The complete chloroplast DNA sequence of Trapa maximowiczii Korsh. (Trapaceae), and comparative analysis with other Myrtales species

Abstract

Trapaceae is an aquatic plant family widely distributed in and around Asia, Europe, and Africa. The fruits, while rich in starch and protein, also have edible and medicinal value. The first complete chloroplast genome in Trapaceae (Trapa maximowiczii Korsh.) has been determined. The genome size is 155,577bp, which includes two inverted repeats (IR) of 24,388bp, one large single copy (LSC) of 88,528bp, and one small single copy (SSC) of 18,273bp. The whole GC content is 36.4%. There are 111 genes in this genome, and 17 are duplicated in the IR. Fourteen genes have one intron, and rps12 and clpP have two introns. The SSR and repeat analysis revealed 61 SSRs, 22 repeat units, and 16 palindromic structures in this chloroplast genome. In a comparative analysis with five species, the detailed boundaries were compared between IR and LSC/SSC that are supposed to be closely related to T. maximowiczii and Lagerstroemia fauriei; gene infA has been lost only in T. maximowiczii and L. fauriei. The mVISTA analysis revealed several variable regions in the Myrtales genome including loci ycf1, ycf2, accD and rpl32-trnL, which can be useful in phylogenetic studies. The phylogenetic position of T. maximowiczii in the whole genome, LSC, SSC, and IR regions has been confirmed using 8 taxa from Myrtales, which is in agreement with other reports that place T. maximowiczii in the same clade as that of Lythraceae. These data represent valuable genetic resources for future research on Trapa population genetics.