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<i>Hydrocotyle</i>, belonging to the Hydrocotyloideae of Araliaceae, consists of 95 perennial and 35 annual species. Due to the lack of stable diagnostic morphological characteristics and high-resolution molecular markers, the phylogenetic relationships of <i>Hydrocotyle</i> need to be further investigated. In this study, we newly sequenced and assembled 13 whole plastid genomes of <i>Hydrocotyle</i> and performed comparative plastid genomic analyses with four previously published <i>Hydrocotyle</i> plastomes and phylogenomic analyses within Araliaceae. The plastid genomes of <i>Hydrocotyle</i> exhibited typical quadripartite structures with lengths from 152,659 bp to 153,669 bp, comprising a large single-copy (LSC) region (83,958–84,792 bp), a small single-copy (SSC) region (18,585–18,768 bp), and a pair of inverted repeats (IRs) (25,058–25,145 bp). Each plastome encoded 113 unique genes, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Comparative analyses showed that the IR boundaries of <i>Hydrocotyle</i> plastomes were highly similar, and the coding and IR regions exhibited more conserved than non-coding and single-copy (SC) regions. A total of 2932 simple sequence repeats and 520 long sequence repeats were identified, with specificity in the number and distribution of repeat sequences. Six hypervariable regions were screened from the SC region, including four intergenic spacers (IGS) (<i>ycf3-trnS</i>, <i>trnS-rps4</i>, <i>petA-psbJ</i>, and <i>ndhF-rpl32</i>) and two coding genes (<i>rpl16</i> and <i>ycf1</i>). Three protein-coding genes (<i>atpE</i>, <i>rpl16</i>, and <i>ycf2</i>) were subjected to positive selection only in a few species, implying that most protein-coding genes were relatively conserved during the plastid evolutionary process. Plastid phylogenomic analyses supported the treatment of <i>Hydrocotyle</i> from Apiaceae to Araliaceae, and topologies with a high resolution indicated that plastome data can be further used in the comprehensive phylogenetic research of <i>Hydrocotyle</i>. The diagnostic characteristics currently used in <i>Hydrocotyle</i> may not accurately reflect the phylogenetic relationships of this genus, and new taxonomic characteristics may need to be evaluated and selected in combination with more comprehensive molecular phylogenetic results.