The global distribution of angiosperm genome size is shaped by climate

New Phytologist, Journal Year: 2024, Volume and Issue: 242(2), P. 744 - 759

Published: Jan. 24, 2024

Angiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of size. These include previously proposed large constraint, mutational hazard, polyploidy-mediated, and climate-mediated hypotheses. We compiled largest size dataset to date, encompassing 16 017 (> 5% known) angiosperm species, analyzed using a comprehensive geographic angiosperms. observed that angiosperms with range sizes generally had small genomes, supporting constraint hypothesis. Climate was shown exert strong influence on along latitudinal gradient, while frequency polyploidy type growth form negligible effects. In contrast unimodal patterns gradient by plant traits polyploid proportions, increase from equator 40-50°N/S is probably mediated different (mostly climatic) mechanisms than decrease 40 50°N northward. Our analysis suggests mainly shaped climatically purifying selection, genetic drift, relaxed environmental filtering.

Language: Английский

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The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: July 12, 2021

Abstract The gymnosperm Welwitschia mirabilis belongs to the ancient, enigmatic gnetophyte lineage. It is a unique desert plant with extreme longevity and two ever-elongating leaves. We present chromosome-level assembly of its genome (6.8 Gb/1 C) together methylome transcriptome data explore astonishing biology. also refined, high-quality Gnetum montanum enhance our understanding evolution. has been shaped by lineage-specific whole duplication (~86 million years ago) more recently (1-2 years) bursts retrotransposon activity. High levels cytosine methylation (particularly at CHH motifs) are associated retrotransposons, whilst long-term deamination resulted in an exceptionally GC-poor genome. Changes copy number and/or expression gene families transcription factors (e.g. R2R3MYB , SAUR ) controlling cell growth, differentiation metabolism underpin plant’s tolerance temperature, nutrient water stress.

Language: Английский

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Application‐based guidelines for best practices in plant flow cytometry

Cytometry Part A, Journal Year: 2021, Volume and Issue: 101(9), P. 749 - 781

Published: Sept. 29, 2021

Abstract Flow cytometry (FCM) is currently the most widely‐used method to establish nuclear DNA content in plants. Since simple, 1‐3‐parameter, flow cytometers, which are sufficient for plant applications, commercially available at a reasonable price, number of laboratories equipped with these instruments, and consequently new FCM users, has greatly increased over last decade. This paper meets an urgent need comprehensive recommendations best practices different science applications. We discuss advantages limitations establishing ploidy, genome size, base composition, cell cycle activity, level endoreduplication. Applications such measurements systematics, ecology, molecular biology research, reproduction biology, tissue cultures, breeding, seed sciences described. Advice included on how obtain accurate reliable results, as well manage troubleshooting that may occur during sample preparation, cytometric measurements, data handling. Each section followed by practice recommendations; tips what specific information should be provided papers also provided.

Language: Английский

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The ecology of palm genomes: repeat‐associated genome size expansion is constrained by aridity

New Phytologist, Journal Year: 2022, Volume and Issue: 236(2), P. 433 - 446

Published: June 19, 2022

Genome size varies 2400-fold across plants, influencing their evolution through changes in cell and division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome diversity, the processes structuring repeat 'communities' are analogous to those ecological communities. However, stressors influence community dynamics has not yet been examined from an perspective. We measured leveraged climatic data for 91% of genera within ecologically diverse palm family (Arecaceae). then generated genomic profiles 141 species, analysed repeats using phylogenetically informed linear models explore relationships between factors. show that 'community' composition best explained by aridity. Specifically, Ty3-gypsy TIR elements were more abundant species wetter environments, generally had larger genomes, suggesting amplification. By contrast, Ty1-copia LINE drier environments. Our results suggest water inhibits selection on upper limits. may associate with stress-response genes (e.g. Ty1-copia) have amplified arid-adapted species. Overall, we provide novel evidence climate assembly 'communities'.

Language: Английский

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Speciation across the Earth driven by global cooling in terrestrial orchids

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(29)

Published: July 10, 2023

Although climate change has been implicated as a major catalyst of diversification, its effects are thought to be inconsistent and much less pervasive than localized or the accumulation species with time. Focused analyses highly speciose clades needed in order disentangle consequences change, geography, Here, we show that global cooling shapes biodiversity terrestrial orchids. Using phylogeny 1,475 Orchidoideae, largest orchid subfamily, find speciation rate is dependent on historic cooling, not time, tropical distributions, elevation, variation chromosome number, other types change. Relative gradual models specifying driven by over 700 times more likely. Evidence ratios estimated for 212 plant animal groups reveal orchids represent one best-supported cases temperature-spurred yet reported. Employing >2.5 million georeferenced records, drove contemporaneous diversification each seven bioregions Earth. With current emphasis understanding predicting immediate impacts warming, our study provides clear case long-term biodiversity.

Language: Английский

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Evolution of genome size and GC content in the tribe Carduinae (Asteraceae)

Preslia, Journal Year: 2023, Volume and Issue: 95(1), P. 185 - 213

Published: Jan. 1, 2023

Genome size and GC content are basic species-specific attributes often delimiting genera or higher taxa, which enable the identification of polyploidy, hybridization other modes genome karyotype evolution. The evolution these genomic traits can occur as a result selective pressure environment. Here, we reconstruct in subtribe Carduinae (Asteraceae) context changes chromosome numbers. Using flow cytometry, were estimated for 119 taxa mapped onto phylogenetic tree constructed using sequences from seven genetic markers. In addition, data compared with length stomatal guard cells achene (length, weight) to evaluate extent characters could evolve adaptively this subtribe. We found strong signals analysed phenotypic traits, delimited most clades agreement reconstructed phylogeny. Monoploid was positively correlated cell length. Cirsium, whose species focus majority analyses, large-genomed subgen. Lophiolepis had smaller cells, might be related it occurring more xeric habitats Cirsium. contrast, achenes larger, possibly response summer drought, whereas weight independent across Thus, under weak environmental control, at least that mediated by achenes. Achene content, have evolved drought. Carduus North American Cirsium there is an increase average reduction monoploid number, suggesting descending dysploidy associated chromosomal fusion. Polyploidy relatively rare confirmed only five studied, including vulgare, invasive likely originated via distant (intersubgeneric) hybridization, suggested its intermediate features combined conflict between morphology position. Phylogenetic reconstruction, differences parameters, well sizes support separation monophyletic remainder results also indicate early diverging italicum separated rest Lophiolepis+Picnomon+Notobasis clade.

Language: Английский

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A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly

Plant Communications, Journal Year: 2022, Volume and Issue: 3(5), P. 100330 - 100330

Published: May 5, 2022

Language: Английский

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RNA barcode segments for SARS-CoV-2 identification from HCoVs and SARSr-CoV-2 lineages

Virologica Sinica, Journal Year: 2024, Volume and Issue: 39(1), P. 156 - 168

Published: Jan. 20, 2024

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for disease 2019 (COVID-19), continues to evolve, giving rise more variants and global reinfections. Previous research has demonstrated that barcode segments can effectively cost-efficiently identify specific species within closely related populations. In this study, we designed tested RNA based on genetic evolutionary relationships facilitate efficient accurate identification of SARS-CoV-2 from extensive virus samples, including human coronaviruses (HCoVs) SARSr-CoV-2 lineages. Nucleotide sequences sourced NCBI GISAID were meticulously selected curated construct training sets, encompassing 1,733 complete genome HCoVs Through genetic-level testing, validated accuracy reliability identifying SARS-CoV-2. Subsequently, 75 main subordinate species-specific SARS-CoV-2, located in ORF1ab, S, E, ORF7a, N coding sequences, intercepted screened single-nucleotide polymorphism sites weighted scores. Post-testing, these exhibited high recall rates (nearly 100%), specificity (almost 30% at nucleotide level), precision (100%) performance identification. They eventually visualized using one two-dimensional combined barcodes deposited an online database (http://virusbarcodedatabase.top/). The successful integration barcoding technology provides valuable insights future studies involving sequence analysis. Moreover, cost-effective approach also reference endeavors surveillance.

Language: Английский

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Genome size evolution is associated with climate seasonality and glucosinolates, but not life history, soil nutrients or range size, across a clade of mustards

Annals of Botany, Journal Year: 2021, Volume and Issue: 127(7), P. 887 - 902

Published: Feb. 21, 2021

We investigate patterns of evolution genome size across a morphologically and ecologically diverse clade Brassicaceae, in relation to ecological life history traits. While numerous hypotheses have been put forward regarding autecological environmental factors that could favour small vs. large genomes, challenge understanding plants is many hypothesized selective agents are intercorrelated.We contribute estimates for 47 species Streptanthus Nutt. close relatives, take advantage data collections this group assemble on climate, history, soil affinity composition, geographic range plant secondary chemistry identify simultaneous correlates variation an evolutionary framework. assess models clades use phylogenetically informed analyses as well model selection information criteria approaches variables can best explain clade.We find differences heterogeneity its rate subclades relatives. show clade-wide positively associated with climate seasonality glucosinolate compounds. Model includes temperature fraction aliphatic glucosinolates, suggesting possible role climatic adaptation or biotic interactions shaping the size. no evidence supporting nutrients forces system.Our findings suggest potential highlight importance evaluating multiple context phylogeny understand effect

Language: Английский

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Genome Size Variation in Dianthus sylvestris Wulfen sensu lato (Caryophyllaceae)

Plants, Journal Year: 2022, Volume and Issue: 11(11), P. 1481 - 1481

Published: May 31, 2022

Genome size (GS) is an important characteristic that may be helpful in delimitation of taxa, and multiple studies have shown correlations between intraspecific GS variation morphological or environmental factors, as well its geographical segregation. We estimated a relative (RGS) 707 individuals from 162 populations Dianthus sylvestris with geographic focus on the Balkan Peninsula, but also including several European Alps. morphologically variable species thriving various habitats six subspecies been recognized Peninsula. Our RGS data backed-up chromosome counts revealed majority were diploid (2n = 30), ten tetraploid recorded D. subsp. Istria (Croatia, Italy). Their monoploid significantly lower than diploids, indicating genome downsizing. In addition, tetraploids differ their counterparts array characteristics. Within populations, geographically only partly taxonomically correlated, highest inferred southern Peninsula demonstrate greater among compared to Alps, which likely result more pronounced evolutionary differentiation within deep divergence Alps points persistence alpine different Pleistocene refugia.

Language: Английский

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