RNA-Seq Analysis of Acacia crassicarpa
Acasia crassicarpa is a fast-growing leguminous tree widely cultivated in tropical areas including Indonasia, Malaysia, Australia and southern part of China. Acacia trees provide versatile utility in timber, furniture, and pulp production. Demands are growing for efficient breeding programs of Acacia trees based on the molecular genetic information, which enables the precise subspecies segregation, identification of useful genes, and altering the genetic traits by genome editing technology. In this study, complementary DNA was prepared from the callus-cultured cells of A. crassicarpa, massive parallel sequencing by paired-end sequencing, and the raw data of 124,410,892 reads containing 12,565,500,092 bases were filtered and assembled de novo into 93,319 contigs, with a total of 84,411,793 base. The unigenes were annotated based on sequence homology by BLAST searches on non-redundant database. Several K+ and Na+-transporter genes annotated in A. crasssicarpa revealed high sequence similarity to those of Prosopis alba, which has the characteristic high tolerance for the drought and barren salt land. Our RNA-seq analysis also revealed the microsatellites, composed of simple-sequence repeat (SSR) loci, representing di-, tri-, and tetra-nucleotide repeat units, in the open-reading frames. Remarkable polymorphism was produced when PCR amplification was applied to the microsatellite loci in auxin-response factors and other transcription factors, which successfully discerned 16 variant species of A. crassicarpa tested. The transcriptomic information of A. crassicarpa generated in this study presents a widely exploitable platform for efficient molecular breeding programs that potentially contributes to the forestry plantation and biomass exploitation.