The Complete Chloroplast Genome of Ficus gasparriniana var. laceratifolia Reveals Discordance Between Morphology-Based Classification and Plastid Phylogeny

The complete chloroplast genome of Hedera helix (Araliaceae): comparative plastome analyses reveal divergence hotspots, selective constraints, and phylogenetic placement

Background Hedera helix: is an ecologically, horticulturally, and medicinally important member of Araliaceae. Although a genome sequence of this species has been reported, detailed chloroplast genome annotation and focused comparative plastome analysis of H. helix remain limited. This study aimed to assemble and annotate the complete chloroplast genome of H. helix and to evaluate its structural features, sequence variation, and phylogenetic position in a comparative family-level context. Methods Approximately 22 Gb of Illumina 150 bp paired-end data were generated for H. helix. The complete chloroplast genome was assembled de novo and annotated using standard plastome assembly and annotation pipelines. Comparative analyses included genome structure characterization, repeat and simple sequence repeat (SSR) detection, codon usage analysis, IR/SC boundary comparison, nucleotide diversity scanning, synteny assessment, and plastome-based phylogenetic reconstruction using representative Araliaceae taxa. Results The H. helix plastome is 156,688 bp in length and exhibits the typical quadripartite structure, comprising a large single-copy region of 86,626 bp, a small single-copy region of 18,180 bp, and two inverted repeats of 25,941 bp each, with an overall GC content of 37.99%. A total of 132 genes were annotated, including 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. Repeat analyses identified 54 long repeats and 47 SSRs, most of which were A/T-rich. Codon usage analysis revealed a preference for codons ending in A or T. Comparative analyses showed that plastome structure and gene order were highly conserved across sampled Araliaceae species, with only minor variation at IR/SC junctions. Most protein-coding genes had Ka/Ks ratios consistent with purifying selection, whereas nucleotide diversity analysis identified several localized divergence hotspots, particularly in ycf1. Phylogenomic analysis based on plastome data strongly supported H. helix as sister to (H. rhombea + H. nepalensis var. sinensis). Conclusion This study provides a complete and curated plastome resource for H. helix and shows that its chloroplast genome is structurally conserved relative to other sampled Araliaceae plastomes. The identified SSRs and highly variable regions, especially ycf1, represent potential candidates for future marker development. In addition, the plastome-based phylogenetic results provide useful evidence for evaluating the placement of Hedera within Araliaceae.

Complete chloroplast genome and phylogenetic analysis of Amorphophallus ochroleucus Hett. & V.D.Nguyen 2001 (Araceae)

Abstract Amorphophallus ochroleucus Hett. & V.D.Nguyen 2001, a perennial herbaceous plant in the genus Amorphophallus (Araceae family), is characterized by a tuberous root system, and is renowned for its unique pale-colored inflorescence and distinctive leaves. It is utilized as an ornamental plant in gardens and indoors. However, the genetic and phylogenetic relationships of this species remain largely unknown, leaving unanswered questions about its evolutionary trajectory. For the first time, this study presents the complete chloroplast genome of A. ochroleucus. The results demonstrate that the chloroplast genome spans 172,779 bp with an overall GC content of 35.15%, comprising a large single-copy (LSC) region of 92,449 bp, a small single-copy (SSC) region of 15,596 bp, and two inverted repeat (IR) regions each 32,367 bp in length. A total of 130 functional genes were annotated, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis revealed that all Amorphophallus species formed a highly supported monophyletic clade, with A. ochroleucus showing closer affinity to A. paeoniifolius and A. titanum. The chloroplast genomic data provide a valuable resource for future taxonomic and evolutionary studies in Amorphophallus.

Comparative plastome analyses of Lewinskya (Orthotrichaceae): insights into genome structure, molecular evolution, and phylogenetic relationships.

The newly assembled Lewinskya plastomes expand genomic resources for Orthotrichaceae and show that chloroplast genome evolution in the sampled species is structurally conservative but contains informative localized variation.

The first complete chloroplast genome of Calamus erectus (Arecaceae): Phylogenetic placement and divergence time estimation

Calamus erectus Roxb. is a medicinally important and vulnerable shrub native to Bangladesh. Despite its ecological and ethnobotanical importance, no complete chloroplast genome has been reported for this species. In this study, we characterized the complete plastome of C. erectus. The assembled plastome was 157,887 bp in length and exhibited a typical quadripartite circular structure, comprising a large single-copy (85,756 bp), a small single-copy (17,593 bp), and a pair of inverted repeats (27,269 bp each). The plastome encoded 131 genes, consisting of 86 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. Seventy simple sequence repeats were identified, mostly mononucleotides (49). A codon usage analysis exhibited a strong preference for codons ending in the adenine or uracil base, reflecting an overall A/T bias in the genome. Plastome-based phylogenetic analyses placed C. erectus within the monophyletic tribe Calameae and indicated a close relationship with C. exilis. A molecular dating analysis indicated that C. erectus diverged approximately 7.6 million years ago during the Tortonian age, while the subfamily Calamoideae originated about 46.2 million years ago in the early Miocene. These findings provide the first complete cp genome resource for C. erectus, offering a foundation for further phylogenomic and conservation studies within Arecaceae.

Comparative plastome analysis and plastomic phylogeny of Moraceae with expanded species-level sampling.

Phylogenetic reconstruction based on complete plastome sequences strongly supported the monophyly of all seven recognized tribes of Moraceae, recovered the non-monophyly of Streblus, and placed Maclura within Chlorophoreae, consistent with recent nuclear and plastid phylogenomic frameworks.

Comparative chloroplast genomics and phylogenomic insights into the genus Zehneria (Cucurbitaceae)