Combining whole plastome and targeted loci data to resolve phylogenetic relationships of Baolia and Corispermoideae (Amaranthaceae s.l.) and exploring morphoanatomical character evolution

Abstract Background Baolia H.W.Kung & G.L.Chu is a monotypic genus only known in Diebu County, Gansu Province, China. Its systematic position is contradictory, and its morphoanatomical characters deviate from all other Chenopodiaceae. We therefore sequenced and compared the chloroplast genomes of this species, and resolved its phylogenetic position based on both chloroplast genomes and marker sequences. Results We sequenced 18 chloroplast genomes of 16 samples from two populations of Baolia bracteata and two Corispermumspecies. These genomes of Baoliaranged in size from 152,499 to 152,508 bp. We also identified between 85 and 87 simple sequence repeats (SSRs) in the chloroplast genomes of B. bracteata. These SSRs were primarily located in the LSC region, and most of them consisted of single-nucleotide A/T repeat sequences. Notably, there were differences in the types and numbers of SSRs between the two populations of B. bracteata. Our phylogenetic analysis, based on both complete chloroplast genomes from 33 species and a combination of three markers (ITS, rbcL, and matK) from 91 species, revealed that Baolia and Corispermoideae (Agriophyllum, Anthochlamys, and Corispermum) form a well-supported clade. This clade was found to be a sister group to Acroglochin. According to our molecular dating results, a major divergence event between Acroglochin, Baolia, and Corispermeae occurred during the Middle Eocene, approximately 46.29–42.12 mya. Conclusions Comparing the chloroplast genomes of B. bracteata with those of eleven typical Chenopodioideae and Corispermoideae species, we observed a high overall similarity and a one notable case of inversion of approximately 6,000 bp of DNA segments. We suggest that Corispermoideae should be considered in a broader sense, it includes Corispermeae (core Corispermoideae: Agriophyllum, Anthochlamys, and Corispermum), as well as two new monotypic tribes, Acroglochineae (Acroglochin) and Baolieae (Baolia). In this new circumscription, these three tribes are distantly related morphologically, but Baolieae and Corispermeae do share certain carpological traits.