Complete mitogenome analysis of Fasciola gigantica from Sudan

Abstract

Complete mitochondrial (mt) genomes are increasingly being used as molecular markers for investigating phylogenetic relationships. We sequenced the complete mt genome of the Fasciola gigantica of 16 samples from cattle, sheep and goats from Sudan using Illumina MiSeq platform. The complete mt genome of F. gigantica was 14,483 bp in length. Its genome is circular, and consists of 36 genes, including 12 protein-coding genes, 2 subunit ribosomal RNA genes (rRNA), and 22 genes for tRNA. The start and stop codons of the12 protein-coding genes are ATG and TAG respectively, which are identical to reference mt genomes except for the ND5 the start codon GTG and the stop codon of the ND4 which was TAA. Additionally, the lengths of the the12 protein-coding genes were identical in 10 genes, however, the ND4L of the reference was 12 bp longer with 273 bp as compared to the Sudan isolates which was 261 bp long and COX1 in the reference was 9 bp shorter which was 1,533 bp long as compared to Sudan isolates which 1,542 bp long. In contrast, the non-coding regions differed by 20 bp and 4 bp length in the long and the short non-coding regions of Sudan isolates. Nucleotide variability in the mt genome among F. gigantica from Sudan is quite different from the reference as revealed by the sliding window analysis. Phylogenetic analysis of the concatenated amino acid sequence data for all 12 protein-coding genes showed that all F. gigantica from Sudan clustered separately from the available F. gigantica. More interestingly, based on stem-loop (non-coding regions) it revealed better resolution on how the evolutionary process has affected host specificity and in particular for the sheep and goats. It is concluded that these novel complete mt genomes of F. gigantica from different host species provide additional genetic markers for studying epidemiology, population genetics, and phylogeographics of F. gigantica, as well as for understanding interplay and the host species.