Phylogenetic studies and comparative chloroplast genome analyses elucidate the basal position of halophyte Nitraria sibirica (Nitrariaceae) in the Sapindales

Abstract

Nitraria sibirica is a halophyte and belongs to the family Nitrariaceae. The chloroplast genome of Nitraria sibirica (159,466 bp) has a quadripartite structure, which consists of a large single-copy (87,914 bp) region, a small single-copy (18,316 bp) region, and a pair of inverted repeats (26,618 bp). Sequencing analyses indicate that the chloroplast genome contains 113 distinct genes, including 79 peptide-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. We also identified 105 perfect simple sequence repeats, 12 most divergent non-coding regions, and 6 most divergent coding regions when compared to the chloroplast genomes of the Sapindales plants. Phylogenetic analyses using the concatenated amino acid sequences of 58 protein-coding genes from 48 species suggest that the ‘basal’ position of Nitraria sibirica belongs to the Sapindales clade. We also found that the inverted repeat expansion resulted in a duplication of rps19 in Nitraria sibirica when comparing its chloroplast genome structure with Theobroma cacao, Vitis vinifera, Eucalyptus erythrocorys and Arabidopsis thaliana. The duplication of rps19 gene was consistent with that in Zanthoxylum piperitum, Azadirachta indica, Sapindus mukorossi and Citrus sinensis, all of which belong to the order Sapindales, but different from most Rosids plants. In summary, the analyses of Nitraria sibirica chloroplast genome not only provide insights into comparative genome analysis, but also pave the way for a better understanding of the phylogenetic relationships within the Sapindales.

Keywords:

• Nitraria sibirica
• phylogenetic analysis
• comparative chloroplast genome
• inverted repeat expansion

Acknowledgments

TC and JS conceived and designed the experiments. JC provided intellectual advice on the project and experimental design. YL prepared the samples. JZ and YP extracted the cp DNA and designed the primers for gap identification and performed the PCR. HX assembled the complete cp genome sequence. XL and ZH performed the genomic annotation and constructed circle map of N. sibirica cp genome. LY interpreted the data and developed the figures. LL wrote the paper. JZ reviewed the paper. All authors contributed to and approved the final manuscript.

Disclosure statement

The authors declare no conflict of interest.

Funding

This work was supported by National High Technology Research and Development Program of China (863 Program, 2013AA102705), National Science Foundation of China (No. 31270707), Qing Lan Project, Doctorate Fellowship Foundation of Nanjing Forestry University grant 163010107, 333 project of Jiangsu Province, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, and Priority Academic Program Development of Jiangsu Higher Education Institutions.