Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8526522_1.fastq.gz | Fastqsanger.gz | |||
| SRR8526522_2.fastq.gz | Fastqsanger.gz | |||
| SRR8526523_1.fastq.gz | Fastqsanger.gz | |||
| SRR8526523_2.fastq.gz | Fastqsanger.gz |
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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.
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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.
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Project description:Diverse dataset of 1247 dogs from many breeds and wolves used to investigate the origins of dog domestication
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Project description:Domestication caused significant differences in morphology and behavior between wild and domestic animals, and gene expression changes played an important role in this event. circRNA is a class of non-coding RNA that exerts a wide range of functions in biological processes through the regulation of gene expression. However, the regulatory role of circRNA in the process of domestication is still unclear. Here, we analyzed circRNA expression patterns in the prefrontal cortices of wild boar and domestic pig to determine the potential role of circRNAs in domestication. We identified a total of 11,375 circRNAs and found that 349 and 354 circRNAs were up-regulated in wild boar and Rongchang pig, respectively. This study lays the groundwork for exploring the regulatory role of circRNA in the process of domestication and provides new insights that contribute to further investigation of the molecular mechanism of pig domestication.
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