Sequencing, de novo assembly ofLudwigiaplastomes, and comparative analysis within the Onagraceae family

Abstract

AbstractThe Onagraceae family, which belongs to the order Myrtales, consists of approximately 657 species and 17 genera, including the genusLudwigiaL., which is comprised of 82 species. There are few genomic resources for Onagraceae, which limits phylogenetic and population genetics, as well as genomic studies. In this study, new complete plastid genomes ofLudwigia grandiflora subps. hexapetala(Lgh) andLudwigia peploides subsp montevidensis(Lpm) were generated using a combination of different sequencing technologies. These plastomes were then compared to the publishedLudwigia octovalvis(Lo) plastid genome, which was re-annotated by the authors. We initially sequenced and assembled the chloroplast (cp) genomes ofLpmandLghusing a hybrid strategy. We observed the existence of twoLghhaplotypes and two potentialLpmhaplotypes.Lgh,Lpm,andLoplastomes were similar in terms of genome size, gene number, structure, and inverted repeat (IR) boundaries, comparable to other species in the Myrtales order. A total of 45 to 65 SSRs (simple sequence repeats), were detected, depending on the species, with the majority consisting solely of A and T, which is common among angiosperms. Four chloroplast genes (matK,accD,ycf2andccsA)were found under positive selection pressure, which is commonly associated with plant development, and especially in aquatic plants such asLgh,andLpm.Our hybrid sequencing approach revealed the presence of twoLghplastome haplotypes which will help to advance phylogenetic and evolutionary studies, not only specifically for Ludwigia, but also the Onagraceae family and Myrtales order. To enhance the robustness of our findings, a larger dataset of chloroplast genomes would be beneficial.