{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T06:04:40Z","timestamp":1789538680594,"version":"build-2803163510"},"reference-count":72,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>\n                      The genus\n                      <jats:italic>Indigofera<\/jats:italic>\n                      is broadly distributed across tropical and subtropical regions and displays high morphological diversity, yet its phylogenetic relationships remain poorly resolved. This study aimed to characterize the complete chloroplast genome of\n                      <jats:italic>Indigofera<\/jats:italic>\n                      argentea from Saudi Arabia and evaluate its comparative genomic and phylogenetic relationships with other\n                      <jats:italic>Indigofera<\/jats:italic>\n                      species.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      The complete chloroplast genome of\n                      <jats:italic>I. argentea<\/jats:italic>\n                      was characterized and compared with seven publicly available\n                      <jats:italic>Indigofera<\/jats:italic>\n                      plastomes. Comparative analyses included genome structure, gene content and organization, GC content, IR boundary variation, codon usage, simple sequence repeats (SSRs), nucleotide diversity, single nucleotide polymorphisms (SNPs), selection pressure, and phylogenetic relationships.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The\n                      <jats:italic>I. argentea<\/jats:italic>\n                      chloroplast genome is 158,639 bp, exhibiting the typical quadripartite structure and encoding 128 genes (83 protein-coding, 37 tRNA, and 8 rRNA genes), with an overall GC content of 35.9%. Comparative analyses revealed strong structural conservation among\n                      <jats:italic>Indigofera<\/jats:italic>\n                      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,\n                      <jats:italic>trn<\/jats:italic>\n                      K-\n                      <jats:italic>rbc<\/jats:italic>\n                      L,\n                      <jats:italic>trn<\/jats:italic>\n                      L-\n                      <jats:italic>rps<\/jats:italic>\n                      4,\n                      <jats:italic>ndh<\/jats:italic>\n                      F-\n                      <jats:italic>trn<\/jats:italic>\n                      L, and\n                      <jats:italic>ycf<\/jats:italic>\n                      1, exhibited elevated nucleotide diversity, and a total of 2,059 SNPs were detected, largely concentrated at the third codon position, with\n                      <jats:italic>ycf<\/jats:italic>\n                      1,\n                      <jats:italic>rpo<\/jats:italic>\n                      C2, and\n                      <jats:italic>ndh<\/jats:italic>\n                      F showing the highest levels of variation. Most protein-coding genes were under strong purifying selection, although 13 genes exhibited signs of positive selection, with\n                      <jats:italic>ycf<\/jats:italic>\n                      1,\n                      <jats:italic>rps<\/jats:italic>\n                      18, and\n                      <jats:italic>rps<\/jats:italic>\n                      19 showing the strongest signals. Phylogenetic analyses resolved\n                      <jats:italic>Indigofera<\/jats:italic>\n                      as a strongly supported monophyletic group, identifying four distinct clades and supporting the use of complete plastomes for resolving relationships within the genus.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>\n                      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\n                      <jats:italic>Indigofera<\/jats:italic>\n                      and highlights informative genomic regions for future comparative and phylogenetic investigations.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fpls.2026.1917737","type":"journal-article","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T05:31:20Z","timestamp":1789536680000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["The complete chloroplast genome of Indigofera argentea from Saudi Arabia: comparative genomic analysis within the genus Indigofera"],"prefix":"10.3389","volume":"17","author":[{"given":"Rana M.","family":"Alshegaihi","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, College of Science, University of Jeddah","place":["Jeddah, Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,16]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.3390\/economies10020049","article-title":"The development of Indigofera spp. as a source of natural dyes to increase community incomes on Timor Island, Indonesia","volume":"10","author":"Agustarini","year":"2022","journal-title":"Economies"},{"key":"B2","doi-asserted-by":"publisher","first-page":"702","DOI":"10.3923\/pjbs.1999.702.711","article-title":"A phytogeographical analysis of the floristic elements in Saudi Arabia","volume":"2","author":"Alfarhan","year":"1999","journal-title":"Pakistan J. 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