Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

Nature Genetics, Journal Year: 2020, Volume and Issue: 52(5), P. 525 - 533

Published: April 20, 2020

Abstract Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection domestication remains elusive. Here we analyze genome evolution diversification five allopolyploid cotton species, including economically important Upland Pima cottons. Although these polyploid genomes are conserved in gene content synteny, they have diversified by subgenomic transposon exchanges that equilibrate size, rate heterogeneities positive between homoeologs within among lineages. These differential trajectories accompanied gene-family homoeolog expression divergence Selection drive parallel similarities fibers of two cultivated cottons, involving coexpression networks N 6 -methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes can be overcome wild introgression. genomic insights will empower efforts to manipulate genetic modify target genes crop improvement.

Language: Английский

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A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant

Horticulture Research, Journal Year: 2020, Volume and Issue: 7(1)

Published: Sept. 21, 2020

Eggplant (Solanum melongena L.) is an economically important vegetable crop in the Solanaceae family, with extensive diversity among landraces and close relatives. Here, we report a high-quality reference genome for eggplant inbred line HQ-1315 (S. melongena-HQ) using combination of Illumina, Nanopore 10X genomics sequencing technologies Hi-C technology assembly. The assembled has total size ~1.17 Gb 12 chromosomes, contig N50 5.26 Mb, consisting 36,582 protein-coding genes. Repetitive sequences comprise 70.09% (811.14 Mb) genome, most which are long terminal repeat (LTR) retrotransposons (65.80%), followed by interspersed nuclear elements (LINEs, 1.54%) DNA transposons (0.85%). S. melongena-HQ carries 563 accession-specific gene families containing 1009 In total, 73 expanded (892 genes) 34 contraction (114 were functionally annotated. Comparative analysis different genomes identified three types variations, including single-nucleotide polymorphisms (SNPs), insertions/deletions (indels) structural variants (SVs). Asymmetric SV accumulation was found potential regulatory regions genes genomes. Furthermore, performed QTL-seq fruit length detected QTL interval 71.29-78.26 Mb on chromosome E03. Smechr0301963, belongs to SUN predicted be key candidate regulation. Moreover, anchored 210 linkage markers associated 71 traits chromosomes finally obtained 26 hotspots. assembly can accessed at http://eggplant-hq.cn. conclusion, presented herein provides global view genomic divergence whole-genome level powerful tools identification eggplant.

Language: Английский

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Current status of structural variation studies in plants

Plant Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19(11), P. 2153 - 2163

Published: June 8, 2021

Structural variations (SVs) including gene presence/absence and copy number are a common feature of genomes in plants and, together with single nucleotide polymorphisms epigenetic differences, responsible for the heritable phenotypic diversity observed within between species. Understanding contribution SVs to plant variation is important breeders assist producing improved varieties. The low resolution early genetic technologies inefficient methods have previously limited our understanding plants. However, rapid expansion genomic technologies, it possible assess an ever-greater accuracy. Here, we review current status SV studies plants, examine roles that play traits, compare future challenges studies.

Language: Английский

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Multi‐Omics Analysis Reveals That AhNHL Contributes to Melatonin‐Mediated Cadmium Tolerance in Peanut Plants

Journal of Pineal Research, Journal Year: 2025, Volume and Issue: 77(2)

Published: Feb. 12, 2025

Cadmium (Cd) pollution significantly hampers cleaner production of peanut (Arachis hypogaea L.). Therefore, exploring tolerance mechanisms to Cd stress and breeding low-Cd cultivars are urgently needed require intense efforts. Herein, multi-omics physiological studies reveal that multiple biological processes, including melatonin (MT) biosynthesis, involved in the plants. Exogenous MT was applied plants under stress, which decreased accumulation roots, shoots seeds for 40%-60%, promoted antioxidant capacity. Integrated investigation reveals MT-mediated is mainly attributed enhanced metabolism linolenic acid, glutathione (GSH), phenylpropanoid (lignin), development casparian strip root cell wall. Defense genes, such as non-race-specific disease resistance gene 1/harpininduced 1 (NDR1/HIN1)-like (AhNHL), were also upregulated by stress. Overexpression AhNHL tobacco reduced 37%-46%, alleviated photosynthesis-inhibition induced Transcriptomic analysis suggested confers through promoting biosynthesis GSH metabolism. Additionally, exogenous effectively improving sequestration capacity plants, while apply inhibitor (buthionine sulfoximine) exacerbated phytotoxicity. improves affecting expression genes transcription regulation, metal ion binding transport. Our findings provide novel insights into molecular underlying would facilitate cultivars.

Language: Английский

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Genome sequencing of three Polyscias species reveals common features in terpene synthase gene family evolution in these species

The Plant Genome, Journal Year: 2025, Volume and Issue: 18(1)

Published: Feb. 19, 2025

Abstract The genus Polyscias , part of the Araliaceae family, is known for its significant ornamental and medicinal value, as well rich variety metabolites. These plants are primarily found in tropical regions, particularly Southeast Asia Pacific islands. diverse geographical environments have led to emergence many unique endangered species, although there limited genomic information available about them. In this study, we generated high‐quality reference genomes three species: two that endemic Hawaiʻi, cf. bisattenuata lallanii one more widespread macgillivrayi . We identified a total 51,083, 60,881, 29,060 genes these respectively. Whole‐genome duplication analysis indicated all species underwent common event. By examining phylogenetic structural characteristics terpene synthase gene family closely related several clusters play crucial roles metabolite synthesis. A mono‐ sesquiterpenoids were detected, with compounds having been validated previous studies. Our findings provide foundation further genetic biochemical investigations which may aid conservation species.

Language: Английский

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Genome-Wide Identification of NAC Transcription Factors and Their Functional Prediction of Abiotic Stress Response in Peanut

Frontiers in Genetics, Journal Year: 2021, Volume and Issue: 12

Published: March 9, 2021

The NAC transcription factor (TF) is one of the most significant TFs in plants and widely involved plant growth, development, responses to biotic abiotic stresses. To date, there are no systematic studies on family peanuts. Herein, 132 AhNACs were identified from genome cultivated peanut, they classified into eight subgroups (I–VIII) based phylogenetic relationships with Arabidopsis proteins their conserved motifs. These genes unevenly scattered all 20 chromosomes, among which 116 pairs fragment duplication events 1 pair tandem duplications existed. Transcriptome analysis showed that many AhNAC responded drought abscisic acid (ABA) stresses, especially members groups IV, VII, VIII, expressed at larger differential levels under polyethylene glycol (PEG) and/or ABA treatment roots or leaves. Furthermore, them selected response PEG evaluated by quantitative real-time polymerase chain reaction. results these significantly This study was helpful for guiding functional characterization improvement drought-resistant germplasms

Language: Английский

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Comparison ofArachis monticolawith Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut

Advanced Science, Journal Year: 2019, Volume and Issue: 7(4)

Published: Nov. 28, 2019

Like many important crops, peanut is a polyploid that underwent polyploidization, evolution, and domestication. The wild allotetraploid species Arachis monticola (A. monticola) an unique link from the diploid to cultivated tetraploid in lineage. However, little known about A. its role evolution domestication of this crop. A fully annotated sequence ≈2.6 Gb genome comparative genomics reported. Genomic reconstruction 17 diploids AA, BB, EE, KK, CC groups 30 tetraploids demonstrates monophyletic origin B subgenomes peanuts. undergo asymmetric subgenome including homoeologous exchanges, homoeolog expression bias, structural variation (SV), leading functional divergence during Significantly, SV-associated homoeologs tend show bias correlation with pod size increase tetraploids. Moreover, genomic analysis disease resistance genes shows alleles present can be introduced into breeding programs improve some traits These resources are valuable for studying domestication, improvement production resistance.

Language: Английский

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Research advances and future perspectives of genomics and genetic improvement in allotetraploid common carp

Reviews in Aquaculture, Journal Year: 2021, Volume and Issue: 14(2), P. 957 - 978

Published: Nov. 26, 2021

Abstract Aquatic species have become an integral part of human culture. As internationally important food fish species, the common carp Cyprinus carpio accounted for over 7% global aquaculture production in 2020. In addition to serving as a source, varieties are used ornamental and valued recreational fisheries. The continuously updated reference genome has recently served foundation both basic genetic studies evolutionary studies. With recent emphasis on allotetraploid signature carp, researchers begun focus how hybridization polyploidization affect successful speciation advantageous behaviour carp. this review, we survey current emerging research topics including genomic tools, germplasm resources, diversity, mechanism improvement economic traits, well multiple breeding technologies employed We also provide overview trends improvements encourage monitor Understanding basis economically traits mechanisms allopolyploidization will be innovation agronomically although road ahead challenging widely domesticated species.

Language: Английский

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The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits

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

Published: July 25, 2023

Abstract Polyploidization can provide a wealth of genetic variation for adaptive evolution and speciation, but understanding the mechanisms subgenome as well its dynamics ultimate consequences remains elusive. Here, we report telomere-to-telomere (T2T) gap-free reference genome allotetraploid horseradish ( Armoracia rusticana ) sequenced using comprehensive strategy. The (epi)genomic architecture 3D chromatin structure A B subgenomes differ significantly, suggesting that both dominant long terminal repeat retrotransposons DNA methylation have played critical roles in diversification. Investigation basis biosynthesis glucosinolates (GSLs) peroxidases reveals important role polyploidization differentiation shaping key traits. Continuous duplication divergence essential genes GSL (e.g., FMO GS-OX , IGMT GH1 gene family) contribute to broad profile horseradish. Overall, T2T assembly expands our polyploid provides fundamental resource breeding improvement

Language: Английский

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PSW1, an LRR receptor kinase, regulates pod size in peanut

Plant Biotechnology Journal, Journal Year: 2023, Volume and Issue: 21(10), P. 2113 - 2124

Published: July 11, 2023

Pod size is a key agronomic trait that greatly determines peanut yield, the regulatory genes and molecular mechanisms controlling pod are still unclear. Here, we used quantitative locus analysis to identify regulator, POD SIZE/WEIGHT1 (PSW1), characterized associated gene protein. PSW1 encoded leucine-rich repeat receptor-like kinase (LRR-RLK) positively regulated stemness. Mechanistically, this allele harbouring 12-bp insertion in promoter point mutation coding region of causing serine-to-isoleucine (S618I) substitution substantially increased mRNA abundance binding affinity for BRASSINOSTEROID INSENSITIVE1-ASSOCIATED RECEPTOR KINASE 1 (BAK1). Notably, PSW1HapII (super-large PSW1) expression led up-regulation positive regulator stemness PLETHORA (PLT1), thereby resulting larger size. Moreover, overexpression seed/fruit multiple plant species. Our work thus discovers conserved function controls provides valuable genetic resource breeding high-yield crops.

Language: Английский

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