Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.

Abstract

AbstractBackgroundThe genusAmaranthusL. consists of 70–80 species distributed across temperate and tropical regions of the world. Nine species are dioecious and native to North America; two of which are agronomically important weeds of row crops. The genus has been described as taxonomically challenging and relationships among species including the dioecious ones are poorly understood. In this study, we investigated the phylogenetic relationships among the dioecious amaranths and sought to gain insights into plastid tree incongruence. A total of 19Amaranthusspecies’ complete plastomes were analyzed. Among these, seven dioeciousAmaranthusplastomes were newly sequenced and assembled, an additional two were assembled from previously published short reads sequences and 10 other plastomes were obtained from a public repository (GenBank).ResultsComparative analysis of the dioeciousAmaranthusspecies’ plastomes revealed sizes ranged from 150,011 to 150,735 bp and consisted of 112 unique genes (78 protein-coding genes, 30 transfer RNAs and 4 ribosomal RNAs). Maximum likelihood trees, Bayesian inference trees and splits graphs support the monophyly of subgeneraAcnida(7 dioecious species) andAmaranthus; however, the relationship ofA. australisandA. cannabinusto the other dioecious species inAcnidacould not be established, as it appears a chloroplast capture occurred from the lineage leading to theAcnida + Amaranthusclades. Our results also revealed intraplastome conflict at some tree branches that were in some cases alleviated with the use of whole chloroplast genome alignment, indicating non-coding regions contribute valuable phylogenetic signals toward shallow relationship resolution. Furthermore, we report a very low evolutionary distance betweenA. palmeriandA. watsonii, indicating that these two species are more genetically related than previously reported.ConclusionsOur study provides valuable plastome resources as well as a framework for further evolutionary analyses of the entireAmaranthusgenus as more species are sequenced.