Molecular Regulatory Mechanism of Ginkgo biloba L. from Next-generation Sequencing Technology

Ginkgo biloba L. is a gymnosperm native to China and has a wide adaptability over more than 100 million years of dramatic climate changes. It is a living fossil for better understanding plant evolutionary history and an ideal model for studying plant phylogeny. The plant is also very important for medical use, food production, and ornamental landscapes. The functional genes related to these characteristics have not been effectively explored due to lacking of the reference sequences of genome and transcriptome. To discover novel functional genes efficiently and understand the development of Ginkgo, we used massive parallel pyrosequencing on the Roche 454 GS-FLX+ System to generate 251,636 and 223,261 reads from two sequenced samples of Ginkgo leaves and strobili. The 474,897 reads combined with the previous 64,057 reads in SRR077423 were assembled into a transcriptome consisting of 12,524 contigs. After functional annotation, domain annotation, GO analysis, and differential expression analysis, a detailed view of the Ginkgo biological systems was displayed, including characterization of unique putative transcripts with homology to known key enzymes and transcription factors involved in ginkgolide/bilobalide and flavonoid biosynthetic pathways. The full-length cDNA sequence of GbGGPS was 1641 bp containing a 1176 bp open reading frame (ORF), which encoding a 391 amino acids. Phylogenetic tree revealed that GbGGPS, TcGGDS, PaGGDS5 and AgGGDS were assigned to the same clade, suggested that high-throughput sequencing technology was superior to traditional gene-by-gene approach in discovery of genes. The results should help to resolve the ambiguous phylogenetic relationship of Ginkgo among the gymnosperms.