The Cycas genome and the early evolution of seed plants

Nature Plants, Journal Year: 2022, Volume and Issue: 8(4), P. 389 - 401

Published: April 18, 2022

Cycads represent one of the most ancient lineages living seed plants. Identifying genomic features uniquely shared by cycads and other extant plants, but not non-seed-producing may shed light on origin key innovations, as well early diversification Here, we report 10.5-Gb reference genome Cycas panzhihuaensis, complemented transcriptomes 339 cycad species. Nuclear plastid phylogenomic analyses strongly suggest that Ginkgo form a clade sister to all gymnosperms, in contrast mitochondrial data, which place alone this position. We found evidence for an whole-genome duplication common ancestor gymnosperms. The contains four homologues fitD gene family were likely acquired via horizontal transfer from fungi, these genes confer herbivore resistance cycads. male-specific region Y chromosome C. panzhihuaensis MADS-box transcription factor expressed exclusively male cones is similar system reported Ginkgo, suggesting sex determination mechanism controlled have originated Ginkgo. provides important new resource broad utility biologists.

Language: Английский

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The giant diploid faba genome unlocks variation in a global protein crop

Nature, Journal Year: 2023, Volume and Issue: 615(7953), P. 652 - 659

Published: March 8, 2023

Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss biodiversity1. However, production is hampered by lack a cool-season legume equivalent to soybean agronomic value2. Faba bean (Vicia faba L.) has high yield potential well suited for cultivation temperate regions, but genomic resources are scarce. Here, we report high-quality chromosome-scale assembly genome show that it expanded massive 13 Gb size through an imbalance between rates amplification elimination retrotransposons satellite repeats. Genes recombination events evenly dispersed across chromosomes gene space remarkably compact considering size, although with substantial copy number variation driven tandem duplication. Demonstrating practical application sequence, develop targeted genotyping assay use high-resolution genome-wide association analysis dissect genetic basis seed hilum colour. The presented constitute genomics-based breeding platform bean, enabling breeders geneticists accelerate improvement sustainable Mediterranean, subtropical northern agroecological zones.

Language: Английский

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Recent advances on phylogenomics of gymnosperms and a new classification

Plant Diversity, Journal Year: 2022, Volume and Issue: 44(4), P. 340 - 350

Published: May 26, 2022

Living gymnosperms comprise four major groups: cycads, Ginkgo, conifers, and gnetophytes. Relationships among/within these lineages have not been fully resolved. Next generation sequencing has made available a large number of sequences, including both plastomes single-copy nuclear genes, for reconstruction solid phylogenetic trees. Recent advances in gymnosperm phylogenomic studies updated our knowledge systematics. Here, we review phylogeny over the past 10 years propose an classification extant gymnosperms. This new includes three classes (Cycadopsida, Ginkgoopsida, Pinopsida), five subclasses (Cycadidae, Ginkgoidae, Cupressidae, Pinidae, Gnetidae), eight orders (Cycadales, Ginkgoales, Araucariales, Cupressales, Pinales, Ephedrales, Gnetales, Welwitschiales), 13 families, 86 genera. We also described six tribes Acmopyleae Y. Yang, Austrocedreae Chamaecyparideae Microcachrydeae Papuacedreae Prumnopityeae 27 combinations genus Sabina.

Language: Английский

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The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights

Cell, Journal Year: 2023, Volume and Issue: 186(6), P. 1279 - 1294.e19

Published: March 1, 2023

Antarctic krill (Euphausia superba) is Earth’s most abundant wild animal, and its enormous biomass vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level genome, whose large genome size appears have resulted from inter-genic transposable element expansions. Our assembly reveals molecular architecture of circadian clock uncovers expanded gene families associated with molting energy metabolism, providing insights into adaptations cold highly seasonal environment. Population-level re-sequencing four geographical sites around continent no clear population structure but highlights natural selection environmental variables. An apparent drastic reduction in 10 mya subsequent rebound 100 thousand years ago coincides climate change events. findings uncover genomic basis provide valuable resources for future research.

Language: Английский

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Phylogenomics shed light on the complex evolutionary history of a gymnosperm genus showing East Asian–Tethyan disjunction

Journal of Systematics and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 3, 2025

Abstract When and how disjunct distributions of biological taxa arose has long attracted interest in biogeography, yet the East Asian–Tethyan disjunction is understudied. Cupressus (Cupressaceae) shows this disjunction, with 10 species Asia three Mediterranean region. Here we used target‐capture sequencing obtained 1991 single‐copy nuclear genes, plus complete plastomes, to infer evolutionary history . Our phylogenomic reconstruction resolved four well supported clades , but revealed significant phylogenetic conflicts, inter‐lineage gene flow, incomplete lineage sorting tree estimation error all making important contributions. The Chengiana clade most likely originated by hybridization between ancestors Himalayan–Hengduan Mountains subtropical clades, whereas orogenic climatic changes may have facilitated flow within clade. Molecular dating suggested that recent common ancestor appeared around middle Eocene period then became continuously distributed across Eurasia. when diverged, been driven Eocene/Oligocene declines global temperature, reinforced ecogeographic barrier created uplift Qinghai–Tibet Plateau. Niche shifts clade, signatures selection genes for drought salt tolerance, probably indicate adaptation local conditions. Overall, our study in‐depth analyses are powerful tools deciphering complex origin organisms, especially gymnosperms.

Language: Английский

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Plant pan-genomics: recent advances, new challenges, and roads ahead

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2022, Volume and Issue: 49(9), P. 833 - 846

Published: June 21, 2022

Pan-genomics can encompass most of the genetic diversity a species or population and has proved to be powerful tool for studying genomic evolution origin domestication species, providing information plant improvement. Plant genomics greatly progressed because improvements in sequencing technologies rapid reduction costs. Nevertheless, pan-genomics still presents many challenges, including computationally intensive assembly methods, high costs with large numbers samples, ineffective integration big data, difficulty applying it downstream multi-omics analysis breeding research. In this review, we summarize definition recent achievements pan-genomics, computational used pan-genome construction, applications pan-genomes molecular breeding. We also discuss challenges perspectives future studies provide detailed pipeline sample selection, genome annotation, structural variation identification, construction application graph-based pan-genomes. The aim is important guidance research better understanding basis evolution, crop domestication, phenotypic studies.

Language: Английский

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Chromosome-level genome assembly of bunching onion illuminates genome evolution and flavor formation in Allium crops

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Nov. 5, 2022

Abstract The Allium genus is cultivated globally as vegetables, condiments, or medicinal plants and characterized by large genomes strong pungency. However, the genome evolution genomic basis underlying their unique flavor formation remain poorly understood. Herein, we report an 11.27-Gb chromosome-scale assembly for bunching onion ( A. fistulosum ). uneven bursts of long-terminal repeats contribute to diversity in constituents, dispersed duplication events largely account gene expansion genomes. extensive differentiation alliinase lachrymatory factor synthase manifest important evolutionary during crops. Furthermore, differential selective preference flavor-related genes likely lead variations isoalliin content onions. Moreover, reveal that China origin domestication center Our findings provide insights into evolution, history enable future genome-assisted breeding traits these

Language: Английский

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The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: March 10, 2023

Abstract Torreya plants produce dry fruits with assorted functions. Here, we report the 19-Gb chromosome-level genome assembly of T. grandis . The is shaped by ancient whole-genome duplications and recurrent LTR retrotransposon bursts. Comparative genomic analyses reveal key genes involved in reproductive organ development, cell wall biosynthesis seed storage. Two encoding a C 18 Δ 9 -elongase 20 5 -desaturase are identified to be responsible for sciadonic acid both present diverse plant lineages except angiosperms. We demonstrate that histidine-rich boxes crucial its catalytic activity. Methylome analysis reveals methylation valleys harbor associated important activities, including lipid biosynthesis. Moreover, development accompanied DNA changes possibly fuel energy production. This study provides resources elucidates evolutionary mechanism land plants.

Language: Английский

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Current status and trends in forest genomics

Forestry Research, Journal Year: 2022, Volume and Issue: 2(1), P. 0 - 0

Published: Jan. 1, 2022

Forests are not only the most predominant of Earth's terrestrial ecosystems, but also core supply for essential products human use. However, global climate change and ongoing population explosion severely threatens health forest ecosystem aggravtes deforestation degradation. Forest genomics has great potential increasing productivity adaptation to changing climate. In last two decades, field advanced quickly owing advent multiple high-throughput sequencing technologies, single cell RNA-seq, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing, spatial transcriptomes, as well bioinformatics analysis which have led generation multidimensional, multilayered, spatiotemporal gene expression data. These together with basic technologies routinely used in plant biotechnology, enable us tackle many important or unique issues biology, provide a panoramic view an integrative elucidation molecular regulatory mechanisms underlying phenotypic changes variations. this review, we recapitulated advancement current status 12 research branches genomics, then provided future directions focuses each area. Evidently, shift from simple biotechnology-based research, setup investigation interpretation development differentiation just begun emerge.

Language: Английский

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The methylation landscape of giga-genome and the epigenetic timer of age in Chinese pine

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: April 7, 2023

Abstract Epigenetics has been revealed to play a crucial role in the long-term memory plants. However, little is known about whether epigenetic modifications occur with age progressively conifers. Here, we present single-base resolution DNA methylation landscapes of 25-gigabase Chinese pine ( Pinus tabuliformis ) genome at different ages. The result shows that closely coupled regulation gene transcription. age-dependent profile linearly increasing trend most significant pattern DMRs between Two segments five-prime end first ultra-long intron DAL1 , conservative biomarker conifers, gradual decline CHG as increased, which highly correlated its expression profile. Similar high correlation also observed nine other marker genes. Our results suggest serves an important signature developmental

Language: Английский

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