Transcriptome analysis of vegetative shoot apex between a thorny blackberry cultivar and its less-thorn variant
Transcriptome sequencing can be used to determine gene sequences and transcript abundance in non-model species. Transcriptome data are especially desirable in Rubus species and limited genomic research has been performed even though blackberry and raspberry play economically important roles in fruit production. Furthermore, thornlessness was an important target in blackberry breeding. Hence, we report the extensive sequence and transcript abundance data for the vegetative shoot apex transcriptome of blackberry Boysenberry and its bud variant with thin and less thorns by the IlluminaHiseq 2500 platform. Approximately, 5,751 Mb sequencing reads were generated and assembled de novo, yielding about 63,632 high-quality unigenes over 200 bp, which had a total length of 38.92 Mb and with an average length of 612 bp and the N50 length of 926 bp. Of these, 39,349 were identified as putative homologs of annotated sequences in the public protein databases. Digital abundance analysis identified 219 transcripts differentially enriched in Boysenberry and its thorn bud variant, with 80 genes upregulated and 139 genes downregulated in the variant. Furthermore, Gene ontology (GO) and KEGG pathway analyses indicated that 31 reliable metabolic pathways were altered in the mutant, including photosynthesis proteins, photosynthesis-antenna proteins, photosynthesis, measles, antigen processing and presentation, chaperones and folding catalysts, which was reflected in the illustration of target differentially expressed genes. This study provided a new sight into the molecular investigation of the thorn formation in blackberry.
Zhang, C.H., Huang, Z.Z., Zhao, H.F., Wu, W.L. and Lyu, L.F. (2019). Transcriptome analysis of vegetative shoot apex between a thorny blackberry cultivar and its less-thorn variant. Acta Hortic. 1265, 19-26
blackberry (Rubus L.), thornlessness, prickles, transcriptome, bud variant