Characterization of Verbesina encelioides (Asteroideae, Asteraceae) Chloroplast Genome and Phylogenetic Insights.

Verbesina encelioides (Cav.) Benth. & Hook.f. ex A.Gray (Asteroideae, Asteraceae) is a widespread annual herb native to southwestern North America that has naturalized globally. Here, we report the first de novo assembly and comprehensive annotation of the complete chloroplast (cp) genome of V. encelioides, generated using Illumina NovaSeq sequencing. The circular genome is 152,213 bp and exhibits the characteristic quadripartite structure, comprising a large single-copy (83,911 bp) region, a small single-copy (18,248 bp) region, and two inverted repeat regions (25,027 bp each). The genome encodes 112 unique genes, including 79 protein-coding genes, 29 tRNAs, and four rRNAs, with 16 genes duplicated in the IRs. Comparative analysis with Verbesina alternifolia revealed high structural conservation regarding gene content and arrangement, codon usage, amino acid frequency, and simple sequence repeats. Codon usage showed bias toward A/T-ending codons (RSCU > 1), whereas leucine was the most abundant amino acid, and cysteine was the least frequent. Simple sequence repeat analysis predominantly identified A/T-rich mononucleotide repeats. Nucleotide diversity analysis highlighted several variable regions-including trnD-trnY, atpA-trnR, rpl32-trnL, ccsA-ndhD, and trnL-ccsA-which may serve as molecular markers. Analysis of adaptive evolution in Verbesina species and related genera identified codons under positive selection in 19 chloroplast genes: atpB, ccsA, clpP, ndhD, ndhI, psaB, psbB, rpl14, rpoB, rpoC1, rps8, ycf3, accD, matK, rbcL, ndhF, rpoC2, ycf2, and ycf1. Maximum likelihood phylogenetic analysis placed Verbesina within the tribe Heliantheae. This complete cp genome provides a valuable genetic resource for phylogenetic studies, DNA barcoding, and population genetics of Verbesina and related Asteraceae taxa.