Ontology highlight
ABSTRACT:
PROVIDER: PRJNA865891 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To further clarify the differences in the potential regulatory mechanisms of cold tolerance between wild and cultivated tomatoes, we subjected cold-sensitive cultivated tomato (Solanum lycopersicum) Ailsa Craig (AC) and cold-tolerant wild tomato (S. habrochaites) LA1777 to cold stress for 6 h, and performed ATAC-Seq and RNA-Seq, respectively.
2024-02-23 | GSE254893 | GEO
Project description:The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication.
2012-08-10 | GSE39308 | GEO
Project description:Peanut (Arachis hypogaea) has a large (~2.7 Gbp) allotetraploid genome with closely related component genomes making its genome very challenging to assemble. Here we report genome sequences of its diploid ancestors (A. duranensis and A. ipaënsis). We show they are similar to the peanutâs A- and B-genomes and use them use them to identify candidate disease resistance genes, create improved tetraploid transcript assemblies, and show genetic exchange between peanutâs component genomes. Based on remarkably high DNA identity and biogeography, we conclude that A. ipaënsis may be a descendant of the very same population that contributed the B-genome to cultivated peanut. Whole Genome Bisulphite Sequencing of the peanut species Arachis duranensis and Arachis ipaensis.
2016-07-03 | E-GEOD-71357 | biostudies-arrayexpress
Project description:Anthocyanins are high value plant antioxidants which are not present in the fruits of cultivated tomato. However, both the dominant gene Anthocyanin fruit (Aft) and the recessive gene atroviolacea (atv), introgressed into domesticated tomato from two different wild Solanum species, stimulate a limited anthocyanin pigmentation. Surprisingly, double mutant Aft/Aft atv/atv tomatoes are characterised by the presence of anthocyanins in the fruit peel, resulting in intensely purple pigmented fruit. We carried out a transcript profiling analysis using GeneChip® Tomato Genome Arrays, in order to identify differentially expressed genes when comparing wild type, Aft/Aft, atv/atv, and Aft/Aft atv/atv fruits. The expression pattern of several genes involved in the anthocyanin pathway was analyzed in detail. Among the fruit peel-associated differentially expressed transcripts, genes involved in phenylpropanoid pathway, cell wall composition, biotic and abiotic stress responses, sugar and hormone metabolism were overrepresented in Aft/Aft atv/atv. Transcriptomic analysis thus revealed that the activation of anthocyanin synthesis in tomato fruit was accompanied by a complex remodulation of gene expression, likely affecting important agronomic and merceological traits.
2010-07-31 | GSE19792 | GEO
Project description:Peanut (Arachis hypogaea) has a large (~2.7 Gbp) allotetraploid genome with closely related component genomes making its genome very challenging to assemble. Here we report genome sequences of its diploid ancestors (A. duranensis and A. ipaënsis). We show they are similar to the peanut’s A- and B-genomes and use them use them to identify candidate disease resistance genes, create improved tetraploid transcript assemblies, and show genetic exchange between peanut’s component genomes. Based on remarkably high DNA identity and biogeography, we conclude that A. ipaënsis may be a descendant of the very same population that contributed the B-genome to cultivated peanut.
2016-01-01 | GSE71357 | GEO
Project description:The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication.In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication.
2012-08-10 | GSE39307 | GEO
Project description:To aid the annotation of the genome of cultivated (ZSZ1) and wild (QYZM) ramie and characterize the expression profiling, the root, stem and leaves from these two varieties were performed for transcriptome sequencing. Our results generated 20,693 and 19,498 predicted genes from QYZM and ZSZ1 genome. of them, 17,983 QYZM genes and 17,998 ZSZ1 expressed in at least one of these three examined tissues.
2020-09-29 | GSE158630 | GEO
Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
2022-06-27 | E-MTAB-11830 | biostudies-arrayexpress
Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
2022-06-27 | E-MTAB-11831 | biostudies-arrayexpress