Hydrocotyle, 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 Hydrocotyle need to be further investigated. In this study, we newly sequenced and assembled 13 whole plastid genomes of Hydrocotyle and performed comparative plastid genomic analyses with four previously published Hydrocotyle plastomes and phylogenomic analyses within Araliaceae. The plastid genomes of Hydrocotyle 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 Hydrocotyle 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) (ycf3-trnS, trnS-rps4, petA-psbJ, and ndhF-rpl32) and two coding genes (rpl16 and ycf1). Three protein-coding genes (atpE, rpl16, and ycf2) 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 Hydrocotyle from Apiaceae to Araliaceae, and topologies with a high resolution indicated that plastome data can be further used in the comprehensive phylogenetic research of Hydrocotyle. The diagnostic characteristics currently used in Hydrocotyle 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.

Tropidia, a type genus of Tropidieae (Orchidaceae, Epidendroideae), represents an important lineage for investigating plastome evolution and phylogenetic relationships within Epidendroideae. Despite its importance, the lack of available plastid genomic data has hindered comprehensive analyses of its genome structure and phylogenetic relationships. In this study, we assembled and characterized the complete plastid genomes of Tropidia angulosa and T. nipponica, providing valuable insights into plastome evolution and phylogenetic placement of Tropidieae. The plastomes of T. angulosa and T. nipponica exhibited a highly conserved quadripartite structure, sharing similar genomic size (161,395 bp and 160,801 bp) and GC content (36.87% and 36.90%). Both plastomes contained identical gene content and gene order, with 79 protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes. A total of 169 simple-sequence repeats (SSRs) and 92 long-sequence repeats (LSRs) were identified, most of which were distributed in large single-copy (63.91% and 66.30%) and non-coding regions (83.43% and 65.22%). Comparative plastomes analyses revealed the overall structural stability among photosynthetic lineages, whereas structural variation was primarily detected in mycoheterotrophic lineages. Phylogenomic reconstruction based on plastid-coding sequences revealed that Tropidieae occupies a relatively isolated phylogenetic position within Epidendroideae. These findings contribute to a more comprehensive understanding of plastome evolution and the phylogenetic framework of Epidendroideae.