Comparative analysis of the complete chloroplast genome of seven Nymphaea species

Abstract Although there has been a long history of cultivation and research on Nymphaea, the taxonomic relationships and evolutionary relationships among Nymphaea species remain controversial. The chloroplast (cp) genome can provide a new method to determine species origin, evolution, and phylogenetic relationships of Nymphaea. The complete cp genomes of seven Nymphaea species were sequenced by high-throughput sequencing technology, and the structural characteristics and phylogenetic relationships of cp genomes were analyzed. The cp genomes of seven species of Nymphaea had rich variation in large single-copy (LSC) and small single-copy (SSC) regions. A comparative cp genomic analysis of seven Nymphaea species showed that the cp gene sequence of Nymphaea was consistent, with no signs of reverse rearrangement. Using N. colorata as the reference sequence, a total of 8328 single nucleotide polymorphisms (SNPs) and 1579 insertions/deletions were obtained. The degree of variation of the cp genome of the seven Nymphaea species in rpoA–rpl20, rbcL–ndhC, ndhD–ndhF, and trnN-GUU–ndhA regions was relatively high. The ycf2 gene was positively selected. The phylogenetic analysis showed that the genus Nymphaea can be further divided into five subgenera.