Sequence characteristics and codon bias analysis of chloroplast genome from Spatholobus suberectus Dunn

【Objective】This work was aimed to clarify the sequence features and codon bias of chloroplast genome from Spatholobus suberectus Dunn， and provide theoretical reference for germplasm identification， molecular breeding and resource conservation and utilization of S. suberectus.【Method】 S. suberectus chloroplast genome was sequenced using high-throughput sequencing technology and then was assembled， annotated and analyzed by means of bioinformatics softwares and tools. A phylogenetic tree was also constructed to understanding the evolution status of S. suberectus.【Result】 The chloroplast genome of S. suberectus was an annular double-chain molecule with a size of 152275 bp， which was successively composed of a large single copy（LSC）with 83924 bp， an inverted repeat A（IRA）with 25113 bp， a small single copy（SSC）with 18125 bp and an inverted repeat B（IRB） with 25113 bp. The chloroplast genome annotated 129 genes， including 84 protein-coding genes（PCGs）， 8 rRNA and 37 tRNA. The chloroplast genome of S. suberectus tended to use the codon ended with A or T under the action of multiple factors dominated by natural selection， and the preference codons were identified as GCT， AGA， CGA， AAT， TGT， CAA， GAA， GGT， CAT， ATA， TTA， AAA， TTT， CCT， TCA， ACT， TAT， GTT. A total of 117 SSR loci were detected from the chloroplast genome of S. suberectus， which were composed of mononucleotide， dinucleotide， trinucleotide and tetranucleotide repeat motifs. The number of mononucleotide and dinucleotide repeat motifs was higher， accounting for 50.4% and 36.8% of the total number of SSR loci respectively， and the mononucleotide， dinucleotide， trinucleotide and tetranucleotide repeat motifs were mainly A or T and their combinations. There were obvious base mutations in the chloroplast genome both within and among the genera Spatholobus. The chloroplast genome sequences of S. suberectus and S. pulcher were the most similar， and the two were most closely related. 【Conclusion】 The chloroplast genome of S. suberectus possesses typical structure of plant chloroplast genome and preferable identification capability among the Spatholobus and other genera. The codon bias of S. suberectus chloroplast genome is a synergistical result of multiple factors. Among them， natural selection contributes most， and the base mutation and others also have a certain impact.