NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes

Bioinformatics, Год журнала: 2023, Номер 39(3)

Опубликована: Март 1, 2023

Abstract Summary Large-scale comparative genomic studies have provided important insights into species evolution and diversity, but also lead to a great challenge visualize. Quick catching or presenting key information hidden in the vast amount of data relationships among multiple genomes requires an efficient visualization tool. However, current tools for such remain inflexible layout and/or require advanced computation skills, especially genome-based synteny. Here, we developed easy-to-use flexible tool, NGenomeSyn [multiple (N) Genome Synteny], publication-ready syntenic whole genome local region features (e.g. repeats, structural variations, genes) across with high customization. provides easy way its users visualize large rich by simply adjusting options moving, scaling, rotation target genomes. Moreover, could be applied on non-genomic similar input formats. Availability implementation is freely available at GitHub (https://github.com/hewm2008/NGenomeSyn) Zenodo (https://doi.org/10.5281/zenodo.7645148).

Язык: Английский

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Meiotic recombination dynamics in plants with repeat-based holocentromeres shed light on the primary drivers of crossover patterning

Nature Plants, Год журнала: 2024, Номер 10(3), С. 423 - 438

Опубликована: Фев. 9, 2024

Abstract Centromeres strongly affect (epi)genomic architecture and meiotic recombination dynamics, influencing the overall distribution frequency of crossovers. Here we show how is regulated distributed in holocentric plant Rhynchospora breviuscula , a species with diffused centromeres. Combining immunocytochemistry, chromatin analysis high-throughput single-pollen sequencing, discovered that crossover distally biased, sharp contrast to hundreds centromeric units features. Remarkably, found crossovers were abolished inside but not their proximity, indicating absence canonical centromere effect. We further propose telomere-led synapsis homologues feature best explains observed landscape. Our results hint at primary influence mechanistic features pairing rather than organization determining biased R. whereas centromeres (epi)genetic properties only positioning locally.

Язык: Английский

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A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity

Nature Genetics, Год журнала: 2025, Номер unknown

Опубликована: Фев. 3, 2025

Abstract A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species. We developed barley using 20 inbred genotypes representing domesticated by generating analyzing short- long-read RNA-sequencing datasets tissues. To overcome single reference bias in transcript quantification, we constructed genotype-specific (RTDs) integrated these into linear pan-genome framework to create pan-RTD, allowing categorization as core, shell or cloud. Focusing on core (expressed all genotypes), observed significant abundance variation among tissues between driven partly RNA processing, gene copy number, structural rearrangements conservation promotor motifs. Network analyses revealed conserved co-expression module::tissue correlations frequent functional diversification. complement pan-transcriptome, comprehensive cultivar (cv.) Morex gene-expression atlas illustrate how combined can be used guide biological inquiry.

Язык: Английский

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A view of the pan‐genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)

The Plant Genome, Год журнала: 2023, Номер 17(1)

Опубликована: Март 22, 2023

Abstract Cowpea, Vigna unguiculata L . Walp., is a diploid warm‐season legume of critical importance as both food and fodder in sub‐Saharan Africa. This species also grown Northern Africa, Europe, Latin America, North East to Southeast Asia. To capture the genomic diversity domesticates this important legume, de novo genome assemblies were produced for representatives six subpopulations cultivated cowpea identified previously from genotyping several hundred diverse accessions. In most complete assembly (IT97K‐499‐35), 26,026 core 4963 noncore genes identified, with 35,436 pan when considering all seven GO terms associated response stress defense highly enriched among genes, while related transcription factor activity, transport metabolic processes. Over 5 million single nucleotide polymorphisms (SNPs) relative each over 40 structural variants >1 Mb size by comparing genomes. Vu10 was chromosome highest frequency SNPs, Vu04 had variants. Noncore harbor larger proportion potentially disruptive than including missense, stop gain, frameshift mutations; suggests that substantially contribute within domesticated cowpea.

Язык: Английский

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Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes

Nature Plants, Год журнала: 2024, Номер 10(8), С. 1184 - 1200

Опубликована: Авг. 5, 2024

Язык: Английский

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Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea

Nature Genetics, Год журнала: 2024, Номер 56(6), С. 1225 - 1234

Опубликована: Май 23, 2024

Язык: Английский

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Grapevine pangenome facilitates trait genetics and genomic breeding

Nature Genetics, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 4, 2024

Grapevine breeding is hindered by a limited understanding of the genetic basis complex agronomic traits. This study constructs graph-based pangenome reference (Grapepan v.1.0) from 18 newly generated phased telomere-to-telomere assemblies and 11 published assemblies. Using Grapepan v.1.0, we build variation map with 9,105,787 short variations 236,449 structural (SVs) resequencing data 466 grapevine cultivars. Integrating SVs into genome-wide association study, 148 quantitative trait loci for 29 traits (50.7% identified), 12 significantly contributed SVs. The estimated heritability improves 22.78% on average when including We discovered locus regions under divergent artificial selection in metabolism berry development between wine table grapes, respectively. Moreover, significant correlations were detected among Under polygenic model, conducted genomic predictions each trait. In general, our facilitates superior cultivars via multiple By constructing incorporating phenotypic maps, investigates traits, empowering breeding.

Язык: Английский

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Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 24, 2024

Cannabis sativa is a globally significant seed-oil, fiber, and drug-producing plant species. However, century of prohibition has severely restricted legal breeding germplasm resource development, leaving potential hemp-based nutritional fiber applications unrealized. Existing cultivars are highly heterozygous lack competitiveness in the overall grain markets, relegating hemp to less than 200,000 hectares globally1. The relaxation drug laws recent decades generated widespread interest expanding reincorporating cannabis into agricultural systems, but progress been impeded by limited understanding genomics potential. No studies date have examined genomic diversity evolution populations using haplotype-resolved, chromosome-scale assemblies from publicly available germplasm. Here we present pangenome, constructed with 181 new 12 previously released genomes total 156 biological samples both male (XY) female (XX) plants, including 42 trio phased 36 assemblies. We discovered regions pangenome that surprisingly diverse for single species, high levels genetic structural variation, propose novel population structure hybridization history. Conversely, cannabinoid synthase genes contain very low diversity, despite being embedded within variable region containing multiple pseudogenized paralogs distinct transposable element arrangements. Additionally, identified variants acyl-lipid thioesterase (ALT) associated fatty acid chain length variation production rare cannabinoids, tetrahydrocannabinol varin (THCV) cannabidiol (CBDV). conclude gene pool only partially characterized, existence wild relatives Asia remains likely, while its as crop species largely

Язык: Английский

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Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape

Journal of Integrative Plant Biology, Год журнала: 2024, Номер 66(7), С. 1408 - 1426

Опубликована: Апрель 5, 2024

ABSTRACT Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on phenotypic traits and local adaptation to abiotic biotic stress. In this study, we employed woolly grape ( Vitis retordii ), species native the tropical subtropical regions East Asia with both coastal inland habitats, as valuable model for examining SVs adaptation. We assembled haplotype‐resolved chromosomal reference genome grape, conducted population genetic analyses based whole‐genome sequencing (WGS) data from populations. The demographic revealed recent bottlenecks in all populations asymmetric gene flow population. total, 1,035 genes associated adaptive regulation salt stress, radiation, environmental were detected underlying selection by SNPs population, which 37.29% 65.26% SNPs, respectively. Candidate such FSD2 , RGA1 AAP8 tolerance found be highly differentiated selected during process habitats SV regions. Our study highlights importance adaptation; candidate related stress climatic environments important genomic resources future breeding programs grapevine its rootstocks.

Язык: Английский

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Integrative genomics reveals the polygenic basis of seedlessness in grapevine

Current Biology, Год журнала: 2024, Номер 34(16), С. 3763 - 3777.e5

Опубликована: Авг. 1, 2024

Seedlessness is a crucial quality trait in table grape (Vitis vinifera L.) breeding. However, the development of seeds involved intricate regulations, and polygenic basis seed abortion remains unclear. Here, we combine comparative genomics, population genetics, quantitative integrative genomics to unravel evolution seedlessness grapes. We generated haplotype-resolved genomes for two seedless cultivars, "Thompson Seedless" (TS, syn. "Sultania") "Black Monukka" (BM). Comparative identified ∼4.25 Mb hemizygous inversion on Chr10 specific with seedless-associated genes VvTT16 VvSUS2 located at breakpoints. Population genomic analyses 548 grapevine accessions revealed distinct clusters identity-by-descent (IBD) results indicated that origin could be traced back "Sultania." Introgression, rather than convergent selection, shaped evolutionary history improvement. Genome-wide association study (GWAS) analysis 110 loci (QTLs) associated 634 candidate genes, including previously unidentified such as three 11S GLOBULIN SEED STORAGE PROTEIN CYTOCHROME P450 well-known like VviAGL11. Integrative resulted 339 core categorized into 13 functional categories related development. Machine learning-based selection achieved remarkable prediction accuracy 97% grapevines. Our findings highlight nature provide molecular genetics an effective

Язык: Английский

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