Complete Plastid Genome Sequencing of Eight Species from <i>Hansenia</i>, <i>Haplosphaera</i> and <i>Sinodielsia</i> (Apiaceae): Comparative Analyses and Phylogenetic Implications

<i>Hansenia</i> Turcz., <i>Haplosphaera</i> Hand.-Mazz. and <i>Sinodielsia</i> H.Wolff are three Apiaceae genera endemic to the Hengduan Mountains and the Himalayas, which usually inhabit elevations greater than 2000 m. The phylogenetic relationships between and within the genera were uncertain, especially the placement of <i>Hap. himalayensis</i> and <i>S. microloba</i>. Therefore, we aimed to conduct comparative (simple sequence repeat (SSR) structure, codon usage bias, nucleotide diversity (Pi) and inverted repeat (IR) boundaries) and phylogenetic analyses of <i>Hansenia</i>, <i>Haplosphaera</i> and <i>Sinodielsia</i> (also compared with <i>Chamaesium</i> and <i>Bupleurum</i>) to reduce uncertainties in intergeneric and interspecific relationships. We newly assembled eight plastid genomes from <i>Hansenia</i>, <i>Haplosphaera</i> and <i>Sinodielsia</i> species, and analyzed them with two plastid genomes from GenBank of <i>Hap. phaea,</i><i>S. yunnanensis</i>. Phylogenetic analyses used these ten genomes and another 22 plastid genome sequences of Apiaceae. We found that the newly assembled eight genomes ranged from 155,435 bp to 157,797 bp in length and all had a typical quadripartite structure. Fifty-five to 75 SSRs were found in <i>Hansenia</i>, <i>Haplosphaera</i> and <i>Sinodielsia</i> species, and the most abundant SSR was mononucleotide, which accounted for 58.47% of <i>Hansenia</i>, 60.21% of <i>Haplosphaera</i> and 48.01% of <i>Sinodielsia.</i> There was no evident divergence of codon usage frequency between the three genera, where codons ranged from 21,134 to 21,254. The Pi analysis showed that <i>trnE(UUC)-trnT(GGU)</i>, <i>trnH(GUG)-psbA</i> and <i>trnE(UUC)-trnT(GGU)</i> spacer regions had the highest Pi values in the plastid genomes of <i>Hansenia</i> (0.01889), <i>Haplosphaera</i> (0.04333) and <i>Sinodielsia</i> (0.01222), respectively. The <i>ndhG-ndhI</i> spacer regions were found in all three genera to have higher diversity values (Pi values: 0.01028–0.2), and thus may provide potential DNA barcodes in phylogenetic analysis. IR boundary analysis showed that the length of <i>rps19</i> and <i>ycf1</i> genes entering IRs were usually stable in the same genus. Our phylogenetic tree demonstrated that <i>Hap. himalayensis</i> is sister to <i>Han. weberbaueriana</i>; meanwhile, <i>Haplosphaera</i> and <i>Hansenia</i> are nested together in the East Asia clade, and <i>S. microloba</i> is nested within individuals of <i>S. yunnanensis</i> in the <i>Acronema</i> clade. This study will enrich the complete plastid genome dataset of the Apiaceae genera and has provided a new insight into phylogeny reconstruction using complete plastid genomes of <i>Hansenia</i>, <i>Haplosphaera</i> and <i>Sinodielsia</i>.