Characterization of genetic difference and phylogenetic relationship between Schizocapsa guangxiensis and Tacca plantaginea based on chloroplast genome

The taxonomy of Tacca remains is controversial all the time. Schizocapsa guangxiensis is considered to be the same species as Tacca plantanginea, but some taxonomists classify them into different species based on their morphological differences. In order to clarify the genetic differences and phylogenetic relationship between Schizocapsa guangxiensis and Tacca plantanginea, this study conducted high-throughput DNA sequencing of Schizocapsa guangxiensis, assembled a complete chloroplast genome using bioinformatics software, and compared it with the published Tacca plantanginea chloroplast genome. The results were as follows:(1)The chloroplast genome size of Schizocapsa guangxiensis and Tacca plantanginea was 162 149 bp and 160 749 bp, respectively, and they had the same GC content(36.90%). Notably, the gene types and gene amount were exactly the same in these two species, including 89 protein-coding genes and 37 tRNA genes, and 6 rRNA genes.(2)Codon preference analysis showed that there were certain differences in the codon frequencies used by the two species, but they both prefered codons ending in A/T(U).(3)Compared with T. plantanginea, the SSC boundary of Schizocapsa guangxiensis had obvious expansion, which was the main factor leading to the length variant in chloroplast genome between the two species.(4)There were some sequence divergences between S. guangxiensis and Tacca plantanginea in the LSC and SSC regions, especially the intergenic region, which can be exploited as species-specific molecular marker.(5)Phylogenetic results showed that Schizocapsa guangxiensis and Tacca plantanginea had a rather distant genetic relationship. Although Schizocapsa guangxiensis was placed in Tacca, they belong to two different species. This study enriches the genetic information of the chloroplast genome of S. guangxiensis and provides a theoretical basis for species classification, genetic diversity analysis and species protection of S. guangxiensis.