Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum

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

Published: April 11, 2023

Abstract Chrysanthemum ( morifolium Ramat.) is a globally important ornamental plant with great economic, cultural, and symbolic value. However, research on chrysanthemum challenging due to its complex genetic background. Here, we report near-complete assembly annotation for C. comprising 27 pseudochromosomes (8.15 Gb; scaffold N50 of 303.69 Mb). Comparative evolutionary analyses reveal whole-genome triplication (WGT) event shared by species approximately 6 million years ago (Mya) the possible lineage-specific polyploidization 3 Mya. Multilevel evidence suggests that likely segmental allopolyploid. Furthermore, combination genomics transcriptomics approaches demonstrate genome can be used identify genes underlying key traits. Phylogenetic analysis CmCCD4a traces flower colour breeding history cultivated chrysanthemum. Genomic resources generated from this study could help accelerate improvement.

Language: Английский

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Plant pan-genomics and its applications

Molecular Plant, Journal Year: 2022, Volume and Issue: 16(1), P. 168 - 186

Published: Dec. 15, 2022

Language: Английский

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The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress

BMC Biology, Journal Year: 2021, Volume and Issue: 19(1)

Published: May 6, 2021

Medicago ruthenica, a wild and perennial legume forage widely distributed in semi-arid grasslands, is distinguished by its outstanding tolerance to environmental stress. It close relative of commonly cultivated alfalfa (Medicago sativa). The high M. ruthenica stress makes this species valuable genetic resource for understanding improving traits associated with harsh environments.We sequenced assembled genome using an integrated approach, including PacBio, Illumina, 10×Genomics, Hi-C. was 904.13 Mb scaffold N50 99.39 Mb, 50,162 protein-coding genes were annotated. Comparative genomics transcriptomic analyses used elucidate mechanisms underlying expanded FHY3/FAR1 family identified be involved drought Many abiotic retained compared other species. Hundreds candidate analyzing variations single nucleotide polymorphism accessions varying drought. Transcriptomic data demonstrated the involvements related transcriptional regulation, response, metabolic regulation ruthenica.We present high-quality assembly identification drought-related providing genomic studies on forages.

Language: Английский

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Genome-wide identification of the MADS-box transcription factor family in autotetraploid cultivated alfalfa (Medicago sativa L.) and expression analysis under abiotic stress

BMC Genomics, Journal Year: 2021, Volume and Issue: 22(1)

Published: Aug. 7, 2021

Alfalfa, the "queen of forage", is most extensively cultivated forage legume in world. The development and yield alfalfa are seriously limited by abiotic stress. MADS-box transcription factors one largest gene families play a pivotal role plant However, little known regarding autotetraploid alfalfa.In present study, we identified 120 MsMADS-box genes genome. Phylogenetic analysis indicated that 75 type-I were classified into Mα, Mβ, Mγ subgroups, 45 type-II 11 subgroups. promoter region containing several hormone stress related elements. Chromosomal location revealed 117 unevenly distributed on 32 chromosomes, remaining three located unmapped scaffolds. A total nine pairs segmental duplications four groups tandem found. Expression showed differentially expressed various tissues under stresses. qRT-PCR expression profiles eight selected distinct stresses.In this genome based level, further confirmed Gene Ontology (GO) analysis, phylogenetic sequence features analysis. Taken together, these findings will provide clues for study functions molecular breeding. Our first to systematically identify characterize (Medicago sativa L.), significantly involved response

Language: Английский

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Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits

Genomics Proteomics & Bioinformatics, Journal Year: 2022, Volume and Issue: 20(1), P. 14 - 28

Published: Jan. 13, 2022

Abstract Alfalfa (Medicago sativa L.) is the most important legume forage crop worldwide with high nutritional value and yield. For a long time, breeding of alfalfa was hampered by lacking reliable information on autotetraploid genome molecular markers linked to agronomic traits. We herein reported de novo assembly allele-aware chromosome-level Zhongmu-4, cultivar widely cultivated in China, comprehensive database genomic variations based resequencing 220 germplasms. Approximate 2.74 Gb contigs (N50 2.06 Mb), accounting for 88.39% estimated genome, were assembled, 2.56 anchored 32 pseudo-chromosomes. A total 34,922 allelic genes identified from genome. observed expansion gene families, especially those related nitrogen metabolism, increase repetitive elements including transposable elements, which probably resulted Zhongmu-4 compared Medicago truncatula. Population structure analysis revealed that accessions Asia South America had relatively lower genetic diversity than Europe, suggesting geography may influence divergence during local adaption. Genome-wide association studies 101 single nucleotide polymorphisms (SNPs) associated 27 Two candidate predicted be correlated fall dormancy salt response. believe sequence combined data diverse germplasms will facilitate research genomics-assisted variety improvement alfalfa.

Language: Английский

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Recent Advances in Assembly of Complex Plant Genomes

Genomics Proteomics & Bioinformatics, Journal Year: 2023, Volume and Issue: 21(3), P. 427 - 439

Published: April 25, 2023

Abstract Over the past 20 years, tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already, ranging from those nonvascular plants to flowering plants. However, complex genome assembly is still challenging remains difficult fully resolve conventional methods due high heterozygosity, highly repetitive sequences, or ploidy characteristics genomes. Herein, we summarize challenges assembly, including feasible experimental strategies, upgrades technology, existing methods, different phasing algorithms. Moreover, list actual cases projects for readers refer draw upon solve future problems related Finally, expect that accurate, gapless, telomere-to-telomere, phased could soon become routine.

Language: Английский

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An alfalfa MYB‐like transcriptional factor MsMYBH positively regulates alfalfa seedling drought resistance and undergoes MsWAV3‐mediated degradation

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(4), P. 683 - 699

Published: Feb. 15, 2024

ABSTRACT Drought is a major threat to alfalfa ( Medicago sativa L.) production. The discovery of important genes regulating drought response will facilitate breeding for drought‐resistant cultivars. Here, we report genome‐wide association study resistance in alfalfa. We identified and functionally characterized an MYB‐like transcription factor gene MsMYBH ), which increases the Compared with wild‐types, biomass forage quality were enhanced overexpressed plants. Combined RNA‐seq, proteomics chromatin immunoprecipitation analysis showed that can directly bind promoters MsMCP1, MsMCP2, MsPRX1A MsCARCAB improve their expression. outcomes such interactions include better water balance, high photosynthetic efficiency scavenge excess H 2 O drought. Furthermore, E3 ubiquitin ligase (MsWAV3) was found induce degradation under long‐term drought, via 26S proteasome pathway. variable‐number tandem repeats promoter among collection germplasms, variation associated activity. Collectively, our findings shed light on functions provide pivotal could be leveraged This also offers new insights into mechanisms

Language: Английский

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An inducible CRISPR activation tool for accelerating plant regeneration

Plant Communications, Journal Year: 2024, Volume and Issue: 5(5), P. 100823 - 100823

Published: Jan. 18, 2024

The inducible CRISPR-activation (CRISPR-a) system offers unparalleled precision and versatility for regulating endogenous genes, making it highly sought after in plant research. In this study, we developed a chemically CRISPR-a tool called ER-Tag by combining the XVE with SunTag system. We systematically compared different induction strategies achieved high efficiency target gene activation. demonstrated that guide RNAs could be multiplexed pooled large-scale screening of effective morphogenic genes pairs involved regeneration. Further experiments showed induced activation these accelerated regeneration improved both eudicot monocot plants, including alfalfa, woodland strawberry sheepgrass. Our study expanded CRISPR toolset plants provided powerful new strategy studying functions when constitutive expression is not feasible or ideal.

Language: Английский

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Genome-Wide Identification of the HIPPs Gene Family and Functional Validation of MsHIPP12 in Enhancing Cadmium Tolerance in Medicago sativa

Journal of Hazardous Materials, Journal Year: 2025, Volume and Issue: 491, P. 137894 - 137894

Published: March 10, 2025

Language: Английский

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Orphan Crops and their Wild Relatives in the Genomic Era

Molecular Plant, Journal Year: 2020, Volume and Issue: 14(1), P. 27 - 39

Published: Dec. 18, 2020

Language: Английский

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