Project description:In the recent years, RNA silencing has been studied extensively to be a conserved regulatory process in plants. In the antiviral silencing, the intermediate double-stranded RNA form during the replication of RNA viruses were recognized and processed into abundant of overlapping viral siRNA (viRNAs). Accordingly, the cloned viRNAs could be conversely assembled into some contigs of viruses, which is recently exploited for identifying new viruses and their genome sequences.To obtain rapidly the complete genome sequence of BYSMV, we carried out deep sequencing of small RNAs from healthy and BYSMV infected wheat, respectively. Thirteen contigs were assembled from the overlapping viRNAs only present in the infected wheat but not in the healthy wheat. The results of BLAST showed that ten contigs shared about 96% identity with the reported L gene of BYSMV isolate Zanjan-1.
Project description:Small RNA libraries were constructed from total RNA from Jasminum sambac plants exhibiting virus-like symptoms. After sequencing, small RNAs were assembled into contigs with MetaVelvet and assembled contigs were aligned against the NR database of NCBI using BLASTx. Top hits that reported a virus as subject were considered putative viral sequences. Based on such alignments, the whole genome of a virus, we tentatively name Jasmine Virus H was recovered and cloned. Two more small RNA libraries were made in a confirmatory experiment. One from Jasminum sambac and another one from Nicotiana benthamiana plants infected with the newly-cloned virus. The small RNA libraries were aligned against the full-length sequence of Jasmine Virus H to determine the spacial distribution of virus-derived small RNAs along the virus genome.
Project description:In the recent years, RNA silencing has been studied extensively to be a conserved regulatory process in plants. In the antiviral silencing, the intermediate double-stranded RNA form during the replication of RNA viruses were recognized and processed into abundant of overlapping viral siRNA (viRNAs). Accordingly, the cloned viRNAs could be conversely assembled into some contigs of viruses, which is recently exploited for identifying new viruses and their genome sequences.To obtain rapidly the complete genome sequence of BYSMV, we carried out deep sequencing of small RNAs from healthy and BYSMV infected wheat, respectively. Thirteen contigs were assembled from the overlapping viRNAs only present in the infected wheat but not in the healthy wheat. The results of BLAST showed that ten contigs shared about 96% identity with the reported L gene of BYSMV isolate Zanjan-1. Viral assembly from the BYSMV infected wheat plants to obtain the full lengh genome and characterise the viral siRNAs
Project description:In this work we used stable isotope probing/proteomics to study uptake of carbon sources by members of the cyanobacterial consortium. The database for protein identification was obtained from assembled metagenomes.
Project description:In this work we used metaproteomics to study the effect of pH and nitrogen source on cyanobacterial growth of the laboratory cultures. The database for protein identification was obtained from assembled metagenomes.
2021-11-02 | PXD024393 | Pride
Project description:The assembled contigs for the chloroplast genome of Typha angustifolia
