Genomic profiling of dioecious Amaranthus species provides novel insights into species relatedness and sex genes

Abstract

AbstractBackgroundAmaranthusL. is a diverse genus consisting of domesticated, weedy, and non-invasive species distributed around the world. Nine species are dioecious, of whichAmaranthus palmeriS. Watson andAmaranthus tuberculatus(Moq.) J.D. Sauer are troublesome weeds of agronomic crops in the USA and elsewhere. Shallow relationships among the dioeciousAmaranthusspecies and the conservation of candidate genes within previously identifiedA. palmeriandA. tuberculatusmale-specific regions of the Y (MSYs) in other dioecious species are poorly understood. In this study, seven genomes of dioecious amaranths were obtained by paired-end short-read sequencing and combined with short reads of seventeen species in the family Amaranthaceae from NCBI database. The species were phylogenomically analyzed to understand their relatedness. Genome characteristics for the dioecious species were evaluated and coverage analysis was used to investigate the conservation of sequences within the MSY regions.ResultsWe provide genome size, heterozygosity, and ploidy level inference for seven newly sequenced dioeciousAmaranthusspecies and two additional dioecious species from the NCBI database. We report a pattern of transposable element proliferation in the species, in which seven species had moreTy3elements thancopiaelements whileA. palmeriandA. watsoniihad morecopiaelements thanTy3elements, similar to the TE pattern in some monoecious amaranths. Using a Mash-based phylogenomic analysis, we accurately recovered taxonomic relationships among the dioeciousAmaranthusspecies that were previously identified based on comparative morphology. Coverage analysis revealed eleven candidate gene models within theA. palmeriMSY region with male-enriched coverages, as well as regions on scaffold 19 with female-enriched coverage, based onA. watsoniiread alignments. A previously reportedFLOWERING LOCUS T(FT) withinA. tuberculatusMSY contig was also found to exhibit male-enriched coverages for three species closely related toA. tuberculatusbut not forA. watsoniireads. Additional characterization of theA. palmeriMSY region revealed that 78% of the region is made of repetitive elements, typical of a sex determination region with reduced recombination.ConclusionsThe results of this study further increase our understanding of the relationships among the dioecious species of theAmaranthusgenus as well as revealed genes with potential roles in sex function in the species.