Comparative analyses of 32 complete plastomes of Tef (Eragrostis tef ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots

Abstract

Eragrostis tef is an important cereal crop in Ethiopia with excellent storage properties, high–quality food, and the unique ability to thrive in extreme environmental conditions. However, the application of advanced molecular tools for breeding and conservation of these species is extremely limited. Therefore, developing chloroplast genome resources and high-resolution molecular markers are valuable to E. tef population and biogeographic studies. In the current study, we assembled and compared the complete plastomes of 32 E. tef accessions. The size of the plastomes ranged from 134,349 to 134,437 bp with similar GC content (∼38.3%). Genomes annotations revealed 112 individual genes, including 77 protein-coding, 31 tRNA, and 4 rRNA genes. Comparison of E. tef plastomes revealed a low degree of intraspecific sequence variations and no structural differentiations. Furthermore, we found 34 polymorphic sites (13 cpSSRs, 12 InDels, and 9 SNPs) that can be used as valuable DNA barcodes. Among them, the majority (88%) of the polymorphic sites were identified in the noncoding genomic regions. Nonsynonymous (ka) and synonymous (ks) substitution analysis showed that all PCGs were under purifying selection (ka/ks <1). The phylogenetic analyses of the whole plastomes and polymorphic region sequences were able to distinguish the accession from the southern population, indicating its potential to be used as a super-barcode. In conclusion, the newly generated plastomes and polymorphic markers developed here could be a useful genomic resource in molecular breeding, population genetics and the biogeographical study of E. tef.