One thousand plant transcriptomes and the phylogenomics of green plants

Nature, Год журнала: 2019, Номер 574(7780), С. 679 - 685

Опубликована: Окт. 23, 2019

Green plants (Viridiplantae) include around 450,000-500,000 species1,2 of great diversity and have important roles in terrestrial aquatic ecosystems. Here, as part the One Thousand Plant Transcriptomes Initiative, we sequenced vegetative transcriptomes 1,124 species that span a broad sense (Archaeplastida), including green (Viridiplantae), glaucophytes (Glaucophyta) red algae (Rhodophyta). Our analysis provides robust phylogenomic framework for examining evolution plants. Most inferred relationships are well supported across multiple tree supermatrix analyses, but discordance among plastid nuclear gene trees at few nodes highlights complexity plant genome evolution, polyploidy, periods rapid speciation, extinction. Incomplete sorting ancestral variation, polyploidization massive expansions families punctuate evolutionary history Notably, find large preceded origins plants, land vascular whereas whole-genome duplications to occurred repeatedly throughout flowering ferns. The increasing availability high-quality sequences advances functional genomics enabling research on life.

Язык: Английский

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Polyploidy: an evolutionary and ecological force in stressful times

The Plant Cell, Год журнала: 2020, Номер 33(1), С. 11 - 26

Опубликована: Дек. 1, 2020

Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for innovation species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests link with environmental conditions. Whole-genome seem correlate periods extinction or global change, while polyploids often thrive in harsh disturbed environments. Evidence is also accumulating that biotic interactions, instance, pathogens mutualists, affect differently than nonpolyploids. Here, we review recent findings insights on effect abiotic stress versus nonpolyploids propose response general important even determining factor success polyploidy.

Язык: Английский

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Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

Nature Plants, Год журнала: 2020, Номер 6(3), С. 259 - 272

Опубликована: Март 13, 2020

Abstract Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including distinct sporophyte architecture, cyanobacterial symbiosis pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as sister clade to liverworts plus mosses with high support. The lack repeat-dense centromeres well whole-genome duplication, contain limited transcription factor repertoire. Several genes involved in angiosperm meristem stomatal function are conserved upregulated during development, suggesting possible homologies at the genetic level. We identified candidate found LCIB , Chlamydomonas CCM gene, is present but absent plant lineages, implying role function. anticipate these hornwort will serve essential references for future research comparative studies across plants.

Язык: Английский

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Polyploidy, the Nucleotype, and Novelty: The Impact of Genome Doubling on the Biology of the Cell

International Journal of Plant Sciences, Год журнала: 2018, Номер 180(1), С. 1 - 52

Опубликована: Дек. 6, 2018

Polyploidy is a key mechanism of genome evolution and speciation, particularly in plants. Many aspects polyploidy have been elucidated with the tools that become available during molecular genetics genomics revolution. Nevertheless, significant questions remain about how doubling per se, absence hybridization, capable generating evolutionary novelty. This true at cellular level, where since discovery it has assumed increased cell size plays role physiological developmental changes associated doubling, usually through changing surface-to-volume ratio. Cell size, nuclear volume, cycle duration hypothesized to be among suite "nucleotypic" characters, defined as phenotypic traits influenced by bulk DNA amount, irrespective genic content. We update this old but still relevant concept, focusing on what current knowledge from biology can elucidate quantitative differences between diploids isogenic autopolyploids could lead differences. Much remains learned before causality correlation distinguished complex network interactions cytoplasm, nucleus other organelles, cycle, metabolism, intra- intercellular transport. It clear many effects are likely type specific conditioned different genomic architectures species which occurs. The rapidly developing ability study processes such transcription movement molecules single cells will enable experiments addressing fundamental potentially nucleotypic these interact genotypes produce

Язык: Английский

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WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

Molecular Plant, Год журнала: 2022, Номер 15(12), С. 1841 - 1851

Опубликована: Окт. 28, 2022

Язык: Английский

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The Angiosperm Terrestrial Revolution and the origins of modern biodiversity

New Phytologist, Год журнала: 2021, Номер 233(5), С. 2017 - 2035

Опубликована: Окт. 26, 2021

Summary Biodiversity today has the unusual property that 85% of plant and animal species live on land rather than in sea, half these tropical rainforests. An explosive boost to terrestrial diversity occurred from c . 100–50 million years ago, Late Cretaceous early Palaeogene. During this interval, Earth‐life system was reset, biosphere expanded a new level productivity, enhancing capacity environments. This biodiversity coincided with innovations flowering biology evolutionary ecology, including their flowers efficiencies reproduction; coevolution animals, especially pollinators herbivores; photosynthetic capacities; adaptability; ability modify habitats. The rise angiosperms triggered macroecological revolution drove modern secular, prolonged shift new, high levels, series processes we name here Angiosperm Terrestrial Revolution.

Язык: Английский

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The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly

Scientific Reports, Год журнала: 2019, Номер 9(1)

Опубликована: Дек. 3, 2019

Abstract Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying expansive ferns unclear, largely due to absence a sequenced homosporous fern genome. The lack this crucial resource has not only hindered investigations evolutionary responsible unusual genome characteristics ferns, but also impeded synthesis evolution across land plants. Here, we used model species Ceratopteris richardii address (e.g., polyploidy, spread repeat elements) by which high chromosome numbers typical may have evolved been maintained. We directly compared compositions in spanning green plant tree life diversity sizes, as well both short- long-read-based assemblies . found evidence consistent with single ancient polyploidy event history based on genomic cytogenetic data, proportions similar those flowering genomes. This study provides major stepping-stone understanding genomics providing first reference genome, insights into formation these massive

Язык: Английский

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Phylogenomics and the rise of the angiosperms

Nature, Год журнала: 2024, Номер 629(8013), С. 843 - 850

Опубликована: Апрель 24, 2024

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods

Язык: Английский

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Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms

Nature Plants, Год журнала: 2021, Номер 7(8), С. 1015 - 1025

Опубликована: Июль 19, 2021

Язык: Английский

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Deep reticulation: the long legacy of hybridization in vascular plant evolution

The Plant Journal, Год журнала: 2023, Номер 114(4), С. 743 - 766

Опубликована: Фев. 13, 2023

Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep scales largely obscure. Over the past decade, genomic phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, common throughout history plants, particularly various lineages flowering plants. However, studies also highlighted challenges disentangling signals ancient hybridization from other sources conflict (in particular, incomplete lineage sorting). Here, we provide critical review vascular outlining well-documented cases plant phylogeny, well unique to documenting versus recent hybridization. We definition for which, knowledge, explicitly attempted before. Further extent reticulation should remain an important research focus, especially because published examples likely represent tip iceberg terms total future increasingly explore macroevolutionary this process, impact on trajectories (e.g. how does influence trait evolution or generation biodiversity over time scales?), life ecological factors shape, shaped, frequency geologic phylogeny. Finally, consider implications ubiquitous conceptualize, analyze, classify Networks, opposed bifurcating trees, more accurate representations many cases, although ability infer, visualize, use networks comparative analyses is highly limited. Developing improved methods generation, visualization, represents direction biology. Current classification systems do generally allow recognition reticulate lineages, classifications themselves are based evidence chloroplast genome. Updating better reflect nuclear phylogenies, considering whether recognize systems, will challenge systematics community.

Язык: Английский

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