Table 1_The complete chloroplast genome of Indigofera argentea from Saudi Arabia: comparative genomic analysis within the genus Indigofera.xlsx

Comparative analyses revealed strong structural conservation among Indigofera plastomes in gene content, gene order, GC content, and IR boundary organization, although minor variations were detected at the LSC, IR, and SSC junctions, which did not affect overall genome structure. Codon usage showed a bias toward A/U-ending codons, consistent with the AT-rich genome composition, and RSCU values varied among genomic regions.

Repeat analysis identified 725 SSRs, predominantly located in the LSC region. Four mutation hotspot regions, trnK-rbcL, trnL-rps4, ndhF-trnL, and ycf1, exhibited elevated nucleotide diversity, and a total of 2,059 SNPs were detected, largely concentrated at the third codon position, with ycf1, rpoC2, and ndhF showing the highest levels of variation. Most protein-coding genes were under strong purifying selection, although 13 genes exhibited signs of positive selection, with ycf1, rps18, and rps19 showing the strongest signals.

Phylogenetic analyses resolved Indigofera as a strongly supported monophyletic group, identifying four distinct clades and supporting the use of complete plastomes for resolving relationships within the genus.</p>Discussion<p>The conserved plastome structure, together with the identified mutation hotspots, SNPs, and genes showing signals of positive selection, provides valuable insights into plastome evolution and lineage diversification within Indigofera and highlights informative genomic regions for future comparative and phylogenetic investigations.</p>