RNA-Seq of Glycine max leaf samples collected near Punjab, Pakistan in 2018
Leaf samples were collected from soybean plants showing virus-like symptoms from a production field in Pakistan and immediately put in RNAlater solution. Total RNAs were extracted from pooled soybean leaf samples using a Qiagen RNeasy Plant Mini kit and treated with Turbo DNase. Ribosomal RNA was removed from total RNAs using an Illumina Ribo-Zero Plus Plant kit. A single-end 100-nt sequencing library was prepared from the rRNA-depleted sample using the Illumina ScriptSeq RNAseq library preparation kit and sequenced on an Illumina NovaSeq 6000 at the University of Illinois. Sequence reads were trimmed and assembled de novo with Trinity. Assembled contigs were compared to the amino acid sequence database having predicted soybean and non-redundant virus amino acid sequences using USEARCH (Edgar, 2010). Contigs with significant similarity to viral sequences were compared to the NCBI non-redundant protein database using BLASTX.