Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae
Abstract Background: Rambutan (Nephelium lappaceum L.) is an important fruit tree belongs to the family Sapindaceae and widely cultivated in Southeast Asia. The chloroplast of plants, as a photosynthetic organelle plays an important role in the photosynthesis and secondary metabolic activities. The chloroplast genome sequencing has become an integral part in understanding the genomic machinery and the phylogenetic histories of rambutan organelles.Results: We sequenced its chloroplast genome and assembled 161,321 bp circular DNA. It is characterized by a typical quadripartite structure composed of a large (86,068 bp) and small (18,153 bp) single-copy region interspersed by two identical inverted repeats (IRs) (28,550 bp). We identified 132 genes including 78 protein-coding, 29 tRNA and 4 rRNA genes, with 21 genes duplicated in the IRs. Sixty-three simple sequence repeats (SSRs) and 98 repetitive sequences were detected. Twenty-nine codons showed biased usage and 49 potential RNA editing sites were predicted across 18 protein-coding genes in the rambutan chloroplast genome. In addition, coding gene sequence divergence analysis of N. lappaceum suggested that ccsA, clpP, rpoA, rps12, psbJ and rps19 were under positive selection, which might reflect specific adaptations of N. lappaceum to its particular living environment. Comparative chloroplast genome analyses from five species in Sapindaceae revealed that a higher similarity was conserved in the IR regions than in the LSC and SSC regions. The phylogenetic analysis showed that N. lappaceum chloroplast genome has the closest relationship with that of Pometia tomentosa. Conclusions: The understanding of the chloroplast genomics of rambutan and comparative analysis of Sapindaceae species would provide insight into future research on the breeding of rambutan and Sapindaceae evolutionary studies.