Vaccinium virgatum transcriptome 2017

Analysis NameVaccinium virgatum transcriptome 2017
MethodTrinity, SOAPdenovo-Trans, TransABySS, Velvet
SourceNCBI Bioproject PRJNA417702
Date performed2018-04-25

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:


Assembly Methods:

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:
Property NameValue
Analysis unigene nameV_virgatum_transcriptome
Analysis unigene num contigs126736
Analysis unigene num reads
Analysis unigene avg length
Analysis unigene num clusters
Analysis unigene num singlets
Analysis Typetranscriptome