De novo assembly of leaf transcriptome, functional annotation and genomic resources development in Prosopis cineraria, a multipurpose tree of Indian Thar Desert

Abstract

Prosopis cineraria (L.) Druce, which belongs to the family Fabaceae, is a key component and one of the most valued trees of the Indian Thar Desert. The genetic improvement of P. cineraria has been hindered owing to very limited availability of genomic or transcriptomic resources. In this study, we present first transcriptome analysis of P. cineraria using RNA-Seq technology. The sequencing output of leaf transcriptome generated > 10 million high quality sequence reads, which assembled de novo in 1,42,711 unigenes. A total 60,583 CDS were predicted from unigenes with maximum and mean CDS length of 15,279 and 904 bp, respectively. Based on the similarity searches against plant non-redundant protein database, 57,249 CDS were annotated. The top-hit species distribution revealed that highest similarity was found to be against the species Glycine max (15,372). Based on sequence homology, 24,424 CDS were assigned GO terms. A total of 18,901 (31%) CDS were annotated with biological process, 12,930 (21%) with cellular components and 19,756 (32%) with molecular function. Annotation of transcripts using KEGG database revealed that 7945 CDSs were enriched in 33 different functional pathway categories including five major pathways i.e. metabolism, genetic information processing, environmental information processing, cellular process and organismal systems. The expression of CDSs ranged from 0 to 41,295.83 RPKM, while 950 CDSs had a high expression level of > 100 RPKM. Transcription factor analysis showed 12,128 unique transcripts belonging to the 79 transcription factor families. In addition, a total of 15,878 SSRs were identified in 13,655 unigenes. The transcriptome data set reported in the current study will serve as an important public information platform for comparative and functional genomic as well as gene expression studies in P. cineraria and other closely related species.