Transcriptome Analysis, Marker Discovery and Pigment Biosynthesis of Red-leaf Juglans regia

Red-leaf trait rarely occurs in Juglans regia , and the genetic mechanism underlying this phenomenon is still unknown. In this study, we attempted to provide insight into the comprehensive transcriptome of red-leaf J. regia by RNA-Seq using Illumina SeqTM2000 platform. A total of 33,488,602 high-quality reads (3.35G cleans bases) were obtained and assembled into 53,782 unigenes. A total of 3,683 unigenes were annotated by using basic local alignment search tool to search against protein databases, All the matched unigenes were categorized by gene ontology analysis, and 3,466 were assigned to metabolism, among which 74 were mapped to anthocyanin, carotenoid, and betalain biosynthetic pathways by Kyoto Encyclopedia of Genes and Genomes analysis. Approximately 656 transcription factors were isolated including MYB, NAC, and bHLH. Additionally, a total of 13,981 simple sequence repeats, 41,088 single nucleotide polymorphisms, and 5,860 insertions and deletions were determined from J. regia transcriptome. Therefore, the current J. regia transcriptome provides deep insight into the molecular basis of red-leaf breeding of J. regia .