Angiosperm‐wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits

Journal of Integrative Plant Biology, Год журнала: 2024, Номер 66(2), С. 228 - 251

Опубликована: Фев. 1, 2024

ABSTRACT Fruit functions in seed protection and dispersal belongs to many dry fleshy types, yet their evolutionary pattern remains unclear part due uncertainties the phylogenetic relationships among several orders families. Thus we used nuclear genes of 502 angiosperm species representing 231 families reconstruct a well supported phylogeny, with resolved for previously uncertain placements. Using this phylogeny as framework, molecular dating supports Triassic origin crown angiosperms, followed by emergence most Jurassic Cretaceous rise ecological dominance during Terrestrial Revolution. The robust allowed an examination fruit ovary revealing trend parallel carpel fusions early diversifications eudicots, monocots, magnoliids. Moreover, taxa same order or family type can develop either fruits strong correlations between specific types fruits; such associations ovary, define ovary‐fruit “modules” each found multiple One frequent modules has containing ovules, capsules berries, another having one two achenes (or other single‐seeded fruits) drupes. This new perspective highlights closeness capsule berry, that from belong module relative (such drupes). Further analyses gene known development identified nodes duplications, supporting possible role whole‐genome combination climate changes animal behaviors, diversification.

Язык: Английский

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

New Phytologist, Год журнала: 2024, Номер 243(2), С. 765 - 780

Опубликована: Май 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.

Язык: Английский

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An Integrative Framework Reveals Widespread Gene Flow During the Early Diversification of Malvaceae S.L

Опубликована: Янв. 1, 2025

Язык: Английский

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Revisiting the backbone phylogeny and inferring the evolutionary trends in inflorescence of Elsholtzieae (Lamiaceae): new insights from orthologous nuclear genes

Cladistics, Год журнала: 2025, Номер unknown

Опубликована: Фев. 18, 2025

Abstract The angiosperm tribe of Elsholtzieae (Lamiaceae) is characterized by complex inflorescences and has notable medicinal economic significance. Relationships within Elsholtzieae, including the monophyly Elsholtzia Keiskea , relationships among Mosla Perilla remain uncertain, hindering insights into inflorescence evolution tribe. Using hybridization capture sequencing deep genome skimming data analysis, we reconstruct a phylogeny using 279 orthologous nuclear loci from 56 species. We evaluated uncertainty concatenation, coalescent network approaches. time‐calibrated phylogeny, reconstructed ancestral traits to elucidate patterns in their Our analyses consistently support paraphyly genus . Phylogenetic analyses, confirmed PhyloNetworks SplitsTree, showed reticulation events major lineages Elsholtzieae. unstable polyphyly observed ASTRAL (accurate species tree algorithm), ML (maximum likelihood) MP parsimony) may be related introgression Based on phylogenetic trees evolutionary trajectory demonstrates pattern diversification, with specialization as one aspect this process. hypothesis that compressed evolved larger more forms through successive compressions axis. Additionally, certain display trend towards simplified inflorescences, reduction number florets. This highlights both diversity structures

Язык: Английский

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Phylogenomic Inference Suggests Differential Deep Time Phylogenetic Signals from Nuclear and Organellar Genomes in Gymnosperms

Plants, Год журнала: 2025, Номер 14(9), С. 1335 - 1335

Опубликована: Апрель 28, 2025

The living gymnosperms include about 1200 species in five major groups: cycads, ginkgo, gnetophytes, Pinaceae (conifers I), and cupressophytes II). Molecular phylogenetic studies have yet to reach a unanimously agreed-upon relationship among them. Moreover, cytonuclear incongruence has been repeatedly observed gymnosperms. We collated comprehensive dataset from available genomes of 17 across the groups added our own high-quality assembly Podocarpaceae (the second largest conifer family) increase sampling width. used these data infer reconciled nuclear phylogenies using two separate methods ensure robustness conclusions. also reconstructed organelle phylogenomic trees 42 mitochondrial 82 plastid genes 38 289 gymnosperm groups, respectively. Our phylogeny consistently recovers Ginkgo-cycads clade as first lineage split other clades sister gnetophytes Gnepines hypothesis). In contrast, tree places cycads earliest Gnecup hypothesis) while plastomic supports cupressophytes. examined effect RNA editing sites on by manipulating nucleotide amino acid sequences at sites. Only complete removal an inference, leading closer congruence between mitogenomic phylogenies. This suggests that carry signal with distinct evolutionary traits.

Язык: Английский

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Evaluating the utility of deep genome skimming for phylogenomic analyses: a case study in the species-rich genus Rhododendron

Plant Diversity, Год журнала: 2025, Номер unknown

Опубликована: Май 1, 2025

Язык: Английский

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Phylogenomics and adaptive evolution of hydrophytic umbellifers (tribe Oenantheae, Apioideae) revealed from chloroplast genomes

BMC Plant Biology, Год журнала: 2024, Номер 24(1)

Опубликована: Ноя. 28, 2024

Tribe Oenantheae consists mainly of aquatic species within the Apioideae. The unique morphology and habitat distinguish this group from other Apioideae groups. However, genomic information these has not been widely developed, molecular mechanisms adaptive evolution remain unclear. We provide comparative analyses on 30 chloroplast genomes tribe representing five genera to explore variation response plant adaptations. presented typical quadripartite structures, with sizes ranging 153,024 bp 155,006 bp. Gene content order were highly conserved no significant expansion or contraction observed. Seven regions (rps16 intron–trnK, rpoB–trnC, trnE–trnT–psbD, petA–psbJ, ndhF–rpl32–trnL, ycf1a–rps15, ycf1a gene) identified as remarkable candidate DNA markers for future studies identification, biogeography, phylogeny Oenantheae. Our study elucidated relationships among subdivided Sium Oenanthe. Oenanthe I clade be further clarified. Eight positively selected genes (accD, rbcL, rps8, ycf1a, ycf1b, ycf2, ndhF, ndhK) persuasively detected under site models tests, might have played roles in adaptation environments. results sufficient subsequent Oenantheae, promote understanding

Язык: Английский

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Ovule initiation in crops characterized by multi-ovulate ovaries

Molecular Horticulture, Год журнала: 2024, Номер 4(1)

Опубликована: Окт. 18, 2024

Язык: Английский

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