Comparative analysis of the complete chloroplast genome of seven Nymphaea species

Abstract

Background: 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. However, there are few studies on the cp genomes of Nymphaea, and the data of their genomes are very scarce. 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.Results: A total of 126–129 genes were annotated in seven Nymphaea species, including 81–84 protein coding genes, eight rRNA, and 37 tRNA genes. 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. The codons preferentially ended with A/U. The cp genomes of seven Nymphaea species contained 147–168 dispersed repeats with a length of 15–19 bp and 979 simple sequence repeats (SSRs). Using N. colorata as the reference sequence, a total of 8,328 single nucleotide polymorphisms (SNPs) and 1,579 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 is relatively high; related regions can be used as potential molecular markers for population genetics research. KaKs analysis showed that the ycf2 gene was positively selected. The results of the phylogenetic analysis showed that the genus Nymphaea can be divided into five branches: subgenus Nymphaea, subgenus Hydrocallis, subgenus Lotos, subgenus Anecphya, and subgenus Brachyceras. Conclusions: The cp genome of Nymphaea is very conservative in structure and composition, but it has rich variation in LSC and SSC regions. The phylogenetic analysis showed that Nymphaea could be further divided into five subgenera, and Euryale and Victoria were most closely related to Nymphaea. This study provided insight on the structure and composition of the cp genome of Nymphaea. Moreover, our results have provided more sequence information and genome resources for follow-up studies on Nymphaea.

Gene coexpression analysis reveals key pathways and hub genes related to late-acting self-incompatibility in Camellia oleifera

“…Our results suggested that the low expression of RALF, UTG and G-type lecRLK in self-pollination treatments was one of the main reasons why pollen tubes stopped growing and failed to fertilize. Cytochrome P450 has wide-range catalytic activity and is involved in the synthesis and metabolism of sterols, terpenoids, fatty acids, alkaloids, isoflavones, flavonoids and plant hormones (Sun et al, 2019). In our study, three cytochrome P450 87A3-like genes (CYPs) were identified as candidate hub genes selected by WGCNA, and the expression of CYPs in cross-pollination was significantly higher than that in self-pollination.…”

“…and Theobroma cacao, in which the pollen tube can grow successfully in the styles, but the inhibition occurs either prezygotically or postzygotically (Hao et al, 2012). Many studies have been performed to identify the key factors involved in the LSI response, but the mechanism remains unclear (Chen et al, 2012;Sun et al, 2019). The genetic basis of LSI was hypothesized to be gametophytic under genetic control (Zhou and Zheng, 2015;Zhang et al, 2016).…”

Plastome evolution and phylogeny of the tribe Ruteae (Rutaceae)

“…GC content is an important genomic and systematic character that describes the nucleotide proportions in the genome. When GC content in the genome is greater, it has a greater density of DNA bases, making the sequence more stable and difficult to mutate (Sun et al, 2021). The overall GC content of the eight plastomes varied from 38.3% to 39.1% (Table 1) and was clearly lower than the AT content.…”

Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution

“…The genome of cp is generally maternal inheritance; there is no problem of gene recombination ( Li et al., 2014 ; Zhao et al., 2015 ). In recent years, the cp genome has been mainly used in phylogenetic, population genetics, and phylogeography studies ( Wang et al., 2022b ), in which plant phylogenetic analysis is the most basic cp genome analysis, which has been widely used in the phylogenetic study of the plant kingdom or one of the groups and to identify the relationships of angiosperm order, family, genus, interspecies, and intraspecies ( Sun et al., 2020 ; Guo et al., 2021 ; Li et al., 2021 ; Xie et al., 2021 ; Liu et al., 2022 ; Raman et al., 2022 ; Wang et al., 2022a ). The cp genome has unique advantages in plant phylogenetic studies.…”