Identification of emerging viral genomes in transcriptomic datasets of alfalfa (Medicago sativa L.).

ABSTRACT:

Background

Publicly available transcriptomic datasets have become a valuable tool for the discovery of new pathogens, particularly viruses. In this study, several coding-complete viral genomes previously not found or experimentally confirmed in alfalfa were identified in the plant datasets retrieved from the NCBI Sequence Read Archive.

Methods

Publicly available Medicago spp. transcriptomic datasets were retrieved from the NCBI SRA database. The raw reads were first mapped to the reference genomes of Medicago sativa and Medigago truncatula followed by the alignment of the unmapped reads to the NCBI viral genome database and de novo assembly using the SPAdes tool. When possible, assemblies were experimentally confirmed using 5'/3' RACE and RT-PCRs.

Results

Twenty three

SUBMITTER: Jiang P 

PROVIDER: S-EPMC6902351 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature