Chloroplast Genomes of <i>Croton alabamensis</i> and <i>Croton bonplandianus</i> (Euphorbiaceae): Comparative Analysis With Related <i>Croton</i> Species

ABSTRACT Croton L. (Crotonoideae, Euphorbiaceae) is one of the largest angiosperm genera, comprising more than 1100 species with a pantropical distribution; however, the chloroplast (cp) genomes of a few species have been reported. In this study, the complete cp genome of Croton bonplandianus Baill. was newly sequenced, and the cp genome of Croton alabamensis E.A.Sm. ex Chapm. was assembled from publicly available data. These genomes were analyzed together with seven previously published Croton cp genomes to investigate structural variation, inverted repeat (IR) boundary dynamics, and phylogenetic relationships. The nine cp genomes exhibited substantial size variation (150,021–177,025 bp), driven primarily by pronounced differences in IR length (10,100–36,116 bp). Six distinct IR boundary configurations were identified, with IR expansion occurring predominantly at the expense of the large single‐copy (LSC) region rather than the small single‐copy (SSC) region. Phylogenomic analysis based on 78 shared protein‐coding genes supported the monophyly of nine Croton species and placed C. alabamensis and C. bonplandianus as successive early‐diverging lineages among the nine sampled species. Comparative analyses further identified 10 highly polymorphic cp genes as candidate molecular markers for phylogenetic and population‐level studies in the nine species examined, though their utility will require validation before application to additional species. Among the nine studied species, IR contraction and expansion in Croton were largely species‐specific and showed limited phylogenetic conservation. IR boundary shifts at cp genome junctions involved predominantly the LSC region, contrasting with the SSC‐driven patterns commonly reported in other angiosperm lineages; however, broader taxon sampling is needed to determine whether this reflects a genus‐wide pattern or is an artifact of limited sampling.