AUTHOR=Li Qin-Qin , Zhang Zhi-Ping , Aogan  , Wen Jun 

TITLE=Comparative chloroplast genomes of Argentina species: genome evolution and phylogenomic implications

JOURNAL=Frontiers in Plant Science

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1349358

DOI=10.3389/fpls.2024.1349358

ISSN=1664-462X

ABSTRACT=<p>The genus <italic>Argentina</italic> Hill belongs to the tribe Potentilleae Sweet and contains approximately 75 species predominantly distributed in the Sino-Himalayan region and the Malesian archipelago. So far we have less knowledge on the phylogenetic relationships within <italic>Argentina</italic> owing to limited sampling of <italic>Argentina</italic> taxa or gene fragments in previous studies. Moreover, to date there is no phylogenetic study on <italic>Argentina</italic> from the perspective of comparative chloroplast (cp) genomics. Here we performed comparative genomic analyses on the cp genomes of 39 accessions representing 18 taxa of <italic>Argentina</italic>. The <italic>Argentina</italic> cp genomes presented the typical quadripartite structure, with the sizes ranging from 155 096 bp to 157 166 bp. The 39 <italic>Argentina</italic> cp genomes contained a set of 112 unique genes, comprising four ribosomal RNA (rRNA) genes, 30 transfer RNA (tRNA) genes, as well as 78 protein-coding genes (PCGs). The cp genome organization, gene content and order in <italic>Argentina</italic> were highly conserved, but some visible divergences were present in IR/SC boundary regions. Ten regions (<italic>trnH-GUG-psbA, trnG-GCC-trnfM-CAU, trnD-GUC-trnY-GUA, rpl32-trnL-UAG, atpH-atpI, rps16-trnQ-UUG, trnS-GCU-trnG-UCC, ndhF-rpl32, trnR-UCU-atpA, and accD-psaI</italic>) were identified as excellent candidate DNA markers for future studies on species identification, population genetics and phylogeny of <italic>Argentina</italic>. Our results indicated that <italic>Argentina</italic> is monophyletic. In the current sampling, the <italic>A. smithiana</italic> - <italic>A. anserina</italic> clade was sister to the remainder of <italic>Argentina</italic>. Our results corroborated the previous taxonomic treatments to transfer <italic>A. phanerophlebia</italic> and <italic>A. micropetala</italic> from the genus <italic>Sibbaldia</italic> L. to <italic>Argentina</italic>. Our results showed close relationships among <italic>A. stenophylla</italic>, <italic>A. microphylla</italic>, <italic>A. taliensis</italic>, and <italic>A. tatsienluensis</italic>, congruent with previous studies based on the morphology of these species. Twenty-six genes (<italic>rps3, rps15, rps16, rps19, rpl16, rpl20, rpl22, rpoA, rpoB, rpoC1, rpoC2, atpA, atpF, psbB, psbF, ndhA, ndhB, ndhC, ndhD, ndhF, rbcL, accD, ccsA, matK, ycf1, ycf2</italic>) were with sites under positive selection, and adaptive evolution of these genes might have played crucial roles in <italic>Argentina</italic> species adaptation to the harsh mountain environment. This study will facilitate future work on taxonomy, phylogenetics, and adaptive evolution of <italic>Argentina</italic>.</p>