Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Eragrostideae (Chloridoideae, Poaceae)

Eragrostideae Stapf, the second-largest tribe in Chloridoideae (Poaceae), is a taxonomically complex tribe. In this study, chloroplast genomes of 13 Eragrostideae species were newly sequenced and used to resolve the phylogenetic relationships within Eragrostideae. Including seven reported chloroplast genomes from Eragrostideae, the genome structure, number and type of genes, codon usage, and repeat sequences of 20 Eragrostideae species were analyzed. The length of these chloroplast genomes varied from 130,773 bp to 135,322 bp. These chloroplast genomes showed a typical quadripartite structure, including a large single-copy region (77,993–80,643 bp), a small single-copy region (12,410–12,668 bp), and a pair of inverted repeats region (19,394–21,074 bp). There were, in total, 129–133 genes annotated in the genome, including 83–87 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Forward and palindromic repeats were the most common repeat types. In total, 10 hypervariable regions (rpl22, rpoA, ndhF, matK, trnG–UCC-trnT–GGU, ndhF–rpl32, ycf4–cemA, rpl32–trnL–UAG, trnG–GCC–trnfM–CAU, and ccsA–ndhD) were found, which can be used as candidate molecular markers for Eragrostideae. Phylogenomic studies concluded that Enneapogon diverged first, and Eragrostis including Harpachne is the sister to Uniola. Furthermore, Harpachne harpachnoides is considered as a species of Eragrostis based on morphological and molecular evidence. In addition, the interspecies relationships within Eragrostis are resolved based on complete chloroplast genomes. This study provides useful chloroplast genomic information for further phylogenetic analysis of Eragrostideae.