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Members of the aquatic plant genus Aponogeton are widely used commercially in aquariums because of their variable leaf shape and unique inflorescences. However, due to extensive similarity between species in this genus, morphological characters are generally inadequate for taxonomic classification. Currently, molecular makers available for taxonomic and phylogenetic studies of Aponogeton are limited. One approach to clarifying relationships between species in these complex groups is to use divergence hotspot regions within the genome. Here, we sequenced and analyzed the plastomes of five Aponogeton species collected from China, Zambia, and Kenya, and subsequently screened these plastomes for divergent DNA hotspots. The five plastomes are circular structures with sizes ranging from 154,167 bp to 154,860 bp. The Large and the Small Single Copies are separated by two Inverted Repeats. One hundred and thirteen unique genes were identified including 79 protein-coding, 30 tRNA, and four rRNA genes. We found that the most abundant repeats in all but one species were mononucleotide repeats (A/T) and that there were 23 potential RNA ending sites. Interestingly, a ~3 kb inversion, which includes the accD gene, was detected within the Asian species of Aponogeton . The inversion may be related to more frequent exchanges between this region and the nuclear genome. Furthermore, we detected mutational hotspot sites among the five Aponogeton species. Three of these hotspots are intergenic spacer regions ( accD-psaI , rbcL-accD and trnH-GUG-psbA ) that might be suitable for use as barcodes to resolve intra-generic relationships. We also identified four highly variable protein-coding genes ( ccsA , rpl22 , rps16 and ycf1 ) may be used as barcodes to resolve the higher-level phylogenies. Our study will provide valuable molecular resources for the taxonomic and phylogenomic study of the complex genus Aponogeton .

Background: Nelumbo nucifera Gaertn., a perennial aquatic macrophyte species, has been cultivated in several Asian countries for its economic importance, and medicinal uses. Two distinct ecotypes of the species are recognized based on the geographical location where the genotypes are adapted, i.e., tropical lotus and temperate lotus. The genetic diversity levels and differentiation of the tropical lotus from poorly studied geographic regions still remain unclear. Here, the population genetic diversity and structure of 15 tropical lotus populations sampled from the previous understudied natural distribution ranges, including India, Thailand, and Australia, were assessed using nine polymorphic SSR markers. Results: The SSR markers used to genotype the 216 individuals yielded 65 alleles. The highest and lowest genetic diversity estimates were found in Thailand and Indian populations, respectively. STRU CTU RE analysis revealed three distinct genetic clusters, with relatively low admixtures, supported by PCoA cluster analysis. Low levels of gene flow (mean N m = 0.346) among the three genetic clusters signified the Mantel test for isolation by distance, revealing the existence of a positive correlation between the genetic and geographic distances (r = 0.448, P = 0.004). Besides, AMOVA analysis revealed a higher variation among populations (59.98%) of the three groups. Overall, the populations used in this study exposed a high level of genetic differentiation (F ST = 0.596). Conclusions: The nine polymorphic microsatellite markers used in our study sufficiently differentiated the fifteen tropical N. nucifera populations based on geography. These populations presented different genetic variability, thereby confirming that populations found in each country are unique. The low genetic diversity (H E = 0.245) could be explained by limited gene flow and clonal propagation. Conserving the available diversity using various conservation approaches is essential to enable the continued utilization of this economically important crop species. We, therefore, propose that complementary conservation approaches ought to be introduced to conserve tropical lotus, depending on the genetic variations and threat levels in populations.

Many aquatic species have restricted dispersal capabilities, making them the most vulnerable organisms to climate change and land use change patterns. These factors deplete Nymphaea species’ suitable habitats, threatening their populations and survival. In addition, the species are poorly documented, which may indicate how scarce they are or will become. Members of Nymphaea are ecologically important as well as having cultural and economic value, making them of conservation interest. Therefore, using the maximum entropy (MaxEnt) approach, climatic variables, land use, and presence points were modeled for seven Nymphaea species in South America, using three general circulation models (CCSM4, HADGEM2-AO, and MIROC5) and in two representative concentration pathways (RCPs 4.5 and 8.5) and two scenarios (2050 and 2070). Our results indicated that mean diurnal range (bio2), precipitation of the wettest month (bio13), temperature seasonality (bio15), and land use (dom_lu) were the main influencing factors. For all species, suitable areas were concentrated east of Brazil, and they were variable in northern parts of the continent. Besides, inconsistent expansion and contraction of suitable habitats were noticed among the species. For example, N. amazonum, N. rudgeana, and N. lasiophylla future habitat expansions declined and habitat contraction increased, while for N. ampla and N. jamesoniana, both future habitat expansion and contraction increased, and for N. pulchella and N. rudgeana it varied in the RCPs. Moreover, the largest projected suitable habitats were projected outside protected areas, characterized by high human impacts, despite our analysis indicating no significant change between protected and unprotected areas in suitable habitat change. Finally, understanding how climate change and land use affect species distribution is critical to developing conservation measures for aquatic species.