Wagutu, G. K. | bioRxiv Science

bioRxiv2021

Comparative analyses and phylogenetic relationships of 15 Trapa (Trapaceae) species based on Complete Chloroplast Genomes

Trapa L. is floating-leaved aquatic plants with important economic and ecological values. However, species identification and phylogenetic relationship are still unresolved for Trapa. In this study, complete chloroplast genomes of 13 Trapa species/taxa were sequenced and annotated. Combined with released sequences of the other two species, comparative analysis of cp genomes was first performed on the 15 Trapa species/taxa. The 15 cp genomes exhibited quadripartite structures with medium size of 155, 453-155, 559 bp. IR/SC junctions were conservative with no obvious change found. Long repetitive repeats and SSRs were mostly detected in the intergenic and LSC regions, providing useful plastid markers for species and relationship identification. Three phylogenetic analyses (MP, ML and BI) consistently showed two clusters within Trapa, including large- and small-seed species/taxa, respectively. This study provided the baseline information for phylogeography of Trapa, which would facilitate the management and utilization of genetic resources of the genus.

genomics↗

bioRxiv2020

Influence of isolation by environment and landscape heterogeneity on genetic structure of wild rice Zizania latifolia along a latitudinal gradient

Global aquatic habitats are undergoing rapid degradation and fragmentation as a result of land-use change and climate change. Understanding the genetic variability and adaptive potential of aquatic plant species is thus important for conservation purposes. In this study, we investigated the role of environment, landscape heterogeneity and geographical distance in shaping the genetic structure of 28 natural populations of Zizania latifolia (Griseb.) Turcz. Ex Stapf in China based on 25 microsatellite markers. Genetic structure was investigated by analysis of molecular variance (AMOVA), estimation of FST, Bayesian clustering and Thermodynamic Integration (TI) methods. Isolation by environment (IBE), isolation by resistance (IBR) and isolation by distance (IBD) hypotheses were compared using a reciprocal causal model (RCM). Further, generalized linear models and spatially explicit mixed models, by using geographic, landscape and genetic variables, were developed to elucidate the role of environment in driving Z. latifolia genetic diversity. The genetic differentiation across all populations was high: FST = 0.579; Opt = 0.578. RCM exclusively supported IBE in shaping genetic structuring, only partial support for IBR, but not for IBD. Maximum temperature of the warmest month and precipitation seasonality were the plausible parameters responsible for genetic diversity. After controlling for spatial effect and landscape complexity, precipitation seasonality was significantly associated with genetic diversity. Based on these findings, genetic structure of Z. latifolia across China seem to be as a result of local adaptation. Environmental gradient and topographical barriers, rather than geographical isolation, influence genetic differentiation of aquatic species across China resulting in instances of local adaptation.

ecology↗