species. Eight native non-native species S. dulcamara L., lycopersicum melongena nigrum rostratum Dunal., sisymbriifolium Lam., tuberosum villosum Mill. recorded Uzbekistan Central Asia. In this article we presented recently diversity, morphological characteristics, global distribution, habitat, population status, phenology, reproduction, pharmacology phytochemistry these Uzbekistan. Furthermore, relying combination literature reviews analyses focus food consumption coupled with ethnopharmacological human diseases growing Since civilization, cultivated non-cultivated provided sustainable resources medicinal plants prevent diseases. Based collected data, it was shown that not studied ethnobotanically ethnomedicinally necessary conduct phytochemical biotechnological them future. Traditional evaluation indicate , one most widely some parts world. Although considerable progress has made comprehend chemical biological properties species, toxicology needed ensure safety, efficacy, quality biologically active extracts isolated bioactive compounds. Additionally, conducting additional structure-activity relationship certain phytochemicals potential enhance efficacy advance utilization traditional applications taxa.

Language: Английский

---

Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster

Science Advances, Journal Year: 2024, Volume and Issue: 10(17)

Published: April 24, 2024

Tremendous plant metabolic diversity arises from phylogenetically restricted specialized pathways. Specialized metabolites are synthesized in dedicated cells or tissues, with pathway genes sometimes colocalizing biosynthetic gene clusters (BGCs). However, the mechanisms by which spatial expression patterns arise and role of BGCs evolution remain underappreciated. In this study, we investigated driving acylsugar Solanaceae. Previously thought to be glandular trichomes, acylsugars were recently found cultivated tomato roots. We demonstrated that roots trichomes have different sugar cores, identified root-enriched paralogs trichome genes, characterized a key paralog required for root biosynthesis,

Language: Английский

---

A highly resolved nuclear phylogeny uncovers strong phylogenetic conservatism and correlated evolution of fruit color and size in Solanum L.

New Phytologist, Journal Year: 2024, Volume and Issue: 243(2), P. 765 - 780

Published: May 27, 2024

Summary Mutualisms between plants and fruit‐eating animals were key to the radiation of angiosperms. Still, phylogenetic uncertainties limit our understanding fleshy‐fruit evolution, as in case Solanum , a genus with remarkable diversity, but unresolved relationships. We used 1786 nuclear genes from 247 species, including 122 newly generated transcriptomes/genomes, reconstruct phylogeny examine tempo mode evolution fruit color size. Our analysis resolved backbone providing high support for its clades. results pushed back origin 53.1 million years ago (Ma), most major clades diverging 35 27 Ma. Evolution size revealed levels trait conservatism, where medium‐sized berries that remain green when ripe are likely ancestral form. analyses evolutionary correlated, dull‐colored fruits two times larger than black/purple red fruits. conclude strong conservatism shown could influences on evolution. findings highlight importance constraints diversification functional traits.

Language: Английский

---

Twenty years of big plant genera

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 291(2023)

Published: May 1, 2024

In 2004, David Frodin published a landmark review of the history and concepts big plant genera. Two decades taxonomic activity have taken place since, coinciding with revolution in phylogenetics bioinformatics. Here we use data from World Flora Online (WFO) to provide an updated list (more than 500 species) megadiverse 1000 flowering genera highlight changes since 2004. The number has increased 57 86; today one every four species is classified as member genus, 14% just 28 Most (71%) growth 2000 result new description, not generic re-circumscription. More 15% all currently accepted described last two are genera, suggesting that groups previously considered intractable now being actively studied taxonomically. Despite this rapid they remain significant yet understudied proportion diversity. They represent global diversity should priority only for taxonomy but understanding patterns evolution general.

Language: Английский

---