Project description:To explore the overall circRNAs involved in growth and development of Arabidopsis thaliana across the lifespan, we deeply sequenced samples of whole plants from different developmental stages (cotyledons emergence, rosette leavesï¹¥1 mm, rosette growth complete, first flower open, flourishing florescence, first silique shattered, senescence). The total RNA was purified by rRNA-depletion and linear RNA removal with RNAseR, and sequenced by the Illumina HiSeq2500 platform. We obtained 31 Gb raw data and identified 1217 circRNAs with expression quantity. We annotated these circRNAs and predicted their targeted microRNA. The circRNAs involved in growth and development of Arabidopsis thaliana across lifespan were identified and analyzed using the Illumina HiSeq2500 platform.
Project description:In the present investigation, the genetic diversity architecture of 96 deep-water rice genotypes of Assam and association mapping strategy was, for the first time, applied to determine the significant SNPsand genes for deep-water rice. These genotypes are known for their unique elongation ability under deep-water condition.The internode elongation under water related genes will be identified here can provide affluent resources for rice breeding especially in flood-prone areas. We investigated the genome-wide association studies (GWAS) using 50 K rice genic SNPchip across 96 deep-water rice genotypes collected from different flood-prone districts/villages of Assam.
Project description:In order to systematically identify the possible regulatory roles of (long nocoding RNAs) lncRNAs and (circular RNAs) cirRNAs in the rice photo-thermosensitive genic male sterile (PTGMS) line that were involved in fertility transition, 18 RNA libraries from rice young panicles of the Wuxiang S sterile line rice (WXS (S)) and its fertile line rice (WXS (F)) at the pollen mother cell (PMC) formation stage (P2), the meiosis stage (P3), and the microspore formation stage (P4) were constructed, with three biological replicates for each condition. These libraries were sequenced using an Illumina Hiseq 2500 platform, and approximately 214.54 Gb clean reads were generated. we performed genome-wide identification and characterization of lncRNAs circRNAs using high-throughput strand-specific RNA sequencing (ssRNA-seq) technology and bioinformatics tools to investigate the expression profiles of circRNAs in the PTGMS rice line WXS and their potential roles in the fertility transition.A total of 3948 lncRNAs and 9994 circRNAs were indentifiled in WXS rice, and our findings clearly revealed that lnRNAs and circRNAs might be endogenous noncoding regulators of flower and pollen development in the PTGMS rice line.
Project description:To explore functional circRNAs during goat muscle development, we systematically investigated the circRNAs profiles using high throughput transcriptome sequencing technology (RNA-seq) at key developmental stages of fetus and Kid in Haimen goat.
Project description:The genome-wide transcriptome analyses using microarray probes containing genes and repeat sequences have been performed to examine response to the low-temperature in rice. We have particularly focused on the rice anther at the booting stage, since the low-temperature at this stage resulted in pollen abortion. The results demonstrated that the low-temperature stress caused genome-wide changes of transcriptional activities not only in genes, but also in repeat sequences of the rice anther. The degrees of the temperature responsive changes varied among the rice strains.
Project description:Detailed analysis of genome-wide transcriptome profiling in rice root is reported here, following Cr-plant interaction. Such studies are important for the identification of genes responsible for tolerance, accumulation and defense response in plants with respect to Cr stress. Rice root metabolome analysis was also carried out to relate differential transcriptome data to biological processes affected by Cr (VI) stress in rice.
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.