Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(3), P. 546 - 578

Published: Jan. 30, 2024

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of angiosperms in fossil record was referred to Darwin as "abominable mystery," hence contributing heightened interest angiosperm evolution. display wide ranges morphological, physiological, and ecological characters, some which have probably influenced their species richness. evolutionary analyses these characteristics help address questions diversification require well resolved phylogeny. Following great successes phylogenetic using plastid sequences, dozens thousands nuclear genes from next-generation sequencing been used phylogenomic analyses, providing phylogenies new insights into evolution angiosperms. In this review we focus on recent large clades, orders, families, subdivisions families provide a summarized Nuclear Phylogenetic Tree Angiosperm Families. newly established relationships highlighted compared previous results. sequenced genomes Amborella, Nymphaea, Chloranthus, Ceratophyllum, monocots, Magnoliids, basal eudicots, facilitated phylogenomics among five major clades. All but one 64 orders were included except placements several orders. Most robust highly supported placements, especially for within important families. Additionally, examine divergence time estimation biogeographic basis frameworks discuss differences analyses. Furthermore, implications ancestral reconstruction characters groups, limitations current studies, taxa that future attention.

Language: Английский

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Cryptic diversity and rampant hybridization in annual gentians on the Qinghai-Tibet Plateau revealed by population genomic analysis

Plant Diversity, Journal Year: 2023, Volume and Issue: 46(2), P. 194 - 205

Published: Oct. 28, 2023

Understanding the evolutionary and ecological processes involved in population differentiation speciation provides critical insights into biodiversity formation. In this study, we employed 29,865 single nucleotide polymorphisms (SNPs) complete plastomes to examine genomic divergence hybridization Gentiana aristata, which is endemic Qinghai-Tibet Plateau (QTP) region. Genetic clustering revealed that G. aristata characterized by geographic genetic structures with five clusters (West, East, Central, South North). The West cluster has a specific morphological character (i.e., blue corolla) higher values of FST compared remaining clusters, likely result geological barrier formed Yangtze River. diverged from other Early Pliocene; these one another Quaternary. Phylogenetic reconstructions based on SNPs plastid data substantial cyto-nuclear conflicts. D-statistics demonstrated rampant between Central North cluster, along Bayankela Mountains, form cluster. Species distribution modeling range expanded since Last Interglacial period. Our findings provide evidence cryptic diversity identified barrier. These suggest barriers climatic fluctuations have an important role triggering diversification as well hybridization, indicating are essential factors formation within QTP

Language: Английский

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Phylogeny, adaptive evolution, and taxonomy of Acronema (Apiaceae): evidence from plastid phylogenomics and morphological data

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Aug. 16, 2024

Introduction The genus Acronema , belonging to Apiaceae, includes approximately 25 species distributed in the high-altitude Sino-Himalayan region from E Nepal SW China. This is a taxonomically complex with often indistinct boundaries and problematic generic delimitation Sinocarum other close genera, largely due varied morphological characteristics. Methods To explore phylogenetic relationships clarify limits of its related we reconstructed reliable framework high support resolution based on two molecular datasets (plastome data ITS sequences) performed analyses. Results Both analyses robustly supported that was non-monophyletic group fell into clades: Clade East-Asia Clade. We also newly sequenced assembled sixteen complete plastomes comprehensively comparative for this genus. results showed plastome structure, gene number, GC content, codon bias patterns were similarity, but borders SC/IR identified six different types border. chienii significantly members which consistent type VI pattern Tongoloa . twelve potential DNA barcode regions ( ccsA matK ndhF ndhG psaI psbI rpl32 rps15 ycf1 ycf3 psaI-ycf4 psbM-trnD ) identification Acronema. evolution relatively conservative only one petG found be under positive selection ω = 1.02489). Discussion genes involved transmission photosynthetic electron chains during photosynthesis, plays crucial role process photosynthesis plants. manifestation adaptive plants areas environment. In conclusion, our study provides novel insights evolution, phylogeny, taxonomy

Language: Английский

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Characteristics of the complete chloroplast genome of Swertia divaricata Harry Sm. (Gentianaceae) and its phylogenetic inference

Mitochondrial DNA Part B, Journal Year: 2023, Volume and Issue: 8(10), P. 1132 - 1136

Published: Oct. 3, 2023

Swertia divaricata Harry Sm., 1965, (Gentianaceae) is a perennial herb endemic to Northwest Yunnan, China, belonging the species-rich genus Swertia. It possesses unique morphological features but its systematic position remains uncertain. To determine phylogenetic placement, complete plastid genome of S. was assembled utilizing high-throughput sequencing data. The circular, spanning 152,073 bp, and comprises large single-copy (LSC) region 82,470 small (SSC) 18,153 two inverted repeats (IR) regions, each 25,725 bp. A total 130 genes were annotated, including 85 protein-coding genes, 37 tRNA eight rRNA genes. plastome exhibits structure gene composition highly similar those other plastomes. Phylogenetic analysis indicated that closely related erythrosticta, sister subclade comprising species from sections Apterae. sequence described herein constitutes valuable contribution evolutionary research on

Language: Английский

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Hybridization and divergent climatic preferences drive divergence of two allopatric Gentiana species on the Qinghai–Tibet Plateau

Annals of Botany, Journal Year: 2023, Volume and Issue: 132(7), P. 1271 - 1288

Published: Nov. 14, 2023

Exploring how species diverge is vital for understanding the drivers of speciation. Factors such as geographical separation and ecological selection, hybridization, polyploidization shifts in mating system are all major mechanisms plant speciation, but their contributions to divergence rarely well understood. Here we test these two species, Gentiana lhassica G. hoae, with goal recent allopatric on Qinghai-Tibet Plateau (QTP).

Language: Английский

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The earliest allopolyploidization in tracheophytes revealed by phylotranscriptomics and morphology of Selaginellaceae

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

Published: Jan. 9, 2024

Abstract Selaginellaceae exhibit extraordinary evolutionary history in which they survived and thrived during the Permian–Triassic extinction did not undergo polyploidization. Here, we reconstructed phylogenetic relationships of by applying large-scale nuclear genes from RNA-seq, found that each group showed incongruences among single-gene trees with different frequencies. In particular, three positions sanguinolenta were recovered gene sets. We evaluated factors might lead to incongruence concluded hybridization between ancestor two superclades is most likely cause. presented supporting evidence flow test, species network inference, plastome-based phylogeny. Furthermore, morphological characters chromosomal also lend support hybrid origin this group. The divergence time estimations, using sets respectively, indicated splits related superclade happened around same period, implying event probably occurred Early Triassic. This study reveals an ancient allopolyploidization integrative robust analyses, sheds new light on recalcitrant problem reports polyploidization basal vascular plants, Selaginellaceae.

Language: Английский

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The Possible Earliest Allopolyploidization in Tracheophytes Revealed by Phylotranscriptomics and Morphology of Selaginellaceae

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(8)

Published: Aug. 1, 2024

Abstract Selaginellaceae, originated in the Carboniferous and survived Permian–Triassic mass extinction, is largest family of lycophyte, which sister to other tracheophytes. It stands out from tracheophytes by exhibiting extraordinary habitat diversity lacking polyploidization. The organelle genome-based phylogenies confirmed monophyly Selaginella, with six or seven subgenera grouped into two superclades, but phylogenetic positions enigmatic Selaginella sanguinolenta clade remained problematic. Here, we conducted a phylogenomic study on Selaginellaceae utilizing large-scale nuclear gene data RNA-seq elucidate phylogeny explore causes incongruence S. clade. Our analyses resolved three different clade, were supported sorted sets, respectively. results flow test, species network inference, plastome-based congruently suggested probable hybrid origin involving each common ancestor superclades Selaginellaceae. hypothesis corroborated evidence rhizophore morphology spore micromorphology. chromosome observation Ks distributions further hybridization accompanied Divergence time estimation based independent datasets sets plastid genome inferred that allopolyploidization occurred Early Triassic. To our best knowledge, Mesozoic reported here represents earliest record revealed unique triad for hybrid-originated group comprehensive proposed retaining both parental alleles through conversion.

Language: Английский

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Plastome characterization and its phylogenetic implications on Lithocarpus (Fagaceae)

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Dec. 30, 2024

The genus Lithocarpus is a species-rich dominant woody lineage in East Asian evergreen broad-leaved forests. Despite its ecological and economic significance, the plastome structure evolutionary history of remain poorly understood. In this study, we comprehensively analyzed 34 plastomes representing 33 species. Of which, 21 were newly assembled. plastome-based phylogenomic tree was reconstructed to reveal maternal patterns genus.

Language: Английский

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