Chromosome-level genome assembly of yellow lupin (Lupinus luteus) provides novel insights into genome evolution, crop adaptation and seed protein in the three most cultivated lupins DOI Creative Commons
Eduardo Martínez,

Haroldo Salvo-Garrido,

Daniela Levicoy

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: March 27, 2024

Abstract Lupinus luteus is a grain legume crop of agricultural importance due to its high seed protein content. In this study, the first chromosome-scale genome assembly L. (962.97 Mb) presented, integrating data from Illumina, PacBio, and Hi-C platforms. The exhibits exceptional completeness (98.9% BUSCO score) repetition rate (76.15%). Genomic annotation identifies 36,884 protein-coding genes, including 2,492 transcription factors 23 microRNA families. Synteny analysis with lupin species reveals important chromosomal rearrangements, indicating complex interactions between conserved regions structural variations. Our analyses suggest that chromosome 8 may have originated translocation event involving two chromosomes during speciation . Orthologous group characterization related indicates an enrichment in gene families associated biotic abiotic stress responses, secondary metabolism, nutrient reservoir activity. Moreover, 911 resistance (R) genes are identified, highlighting their pathogen defence. Exploration alkaloid biosynthesis regulation 16 quinolizidine alkaloids (QAs) expression revealing tissue-specific patterns for key enzymes QA biosynthesis. Furthermore, metabolite transporters explored, angustifolius PUP1 ortholog, providing insights into mechanisms. This comprehensive provides valuable resources further understanding genetic basis traits , facilitating advancements adaptation, improvement, sustainability.

Language: Английский

Systematic analysis of Heat Shock Protein 70 (HSP70) gene family in radish and potential roles in stress tolerance DOI Creative Commons

Xiaoxue Pan,

Yang Zheng, Kairong Lei

et al.

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Jan. 2, 2024

Abstract The 70 kD heat shock proteins (HSP70s) represent a class of molecular chaperones that are widely distributed in all kingdoms life, which play important biological roles plant growth, development, and stress resistance. However, this family has not been systematically characterized radish ( Raphanus sativus L.). In study, we identified 34 RsHSP70 genes unevenly within nine chromosomes R. . Phylogenetic multiple sequence alignment analyses classified the into six distinct groups (Group A–F). characteristics gene structures, motif distributions, corresponding cellular compartments were more similar closely linked groups. Duplication analysis revealed segmental duplication was major driving force for expansion RsHSP70s radish, particularly Group C. Synteny eight paralogs (Rs-Rs) genome 19 orthologs (Rs-At) between Arabidopsis , 23 (Rs-Br) Chinese cabbage. RNA-seq showed expression change some related to responses heat, drought, cadmium, chilling, salt stresses Plasmodiophora brassicae infection, patterns these significantly different among 14 tissues. Furthermore, targeted candidate gene, RsHSP70–23 product is localized cytoplasm involved certain abiotic P infection. These findings provide reference further studies improve yield tolerance radish.

Language: Английский

Citations

10
Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.) DOI Creative Commons
Yadong Li,

Xiaobo Luo,

Xiao Peng

et al.

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Aug. 8, 2023

Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the most abundant genetic variations widely distribute across genomes in plant. Development of SNP InDel markers is a valuable tool for genetics genomic research radish (Raphanus sativus L.).In this study, total 366,679 single 97,973 insertion-deletion (InDel) were identified based on genome resequencing between 'YZH' 'XHT'. In all, 53,343 SNPs 4,257 InDels detected two cultivars by transcriptome sequencing. Among variations, 85 15 transcriptomic newly developed validated PCR. The 100 polymorphic generated 207 alleles among 200 Chinese germplasm, with an average 2.07 number (Na) 0.33 polymorphism information content (PIC). Population structure phylogenetic relationship revealed that from northern China clustered together southwest together. RNA-Seq analysis 11,003 differentially expressed genes (DEGs) cultivars, which 5,020 upregulated 5,983 downregulated. total, 145 flowering time-related DGEs detected, involved time integrator, circadian clock/photoperiod autonomous, vernalization pathways. region, 150 9 obtained.The large amount study will provide marker resource studies. within fundamental insight into dissecting molecular mechanism bolting radish.

Language: Английский

Citations

11
The mechanism by which oriented polypropylene packaging alleviates postharvest ‘Black Spot’ in radish root (Raphanus sativus) DOI Creative Commons
Zixin Lin, Bihong Feng,

Shibei Fang

et al.

Journal of Advanced Research, Journal Year: 2024, Volume and Issue: unknown

Published: June 1, 2024

The postharvest physiological disorder known as 'black spot' in radish roots (Raphanus sativus) poses a significant challenge to quality maintenance during storage, particularly under summer conditions. cause of this disorder, however, is poorly understood.

Language: Английский

Citations

4
Genome-wide characterization of RsHSP70 gene family reveals positive role of RsHSP70-20 gene in heat stress response in radish (Raphanus sativus L.) DOI
Qing He, Xinyu Zhang, Min He

et al.

Plant Physiology and Biochemistry, Journal Year: 2023, Volume and Issue: 199, P. 107710 - 107710

Published: April 14, 2023

Language: Английский

Citations

10
Apiaceae Medicinal Plants in China: A Review of Traditional Uses, Phytochemistry, Bolting and Flowering (BF), and BF Control Methods DOI Creative Commons
Meiling Li, Min Li, Li Wang

et al.

Molecules, Journal Year: 2023, Volume and Issue: 28(11), P. 4384 - 4384

Published: May 27, 2023

Apiaceae plants have been widely used in traditional Chinese medicine (TCM) for the removing dampness, relieving superficies, and dispelling cold, etc. In order to exploit potential applications as well improve yield quality of medicinal (AMPs), use, modern pharmacological phytochemistry, effect bolting flowering (BF), approaches controlling BF were summarized. Currently, about 228 AMPs recorded TCMs, with 6 parts, 79 uses, 62 5 main kinds metabolites. Three different degrees (i.e., significantly affected, affected some extent, not affected) could be classed based on quality. Although (e.g., Angelica sinensis) effectively controlled by standard cultivation techniques, mechanism has yet systemically revealed. This review will provide useful references reasonable exploration high-quality production AMPs.

Language: Английский

Citations

10
Two long read-based genome assembly and annotation of polyploidy woody plants, Hibiscus syriacus L. using PacBio and Nanopore platforms DOI Creative Commons
Hyunjin Koo, Gir-Won Lee, Seo-Rin Ko

et al.

Scientific Data, Journal Year: 2023, Volume and Issue: 10(1)

Published: Oct. 18, 2023

Abstract Improvements in long read DNA sequencing and related techniques facilitated the generation of complex eukaryotic genomes. Despite these advances, quality constructed plant reference genomes remains relatively poor due to large size genomes, high content repetitive sequences, wide variety ploidy. Here, we developed de novo assembly polyploid genome, Hibiscus syriacus , a flowering species Malvaceae family, using Oxford Nanopore Technologies Pacific Biosciences Sequel platforms. We investigated an efficient combination high-quality high-molecular-weight isolation procedure suitable assembler achieve optimal results data. found that abundant ultra-long reads allow for genome assemblies with great recovery sequences error correction even at low depth data polishing compared previous studies. Collectively, our provides cost effective methods improve continuity previously reported by accessing highly regions. The application this may enable genetic research breeding crops, thus leading improvements crop production.

Language: Английский

Citations

10
Pancentromere landscape and dynamic evolution in Brassica plants DOI Creative Commons
Li Guo, Weikai Chen, Jingxuan Wang

et al.

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

Published: Jan. 14, 2025

Abstract Centromere paradox where functionally conserved centromeres exhibit rapid evolution has long intrigued geneticists and evolutionary biologists. Despite its importance, centromeric landscape remains poorly understood due to assembling challenge. Here, we dissect the dynamic of Brassica by generating telomere-to-telomere assemblies from seven morphotypes B. rapa (AA) two tetroploids juncea (AABB) napus (AACC). Pan-centromere analysis reveal that are extensively invaded retrotransposons show remarkable diversity in size structure. While A- C-genome featured distinct patterns satellites, B-genome devoid satellites. Interestingly, satellite expansion is reminiscent layered expansions observed human centromeres. Accordingly, propose a working model centromere reconstructing key events leading current structures. These insights will illuminate plant guide design crop synthetic chromosomes.

Language: Английский

Citations

0
RsWRKY75 promotes ROS scavenging and cadmium efflux via activating the transcription of RsAPX1 and RsPDR8 in radish (Raphanus sativus L.) DOI
Xinyu Zhang,

Yingfei Ma,

Weilan Zhang

et al.

Plant Cell Reports, Journal Year: 2025, Volume and Issue: 44(3)

Published: Feb. 24, 2025

Language: Английский

Citations

0
RsWRKY40 coordinates the cold stress response by integrating RsSPS1-mediated sucrose accumulation and the CBF-dependent pathway in radish (Raphanus sativus L.) DOI Creative Commons
Sen Chen, Liang Xu, Yan Wang

et al.

Molecular Horticulture, Journal Year: 2025, Volume and Issue: 5(1)

Published: March 2, 2025

Abstract Cold stress adversely affects crop growth and development. Radish is an important root vegetable crop, its taproot formation susceptible to low temperatures. However, the molecular basis of cold response has not yet been fully dissected in radish. Here, a sucrose phosphate synthase gene ( RsSPS1 ) was identified through genome-wide association study transcriptome analysis. responsible for synthesis, shown be involved growth, cambium activity, tolerance regulated activity by modulating content. Moreover, RsWRKY40 as upstream transcription activator binding promoter. functioned -mediated accumulation. Furthermore, promoted RsCBF1 RsCBF2 expression levels, resulting elevated resilience. also enhanced own transcription, forming positive auto-regulatory loop regulate Together, module orchestrated integrating accumulation CBF-dependent pathway uncovered. These findings would provide novel insight into mechanism underlying cold-responsive facilitate genetic improvement radish breeding programs.

Language: Английский

Citations

0
Integrated genomic and transcriptomic analyses reveal the genetic and molecular mechanisms underlying hawthorn peel color and seed hardness diversity DOI
Jiaxin Meng, Yan Wang,

Rongkun Guo

et al.

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

Citations

0