Intraspecific Genetic Distance and Phylogenetic Evolution of Schizothorax Plagiostomus Inferred from Mitochondrial D-Loop Sequences

The fish in the genus Schizothorax from the Cyprinidae family live in high-altitude Rivers andstreams, are threatened by various anthropogenic stressors. This study aims to characterize S. plagiostomus across Pakistan and throughout the world available on NCBI using the mitochondrial D-loop region, and in particular, to assess the degree of intra-specific pairwise distance among these sequences, as well as to establish their phylogenetic relationships. The percent overall nucleotide composition was 32.6% (A), 33.6% (T), 19.8% (C), and 14.0% (G), which infers that S. plagiostomus control regions is AT-rich (66.2%) and poor in G contents. The mean pair-wise intra-specific nucleotide diversity (Pi)of all the S. plagiostomus was 0.022. While, the inter-specific nucleotide diversity of all the Schizothorax species was 0.049. D-loop sequences for intra-specific variations revealed 765 sites were invariable and 10 were variable, 8 parsimony informative sites and only 2 were singletons. The overall transition/transversion ratio is R = 7.135. Three domains in S. plagiostomus were observed, namely, the termination associated sequence (TAS) domain, the central conserved sequence block (CSB) domain, and the conserved sequence block (CSB) domain. No substitution saturation was detected as an Iss value was significantly (𝑃< 0.001) lower than the Iss.c in all cases indicating the suitability of the data for phylogenetic analysis. This study signifies the importance of the control region for the genetic analysis of S. plagiostomus and also provides a hypothesis of their phylogenetic relationships.

Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes using 5’ and 3’ end small RNAs

Using 5’ and 3’ end small RNAs, we annotated human, chimpanzee, rhesus macaque and mouse mitochondrial genomes at 1 base-pair (bp) resolution to cover both strands of the mammalian mitochondrial genome entirely without leaving any gaps or overlaps. The precise annotation of all coding and non-coding genes (e.g. ncMT1, MDL2 and MDL1AS) led to the discovery of novel functions and mechanisms of mitochondrion. In this study, we defined the conserved sequence block (CSB) region to span five CSBs (CSB1, CSB2, CSB3, LSP and HSP) and identified the motifs of five CSBs in the mitochondrial displacement loop (D-loop) regions of 52 mammals. The conserved arrangement of these five CSBs in 17 primates inspired us to investigate the function of the mtDNA D-loop, which has been puzzling scientists for more than 50 years. We found that 5’ sRNAs of MDL1AS control the expression levels of mitochondrial genes as a whole by a negative feedback mechanism. Thus, the precise annotations of three CSBs (CSB2, LSP and HSP) in more species will help to understand the function of the mtDNA D-loop. The precision annotation of animal mitochondrial genomes also provides abundant information for studying the molecular phylogenetics and evolution of animals.