Genomic and transcriptomic analyses of valencia orange provide insights into its domestication and traits formation
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA689213 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13341800_1.fastq.gz | Fastqsanger.gz | |||
| SRR13341800_2.fastq.gz | Fastqsanger.gz | |||
| SRR13341801_1.fastq.gz | Fastqsanger.gz | |||
| SRR13341801_2.fastq.gz | Fastqsanger.gz | |||
| SRR13341802_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 72 |
Similar Datasets
Project description:Valencia orange (Citrus sinensis Osbeck), namely summer orange (SO), is a type of late-ripening sweet oranges, the ripening time of which is 4 to 5 months later than that of the middle-ripening common sweet orange (CO). The mastication of SO fruit pulp is worse than that of CO. To date, how the late-ripening and poor pulp mastication traits were domesticated in SO is unknown. In this study, 13 SO cultivars and 12 CO cultivars were used for whole-genome resequencing. Population genetic diversity analysis divided these 25 samples into SO and CO subgroups, respectively. There were 144 and 141 genes identified by selective sweep analysis to be strongly selected during SO and CO evolutionary processes, respectively. Based on gene functional annotation and pathway enrichment analysis, most of these selected genes in SO were related to resistance and lignin biosynthesis. Simultaneously, we comparatively analyzed the transcriptome profiles of the peel and pulp tissues among three SO cultivars and three CO cultivars, which also revealed the difference of lignin synthesis between SO and CO fruits. Moreover, according to the comparative analysis of the lignin content and the expressions of the genes related to lignin biosynthesis in SO and CO fruits, we suggested that lignin may play an important role in the pulp mastication trait of SO. In addition, a SNP molecular marker was developed to distinguish SO and CO. This study reveals that the mastication trait may be formed in the process of SO domestication, while the late-ripening trait may be formed in a genetic mutation event.
2021-08-26 | GSE164142 | GEO
Project description:Citrus sinensis cultivar:Valencia sweet orange Raw sequence reads
| PRJNA1076522 | ENA
Project description:Valencia orange (Citrus sinensis Osbeck) (VO) is a type of late-ripening sweet orange whose ripening occurs 4 to 5 months later than that of the mid-ripening common sweet orange (CO). Notably, the mastication trait of VO fruit is inferior to that of CO fruit. To date, how inferior pulp mastication trait forms in VO has not been determined. In this study, 13 VO varieties and 12 CO varieties were subjected to whole-genome resequencing. A total of 2.98 million SNPs were identified from 25 varieties, and a SNP molecular marker was developed to distinguish VO and CO. Moreover, 144 and 141 genes identified by selective sweep analysis were selected during VO and CO evolution, respectively. Based on gene functional enrichment analysis, most of the selected VO genes were related to the stress response and lignin biosynthesis. Simultaneously, we comparatively analyzed the transcriptome profiles of peel and pulp tissues among three VO varieties and three CO varieties, and the results demonstrated differences in lignin biosynthesis between VO and CO fruits. Furthermore, coexpression network analysis was performed to identify hub genes of lignin-related and variety-specific networks, which included CsERF74, CsNAC25, CsHSFB3, CsSPL4/13, etc. Overall, this study provides important insights into the mastication trait formation of Valencia orange fruit.
| S-EPMC8484299 | biostudies-literature
Project description:Chromosome set A (primarily mandarin-origin) of diploid Valencia sweet orange genome
| PRJNA736174 | ENA
Project description:Chromosome set B (primarily pummelo-origin) of diploid Valencia sweet orange genome
| PRJNA736176 | ENA
Project description:Genome assemblies and transcriptomes of an ordinary Valencia sweet orange and three irradiation-induced mutants
| PRJNA735893 | ENA
Project description:Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. A wealth of archeological and population genetic data has established maize as a model system for studying domestication , genome evolution and the genetics and evolution of complex traits. We used expression profiling of 18,242 genes for 38 diverse maize genotypes and 18 teosinte genotypes to examine how domestication has re-shaped the transcriptome of maize seedlings. We detected evidence for more than 600 genes having significantly different expression levels in maize compared to teosinte as well as 800 genes with significantly altered co-expression profiles reflective of substantial rewiring of the transcriptome since domestication. These genes likely include loci with altered expression due to domestication. The genes with altered expression show a significant enrichment for genes located in regions that previous population genetic analyses have identified as having undergone a selective sweep during maize domestication; thirty-two genes previously identified as putative targets of selection also exhibit altered expression levels and co-expression relationships. We also identified 45 genes with altered, primarily higher, expression in inbred relative to out-crossed teosinte. These genes are over-represented for genes that function in response to biotic stress and may reflect responses to the effects of inbreeding. This study not only documents alterations in the maize transcriptome following domestication and identifies several genes that may have contributed to the evolution of maize but also highlights the complementary information that can be gained by combining gene expression with population genetic analyses.
2012-04-01 | GSE30036 | GEO
Project description:Spinach is a nutritious leafy vegetable belonging to the family Chenopodiaceae. Here we report a high-quality chromosome-scale reference genome assembly of spinach and genome resequencing of 305 cultivated and wild spinach accessions. Reconstruction of ancestral Chenopodiaceae karyotype indicates substantial genome rearrangements in spinach after its divergence from ancestral Chenopodiaceae, coinciding with high repeat content in the spinach genome. Population genomic analyses provide insights into spinach genetic diversity and population differentiation. Genome-wide association studies of 20 agronomical traits identify numerous significantly associated regions and candidate genes for these traits. Domestication sweeps in the spinach genome are identified, some of which are associated with important traits (e.g., leaf phenotype, bolting and flowering), demonstrating the role of artificial selection in shaping spinach phenotypic evolution. This study provides not only insights into the spinach evolution and domestication but also valuable resources for facilitating spinach breeding.
| S-EPMC8668906 | biostudies-literature
Project description:Transposable elements (TEs) are genomic parasites that constitute the most abundant portions of higher plant genomes. However, whether TE selection occurred during crop domestication remains unknown. HUO is active under normal growth conditions, present at low copy numbers, inserts preferentially into regions capable of transcription, but absent in almost all modern varieties, indicating its removal during rice domestication and modern rice breeding. HUO triggers genomic immunity and dramatically alters genome-wide methylation levels and small RNA biogenesis, as well as global gene expression. Its presence specifically affects agronomic traits by decreasing yield performance and disease resistance but enhancing salt tolerance, which mechanistically explains its domestication removal. Thus, our study reveals a unique retrotransposon as a negative target for maintaining genetic and epigenetic stability during crop domestication and selection.
2018-03-08 | GSE79155 | GEO
Project description:Transposable elements (TEs) are genomic parasites that constitute the most abundant portions of higher plant genomes. However, whether TE selection occurred during crop domestication remains unknown. HUO is active under normal growth conditions, present at low copy numbers, inserts preferentially into regions capable of transcription, but absent in almost all modern varieties, indicating its removal during rice domestication and modern rice breeding. HUO triggers genomic immunity and dramatically alters genome-wide methylation levels and small RNA biogenesis, as well as global gene expression. Its presence specifically affects agronomic traits by decreasing yield performance and disease resistance but enhancing salt tolerance, which mechanistically explains its domestication removal. Thus, our study reveals a unique retrotransposon as a negative target for maintaining genetic and epigenetic stability during crop domestication and selection.
2018-03-08 | GSE79154 | GEO