Whole-body transcriptome mining for candidate effectors from Diuraphis noxia

RNA was extracted from a pooled sample of salivary glands that were excised from adult Diuraphis noxia aphids of two biotypes SA1 and SAM2.0. South African D. noxia biotype SA1 is known to be the least virulent aphid, while its offspring, the South African D. noxia biotype SAM2.0 is a newly developed biotype that is capable of feeding on several resistant cultivars. The overall purpose of the experiment was to establish a baseline availability of transcripts contained in the salivary glands of D. noxia aphids as well as help improve on current genome assemblies. In total, 200 glands were excised from both biotypes feeding on various wheat hosts (Tugela, Tugela Dn1, Gamtoss R, SST387). Aphid glands were excised in PBS buffer and stored in RNA-later until RNA extraction with a Qiagen Rneasy kit could commence. Library preparation for sequencing was performed using an Illumina TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E protocol. The single library was then sequenced on a NovaSeq6000 system. De novoassembly was performed making use of the Trinity package. Assembly of combined salivary transcriptome of two Diuraphis noxia biotypes that fed on wheat cultivars Tugela, Tugela Dn1, Gamtoos R, SST387. Salivary glands were excised from both biotypes feeding on various hosts and pooled together before RNA extraction.