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

<p><i>Nitraria sibirica</i> is a halophyte and belongs to the family Nitrariaceae. The chloroplast genome of <i>Nitraria sibirica</i> (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 <i>Nitraria sibirica</i> belongs to the Sapindales clade. We also found that the inverted repeat expansion resulted in a duplication of <i>rps19</i> in <i>Nitraria sibirica</i> when comparing its chloroplast genome structure with <i>Theobroma cacao</i>, <i>Vitis vinifera</i>, <i>Eucalyptus erythrocorys</i> and <i>Arabidopsis thaliana</i>. The duplication of <i>rps19</i> gene was consistent with that in <i>Zanthoxylum piperitum</i>, <i>Azadirachta indica</i>, <i>Sapindus mukorossi</i> and <i>Citrus sinensis</i>, all of which belong to the order Sapindales, but different from most Rosids plants. In summary, the analyses of <i>Nitraria sibirica</i> 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.</p>