Sequencing, de novo assembly of Ludwigia plastomes, and comparative analysis within the Onagraceae family

The Onagraceae family, which belongs to the order Myrtales, consists of approximately 657 species and 17 genera. This family includes the genus Ludwigia  L., which is comprised of 82 species. In this study, we focused on the two aquatic invasive species Ludwigia grandiflora subsp. hexapetala ( Lgh ) and Ludwigia peploides subsp. montevidensis ( Lpm ) largely distributed in aquatic environments in North America and in Europe. Both species have been found to degrade major watersheds leading ecological and economical damages. Genomic resources for Onagraceae are limited, with only Ludwigia octovalvis (Lo) plastid genome available for the genus Ludwigia L. at the time of our study. This scarcity constrains phylogenetic, population genetics, and genomic studies. To brush up genomic ressources, new complete plastid genomes of Ludwigia grandiflora subps . hexapetala ( Lgh ) and Ludwigia peploides subsp.   montevidensis ( Lpm ) were generated using a combination of MiSeq (Illumina) and GridION (Oxford Nanopore) sequencing technologies. These plastomes were then compared to the published Ludwigia octovalvis ( Lo ) plastid genome, which was re-annotated by the authors. We initially sequenced and assembled the chloroplast (cp) genomes of Lpm and Lgh using a hybrid strategy combining short and long reads sequences. We observed the existence of two Lgh haplotypes and two potential Lpm haplotypes. Lgh , Lpm, and Lo plastomes were similar in terms of genome size (around 159 Kb), 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 , ycf2 and ccsA) were found under positive selection pressure, which is commonly associated with plant development, and especially in aquatic plants such as Lgh, and Lpm. Our hybrid sequencing approach revealed the presence of two Lgh plastome 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.