Telomere-to-telomere, gap-free genome of mung bean (Vigna radiata) provides insights into domestication under structural variation DOI Creative Commons
Kai‐Hua Jia, Guangyong Li,

Longxin Wang

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: 12(3)

Published: Dec. 2, 2024

Abstract Mung bean (Vigna radiata), an essential annual legume, holds substantial value in global agriculture due to its short growth cycle, low input requirements, and nutritional benefits. Despite extensive domestication, the genetic mechanisms underlying morphological physiological evolution remain incompletely understood. In this study, we present a gap-free, telomere-to-telomere genome assembly of mung cultivar 'Weilv-9′, achieved through integration PacBio HiFi, Oxford Nanopore, high-throughput chromosome conformation capture (Hi-C) sequencing technologies. The 500-Mb assembly, encompassing 11 chromosomes containing 28 740 protein-coding genes, reveals that 49.17% comprises repetitive sequences. Within genome, found recent amplification transposable elements significantly impacts expression nearby genes. Furthermore, integrating structural variation single-nucleotide polymorphism (SNP) data from resequencing, identified fatty acid synthesis, suberin biosynthetic, phenylpropanoid metabolic processes have undergone strong selection during domestication. These findings provide valuable insights into driving domestication offer foundation for future enhancement breeding programs beans related species.

Language: Английский

Pangenome analysis reveals transposon-driven genome evolution in cotton DOI Creative Commons
Xin He, Zhengyang Qi, Zhenping Liu

et al.

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: April 23, 2024

Transposable elements (TEs) have a profound influence on the trajectory of plant evolution, driving genome expansion and catalyzing phenotypic diversification. The pangenome, comprehensive genetic pool encompassing all variations within species, serves as an invaluable tool, unaffected by confounding factors intraspecific diversity. This allows for more nuanced exploration TE evolution.

Language: Английский

Citations

8
The transposition of a heat-activated retrotransposon <i>ONSEN</i> resulted in changes in the hypocotyl elongation DOI Creative Commons

Ryu Hasegawa,

Hidetaka Ito

Genes & Genetic Systems, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

In our study, we aimed to identify new mutants resulting from ONSEN transposition in Arabidopsis thaliana by subjecting nrpd1 heat stress. We isolated a mutant with significantly elongated hypocotyl, named "Long hypocotyl inserted line 1" (HYO1). This phenotype was heritable, progeny consistently displaying longer hypocotyls than the wild type. Genetic analysis revealed that this trait due single recessive mutation. Further mapping and sequencing identified insertion of HY2 gene, crucial regulator elongation. The disrupted transcription, as confirmed quantitative PCR, leading observed phenotype. To assess influence background, generated lines backcrossed twice wild-type Col-0, results were consistent those original lines. Furthermore, examined effect HYO1 mutations on flowering time analyzing expression levels FT. hyo1 exhibited earlier compared both type mutants, increased FT levels. research underscores significant impact gene function phenotypic variation thaliana, providing insights into mutagenic potential transposons their role shaping plant traits.

Language: Английский

Citations

0
Chromosome-scale assembly of European flax (Linum usitatissimum L.) genotypes and pangenomic analysis provide genomic tools to improve breeding DOI
Boris B. Demenou,

Adama Ndar,

Christophe Pineau

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: March 7, 2025

Abstract Decoding the genome of cultivated species is one key starting points for supporting marker-assisted selection to accelerate breeding programmes. To date, five six flax genotypes, including fiber flax, linseed and related wild mainly from Canada, China Russia, have been sequenced assembled. But no assembly was available Western European cultivar, although France world's leading producer (85% world production). The Canadian oilseed cultivars CDC Bethune used as reference studies activities. best date Chinese Yiya5 assembly, which had metric all assemblies available. Recent analyses shown that up 30% reads different origins do not map genome. Thus, much genetic information could be neglected using a reference. aim this study sequence, assemble annotate genomes four (two Bolchoï Idéo; two Marquise Attila) provide pangenome genotype characterization breeding. From 21 46 Gb ONT Minion long sequence data were -sequenced - assembled Flye, -polished, validated organised into hybrid scaffolds 100 197 optical (Bionano Genomics), finally anchored fifteen T2T pseudomolecules each assembly. final size reached 437, 441, 442 453 Mb Idéo, Marquise, Attila respectively. annotated ab initio predictions genomic sequences evidence transcriptomic data. A graph constructed ten cultivars, previous publicly (CDC Bethune, Longya10 Line 3896, Heiya-14, Atlant). total 835.77 Mbp (74,123 non-redundant orthologous proteins) with core 172.2 Mbp. resources generated development tools useful breeders improve efficiency variety evaluation.

Language: Английский

Citations

0
Differential LTR-retrotransposon dynamics across polyploidization, speciation, domestication and improvement of cotton (Gossypium) DOI Creative Commons
Lucía Campos, Raúl Castanera, Corrinne E. Grover

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: March 21, 2025

Abstract Background Transposable elements (TEs) are major components of plant genomes and drivers genome evolution. The cotton genus (Gossypium) is an excellent evolutionary model for polyploidization, speciation, domestication crop improvement. Here, we implement pangenome analyses to study in detail the dynamics LTR-retrotransposons (LTR-RT) during Results We show that some LTR-RT lineages amplified tetraploid compared their diploid progenitors, whereas others stayed stable or but were removed through solo-LTR formation. Using species-level pangenomes only a few (CRM, Tekay, Ivana Tork) remained active after polyploidization still transposing. Tekay CRM have re-shaped centromeric pericentromeric regions cottons subgenome specific manner, new insertions also selective eliminations On other hand, Tork actively inserted within close genes. Finally, population-level using two data from 283 223 varieties G. hirsutum barbandense reveal changes Transposon Insertion Polymorphism (TIP) frequencies accompanying improvement both species, suggesting possibility selection on linked regions. Conclusions Our findings followed differential evolution, displaying differences among species coresident allopolyploid cotton. A handful expanded polyploidisation helped shape hirstutum barbadense, impacting centromere as well protein- coding

Language: Английский

Citations

0
Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome DOI Creative Commons

Yafang Xiao,

Jianbo Wang

Plants, Journal Year: 2025, Volume and Issue: 14(8), P. 1160 - 1160

Published: April 8, 2025

Transposon is the main component of eukaryotic genome, and more plant genome data show that transposons are diverse in regulating structure, variation, function evolution, with different transposition mechanisms genome. Hybridization polyploidy play an important role promoting speciation recent studies have shown usually accompanied by expansion transposons, which affect size structure polyploid plants. Transposons can insert into genes intergenic regions, resulting great differences overall closely related species, it also capture gene segments to increase copy number genes. In addition, influence epigenetic modification state regulate expression gene, while phenotype, biological abiotic stress response regulated transposons. Overall, especially adaptation evolution.

Language: Английский

Citations

0
Advances in genome sequencing and artificially induced mutation provides new avenues for cotton breeding DOI Creative Commons
Peilin Wang,

Mubashir Abbas,

Jianhan He

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: July 2, 2024

Cotton production faces challenges in fluctuating environmental conditions due to limited genetic variation cultivated cotton species. To enhance the diversity crucial for this primary fiber crop, it is essential augment current germplasm resources. High-throughput sequencing has significantly impacted functional genomics, enabling creation of diverse mutant libraries and identification genes new Artificial mutation, established through physical or chemical methods, stands as a highly efficient strategy enrich resources, yielding stable high-quality raw materials. In paper, we discuss good foundation laid by high-throughput genome genome, focus on construction methods strategies based mutants. addition, important identified library have greatly enriched resources promoted development genomes. Finally, an innovative constructing CRISPR was proposed, possibility screening mutants UAV phenotyping platform discussed. The aim review expand mine genes, develop adaptable materials variety complex environments.

Language: Английский

Citations

0
Pangenome Identification and Analysis of Terpene Synthase Gene Family Members in Gossypium DOI Open Access

Yue‐Qin Song,

Sheng‐Jie Han,

Mengting Wang

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(17), P. 9677 - 9677

Published: Sept. 6, 2024

Terpene synthases (TPSs), key gatekeepers in the biosynthesis of herbivore-induced terpenes, are pivotal diversity terpene chemotypes across and within plant species. Here, we constructed a gene-based pangenome Gossypium genus by integrating genomes 17 diploid 10 tetraploid Within this pangenome, 208 TPS syntelog groups (SGs) were identified, comprising 2 core SGs (TPS5 TPS42) present all 27 analyzed genomes, 6 softcore (TPS11, TPS12, TPS13, TPS35, TPS37, TPS47) found 25 to 26 131 dispensable identified 24 69 private exclusive single genome. The mutational load analysis these genes 216 cotton accessions revealed great number splicing variants complex patterns. nonsynonymous/synonymous Ka/Ks value for 52 was less than one, indicating that subject purifying selection. Of encompassing 1795 genes, 362 derived from 102 as atypical truncated. structural gene truncation is major mechanism contributing formation genes. An integrated three RNA-seq datasets plants subjected herbivore infestation highlighted nine upregulated TPSs, which included six previously characterized TPSs G. hirsutum (AD1_TPS10, AD1_TPS12, AD1_TPS40, AD1_TPS42, AD1_TPS89, AD1_TPS104), two (AD1_TPS100 AD2_TPS125), one (AD2_TPS41). Also, TPS-associated coexpression module eight involved terpenoid pathway transcriptomic data herbivore-infested hirsutum. These findings will help us understand contributions family members interspecific offer valuable resources breeding insect-resistant cultivars.

Language: Английский

Citations

0
Telomere-to-telomere, gap-free genome of mung bean (Vigna radiata) provides insights into domestication under structural variation DOI Creative Commons
Kai‐Hua Jia, Guangyong Li,

Longxin Wang

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: 12(3)

Published: Dec. 2, 2024

Abstract Mung bean (Vigna radiata), an essential annual legume, holds substantial value in global agriculture due to its short growth cycle, low input requirements, and nutritional benefits. Despite extensive domestication, the genetic mechanisms underlying morphological physiological evolution remain incompletely understood. In this study, we present a gap-free, telomere-to-telomere genome assembly of mung cultivar 'Weilv-9′, achieved through integration PacBio HiFi, Oxford Nanopore, high-throughput chromosome conformation capture (Hi-C) sequencing technologies. The 500-Mb assembly, encompassing 11 chromosomes containing 28 740 protein-coding genes, reveals that 49.17% comprises repetitive sequences. Within genome, found recent amplification transposable elements significantly impacts expression nearby genes. Furthermore, integrating structural variation single-nucleotide polymorphism (SNP) data from resequencing, identified fatty acid synthesis, suberin biosynthetic, phenylpropanoid metabolic processes have undergone strong selection during domestication. These findings provide valuable insights into driving domestication offer foundation for future enhancement breeding programs beans related species.

Language: Английский

Citations

0