Comparative analysis of chloroplast genomes in 48 samples from 5 species and 2 varieties of Agropyron Gaertn. (Poaceae, Triticeae)

Background Agropyron belongs to Triticeae of the Poaceae family. Its plants are rich in nutrients and have good palatability. They are important forage grasses in the temperate zone of the Northern Hemisphere. Accurate identification of Agropyron germplasm resources is the basic guarantee for breeding. However, the morphological variation of Agropyron is complex, making identification based on traditional morphological characteristics difficult. Molecular markers are an effective tool for rapid and accurate identification of many forage plants. Therefore, this study conducted second-generation high-throughput sequencing, chloroplast genome assembly, chloroplast genome comparison, and phylogenetic analysis on 48 Agropyron samples of 5 species and 2 varieties. Results The chloroplast genome was assembled and annotated based on next-generation sequencing reads. Analysis of repetitive sequences, codon usage bias, boundary variation, and nucleotide diversity indicates that the chloroplast genome of Agropyron is highly conserved: the total length was 135,321–135,564 bp, the GC content was stable at 38%, and the gene composition was consistent (132 genes). The study found that the simple repeat sequence (SSR) was mainly A/T type (21–28), and the direct repeat dominated in the long repeat sequence (29–31). Each sample of Agropyron had 29 to 34 tandem repeat sequences, among which A. mongolicum (0506) had the most, reaching 34. In long interspersed nuclear elements, most samples had 13 palindromic repeat sequences and 29 to 31 forward repeat sequences. There were no reverse and complementary repeat sequences in the sequenced samples. The codons preferred A/U ending (RSCU>1 codons accounted for 48.4%). Nucleotide diversity analysis identified 8 hypervariable regions (such as psbA in the LSC region and rpl32 in the SSC region), but the hypervariable regions were still not enough to distinguish the five species of Agropyron. In the phylogenetic tree, all Agropyron samples clustered into a monophyletic clade with high support (bootstrap = 100), but within the genus Agropyron, the phylogenetic relationships among the five species and two varieties were not resolved. Further analysis showed that the number of phylogenetically informative sites within Agropyron was only 178, accounting for 0.13% of the total effective sites in the entire chloroplast, and the number of such sites in the hypervariable region was only 68, accounting for 0.45% of the effective sites there. Conclusion Our study comprehensively revealed the chloroplast genome information of Agropyron plants and its consistency across the genus.