Vaccinium virgatum transcriptome 2017
DNA from leaves, green berries, and bud tips from Vaccinium virgatum cv. Premier were sequenced and assembled. The manuscript is currently in preparation. Data was provided pre-publication by Miriam Paya-Milans and Meg Staton from the University of Tennessee, Knoxville. Also see the expression analysis project page.
Reference: Payá-Milans M, Nunez GH, Olmstead JW, Rinehart TA, Staton M. Regulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq. BMC genomics. 2017 Aug 07; 18(1):580.
NCBI Biomaterial Accessions:
Two settings of k-mer 25 and k-mer 31 were applied in Trinity de novo assembly, and default settings on genome guided assembly. k-mer range of 25 to 55 with a step size of 10 were used in SOAPdenovo-Trans, TransABySS and velvet. To remove the redundancy on Trinity and SOAPdenovo-Trans, all contigs were pooled by software and clustered using CD-HIT-EST v4.6.6 with 95% identity. On velvet and TransABySS, reduced assemblies were obtained with Oases and transabyss-merge, respectively. The result of the four programs were pooled and reduced with CD-HIT to obtain the final transcriptome.
Additional information about this analysis: