Phylotranscriptomics Resolves the Phylogeny of Pooideae and Uncovers Factors for Their Adaptive Evolution

Molecular Biology and Evolution, Год журнала: 2022, Номер 39(2)

Опубликована: Янв. 29, 2022

Adaptation to cool climates has occurred several times in different angiosperm groups. Among them, Pooideae, the largest grass subfamily with ∼3,900 species including wheat and barley, have successfully occupied many temperate regions play a prominent role ecosystems. To investigate possible factors contributing Pooideae adaptive evolution cooling climates, we performed phylogenetic reconstruction using five gene sets (with 1,234 nuclear genes their subsets) from 157 transcriptomes/genomes representing all 15 tribes 24 of 26 subtribes. Our phylogeny supports monophyly (except Diarrheneae) subtribes at least two species, strongly supported resolution relationships. Molecular dating suggests that originated late Cretaceous, subsequent divergences under conditions first among early middle Eocene again genera Miocene later periods. We identified cluster duplications (CGD5) shared by core 80% species) near Eocene-Oligocene transition, coinciding transition closed open habitat an upshift diversification rate. evolutionary analyses homologs CBF for cold resistance uncovered tandem during history, dramatically increasing copy number possibly promoting adaptation habitats. Moreover, duplication AP1/FUL-like before origin might facilitated regulation vernalization pathway environments. These other results provide new insights into likely contributed successful members regions.

Язык: Английский

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The chromosome-based lavender genome provides new insights into Lamiaceae evolution and terpenoid biosynthesis

Horticulture Research, Год журнала: 2021, Номер 8

Опубликована: Март 1, 2021

Язык: Английский

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The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(41)

Опубликована: Окт. 3, 2023

The importance of whole-genome duplication (WGD) for evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary dead end, there growing evidence that polyploidization can help overcome environmental change, stressful conditions, or periods extinction. However, despite much research, the mechanistic underpinnings why how polyploids might be able to outcompete outlive nonpolyploids at times upheaval remain elusive, especially autopolyploids, in which heterosis effects are limited. On longer term, increase both mutational robustness due redundancy increased genetic variation, but on short-or even immediate-term, selective advantages WGDs harder explain. Here, by duplicating artificially generated Gene Regulatory Networks (GRNs), we show duplicated GRNs-and thus genomes-show higher signal output variation than nonduplicated GRNs. This leads niche expansion provide polyploid populations with substantial survive turmoil. In contrast, under stable environments, GRNs maladaptive changes, a phenomenon exacerbated We believe these results insights into genome (auto)polyploidy organisms adapt quickly novel conditions ecological uproar cataclysmic events.

Язык: Английский

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Chromosome number variation and phylogenetic divergence of East Asian Cirsium sect. Onotrophe subsect. Nipponocirsium (Compositae), with a new species from Taiwan

Botanical studies, Год журнала: 2025, Номер 66(1)

Опубликована: Фев. 14, 2025

Abstract Background This study explored chromosome number variation, phylogenetic divergence, and mechanisms underlying speciation in East Asian thistle Cirsium Mill. sect. Onotrophe (Cass.) DC. subsect. Nipponocirsium Kitam. (Compositae). The focused on the newly identified species from Taiwan: pengii Y.H. Tseng, P.C. Liao & Chih Y. Chang. Utilizing phylotranscriptomic data to reconstruct evolutionary relationships between Taiwanese Japanese taxa of as well their divergence times chromosomal characteristics. Additionally, number, morphology, pollen morphology unknown taxon are compared with other known Taiwan. Results Phylotranscriptomic analysis reveals a division within into clades. In clade, C. is basal, while tatakaense remains monophyletic despite higher genetic diversity. prevalent this subsection tetraploid (2 n = 4 x 68), common taxa, members have 2 64. Notably, has diploid 32), indicating descending dysploidy followed by polyploidization polyploidization, driven glaciations, likely shaped evolution . Divergence time estimates suggest separation clades around 0.74 million years ago (Myr) during glacial periods. diverged 0.47 Myr, kawakamii 0.35 Myr. These evolved separate refugia, distinct boundaries confirmed through delimitation analysis, karyotype, comparisons. Conclusions findings enhance our understanding underscore importance integrating transcriptomic studies. provides comprehensive framework for further investigations diversity adaptive ecologically vital group.

Язык: Английский

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Which factors contribute most to genome size variation within angiosperms?

Ecology and Evolution, Год журнала: 2021, Номер 11(6), С. 2660 - 2668

Опубликована: Янв. 31, 2021

Abstract Genome size varies greatly across the flowering plants and has played an important role in shaping their evolution. It been reported that many factors correlate with variation genome size, but few studies have systematically explored this at genomic level. Here, we scan information for 74 species from families 38 orders covering major groups of angiosperms (the taxonomic was acquired latest Angiosperm Phylogeny Group (APG IV) system) to evaluate correlation between different characteristics: polyploidization, types repeat sequence content, dynamics long terminal retrotransposons (LTRs). Surprisingly, found polyploidization shows no significant while LTR content demonstrates a significantly positive correlation. This may be due instability after since LTRs occupy most it directly result variation. We insertion time is negatively correlated which reflect competition deletion each genome, old insertions are usually easy recognize eliminate. also noticed burst occurred within last 3 million years, timeframe consistent violent climate fluctuations Pleistocene. Our findings enhance our understanding evolution angiosperms, methods offer immediate implications corresponding research other datasets.

Язык: Английский

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Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae

Current Opinion in Plant Biology, Год журнала: 2020, Номер 55, С. 74 - 83

Опубликована: Апрель 27, 2020

Язык: Английский

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Diversity, phylogeny, and adaptation of bryophytes: insights from genomic and transcriptomic data

Journal of Experimental Botany, Год журнала: 2022, Номер 73(13), С. 4306 - 4322

Опубликована: Март 24, 2022

Bryophytes including mosses, liverworts, and hornworts are among the earliest land plants, occupy a crucial phylogenetic position to aid in understanding of plant terrestrialization. Despite their small size simple structure, bryophytes second largest group extant plants. They live ubiquitously various habitats highly diversified, with adaptive strategies modern ecosystems on Earth. More more genomes transcriptomes have been assembled address fundamental questions biology. Here, we review recent advances associated diversity, phylogeny, ecological adaptation. Phylogenomic studies provided increasing supports for monophyly bryophytes, sister Setaphyta clade liverworts mosses. Further comparative genomic analyses revealed that multiple whole-genome duplications might contributed species richness morphological diversity We highlight biological changes through gene gain or neofunctionalization primarily evolved facilitated adaptation early environments; adapt desiccation tolerance is most remarkable. information would shed light key mechanisms success these 'dwarfs' kingdom.

Язык: Английский

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Divergence in cold tolerance promotes niche differentiation between diploid and polyploid kiwifruits along an altitudinal gradient in Southwest China

Oikos, Год журнала: 2024, Номер 2024(5)

Опубликована: Янв. 11, 2024

Polyploidization is hypothesized to improve the freezing resistance of plants in cold regions. However, adaptive strategies and key physiological mechanisms involved resistant ability polyploids remain unclear. In Actinidia chinensis (kiwifruits), tetraploids hexaploids occupy higher altitude habitats with colder climates than diploids, providing a study system investigate responsible for differentiation between cytotypes. We characterized environmental conditions their natural distribution areas, measured leaf‐level traits damages water relations at typical sites each cytotype along an altitudinal gradient. Polyploids showed lower semi‐lethal temperature (LT 50 ) ice nucleation (INT), reflecting tolerance strategy cope events plateau More negative turgor loss points larger cell elastic modulus could help alleviate from freezing‐induced dehydration, thus strengthening subzero temperatures (lower LT ). The increased supercooling capacity INT) might correlate less extracellular formation due osmotic potential full turgor, apoplastic fraction tissue capacitance. Our uncovers greater polyploid kiwifruits suggests linkage relations. Taken together, such divergence stress may underlie niche shift towards harsh environments.

Язык: Английский

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Influence of polyploidy on morphology and distribution of the Cypress Spurge (Euphorbia cyparissias, Euphorbiaceae)

Plant Biology, Год журнала: 2024, Номер 26(6), С. 998 - 1007

Опубликована: Июль 9, 2024

Abstract Polyploidy can cause differences in phenotypic and physiological traits among different cytotypes of the same species. Polyploids may have larger organs or occupy ecological niches than their diploid counterparts, therefore they are hypothesized to distributions prosper stressful environments, such as higher elevations. The Cypress spurge ( Euphorbia cyparissias L.; Euphorbiaceae) is a widespread European heteroploid species including di‐ (2 x ), tetra‐ (4 ) hexaploid (6 cytotypes. We tested hypotheses that polyploids more abundant at elevations ancestors case E. . also analysed whether genome downsizing had occurred after polyploidisation. conducted comprehensive geographic sampling 617 populations throughout Europe. estimated relative size using flow cytometry inferred ploidy level each population. scored 13 morphological vegetative seed characters performed statistical analyses. study indicates polyploidisation facilitated colonisation new areas , where tetraploids most widespread, whereas diploids limited putative Pleistocene refugia, mostly southern On other hand, three ploidies do not differ elevational distribution. Although some quantitative exhibited an increasing trend with ploidy, did significantly ploidies, there was no overall differentiation them. Given individuals thrive similar habitats across elevations, we suggest segregation following important trigger for itself autopolyploid plants. demonstrates be crucial range expansion, but it does necessarily influence distribution nor confer phenotype.

Язык: Английский

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Plastid Genomes of Five Species of Riverweeds (Podostemaceae): Structural Organization and Comparative Analysis in Malpighiales

Frontiers in Plant Science, Год журнала: 2019, Номер 10

Опубликована: Авг. 20, 2019

With the advent of next generation sequencing technologies, whole plastome data can be obtained as a byproduct low coverage plant genomic DNA. This provides an opportunity to study plastid evolution across groups, well testing phylogenetic relationships among taxa. Within order Malpighiales (~16,000 spp.), Podostemaceae (~300 spp.) stand out for their unique habit, living attached rocks in fast-flowing aquatic habitats, and displaying highly modified morphologies that confound our understanding classification, biology evolution. In this study, we used genome skimming assemble full five species within Podostemaceae. We analyzed comparative framework determine structure, gene content rearrangements plastomes family. The have smallest reported so far Malpighiales, possibly due variation length IR regions, loss, intergenic region variation. also detected major inversion large single copy uncommon loss or pseudogenization ycf1 ycf2 land plants is found characteristic Podostemaceae, but compensatory mechanisms implications accD, rpl22 clpP, rps16 remain explained group. addition, estimated tree selected Malpighiales. Our findings indicate are distinct lineage with long branches suggest faster rates group, compared other taxa order. lays foundations future phylogenomic studies

Язык: Английский

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