Analysis of the ycf1 Gene within the Fabaceae (Leguminosae) Family

Fabaceae (Leguminosae) is one of the largest angiosperm families and includes many ecologically and economically important crops and wild species. However, the family’s rapid radiations and plastome structural rearrangements can complicate phylogenetic inference when only a small number of traditional plastid markers are used. Here, we evaluate the chloroplast ycf1 locus as a source of phylogenetic signal and sequence diversity across 146 Fabaceae plastomes. Whole chloroplast genomes and the extracted ycf1 region were aligned, and phylogenetic trees were reconstructed for comparative purposes, with the ycf1 topology inferred using a filtered Maximum Likelihood framework to reduce artifacts from highly incomplete sequences. In addition, descriptive diversity statistics (GC content 28.5%, overall similarity 51.9%, Shannon information index 0.23, and Nei’s gene diversity He = 0.29) were calculated for the ycf1 dataset, and codon-based dN/dS analyses were performed to quantify selective constraint. The results show that ycf1 contains both highly conserved segments and strongly variable domains, consistent with predominant purifying selection across the gene and localized codons exhibiting evidence consistent with diversifying selection. The ycf1-only maximum-likelihood (ML) tree retained reduced support for a subset of short internal nodes, indicating that ycf1 is most informative as a complementary marker rather than a stand-alone locus for family-wide resolution. Together, these analyses highlight ycf1 as a useful locus for Fabaceae comparative studies, especially when integrated with genome-scale or multi-locus phylogenetic frameworks.