Analysis of RNAseq reads from orchard trees and seed-borne seedlings for virus detection in apricot (Prunus armeniaca)
In this study, RNAseq reads of apricots (Prunus armeniaca) were analyzed to see reliability of High-throughput sequencing (HTS) for virus detection. HTS reads produced from the tissues of 7 trees (7 leaves, 1 immature fruit and 1 petal) grown in Kayseri naturally infected by Plum pox virus (PPV) and from the tissues of 3 seed-borne seedlings (1 leaf, 1 root, and 1 cotyledon) grown in screen house were local blasted against to the complete RefSeq release of virus sequences of NCBI. The all 9 samples form the outdoor trees depicted fragments of PPV and also 7 of them showed Apricot latent virus (ALV) in their total RNA reads. The number of reads of PPV ranged from 215 437 in Esen3 to 4 in Roxana. The highest number of ALV fragments (35,070) were observed in the total reads of SEO accession. The three samples obtained from tissues from seed-borne seedlings protected in the screen house against to virus infection did not display fragments of PPV and ALV. The results pointed that HTS sequencing does not produce virus reads if the tissue is not infected, suggesting that HTS is reliable source for virus detection.
Canbulat, O., Gürcan, K. and Teber, S. (2020). Analysis of RNAseq reads from orchard trees and seed-borne seedlings for virus detection in apricot (Prunus armeniaca). Acta Hortic. 1290, 123-128
next generation sequencing (NGS), virus detection, virus resistance