RNA-Seq analysis for transcriptome assembly, gene identification, and SSR mining in ginkgo (Ginkgo biloba L.)

Ginkgo (Ginkgo biloba L.) is a unique tree due to its distinctive classification in the plant kingdom and a long history as a medicinal plant, yet the genetic information and molecular processes in ginkgo have been largely lacking. In this study, 63.68 million paired-end reads from the asepsis seedling of ginkgo with lengths of 75 bp were assembled using Trinity, and 70,752 transcripts and 49,396 unique transcripts were generated. Among the 39,941 unique transcripts with coding regions, 24,645 unique transcripts had at least one hit in the public databases. And only 15,154 unique transcripts were annotated into 52 gene ontology (GO) functional categories. There were 50 and 43 sequences analyzed to be involved in the synthesis of flavonoids and ginkgolide/bilobalide, respectively, uncovering the putative enzymes catalyzing each step of the metabolic pathways. Sequence analysis identified a ginkgo chalcone isomerase gene (GbCHI1) encoding one of the key enzymes in the flavonoid biosynthesis pathway and exhibiting differences on protein sequences from the previously identified GbCHI. Phylogenetic analysis showed that GbCHI1 is close to GbCHI and the chalcone isomerase from Picea sitchensis, and the expression levels of GbCHI1 are coincided with the contents of flavonoids in different tissues. Furthermore, 4000 simple sequence repeats (SSRs) were found in the transcript library, and 1513 PCR primers of the SSR loci were designed. This study generated rich genetic and genomic information about the complex transcriptome of ginkgo, which would be valuable in helping with molecular study in this unique species in the future.