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SSR repeat dynamics in mitochondrial genomes of five domestic animal species.

ABSTRACT: SSR (simple sequence repeats) are ubiquitously abundant in genomes. In organellar mitochondrial genome of animals, its distribution, size dynamics and effectiveness for phylogenetic relationship have not been understood. Present investigation reveals organisation of SSR in genic and intergenic region, its length and repeat motif dynamics, extent of conservation of flanking regions, appropriateness of these SSR data in establishing phylogenetic relationship. Contrary to eukaryotic nuclear abundance of SSR in non-coding region, we found abundance in coding region. Like nuclear SSR, most hyper mutable repeats were found in non coding region having di nucleotide motifs of mitochondrial genome but contrary to human having high mutable tetra repeats in case of mitochondrial genomes this was found to be with tri-motif repeats. SSR of mitochondrial genomes also show cyclical expansion and shrinkage in pattern of SHM (simple harmonic motion) with respect to time its non- linear thus not appropriate for phylogenetic analysis though the flanking regions of these SSR also conserved like nuclear SSR.

SUBMITTER: Shakyawar SK

PROVIDER: S-EPMC2825591 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature

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SSR repeat dynamics in mitochondrial genomes of five domestic animal species.

Shakyawar Sushil Kumar SK Joshi Balwindar Kumar BK Kumar Dinesh D

Bioinformation 20091015 4

SSR (simple sequence repeats) are ubiquitously abundant in genomes. In organellar mitochondrial genome of animals, its distribution, size dynamics and effectiveness for phylogenetic relationship have not been understood. Present investigation reveals organisation of SSR in genic and intergenic region, its length and repeat motif dynamics, extent of conservation of flanking regions, appropriateness of these SSR data in establishing phylogenetic relationship. Contrary to eukaryotic nuclear abundan ...[more]

PMID: 20198193

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Project description:BACKGROUND: Studying mitochondrial (mt) genomics has important implications for various fundamental areas, including mt biochemistry, physiology and molecular biology. In addition, mt genome sequences have provided useful markers for investigating population genetic structures, systematics and phylogenetics of organisms. Toxocara canis, Toxocara cati and Toxocara malaysiensis cause significant health problems in animals and humans. Although they are of importance in human and animal health, no information on the mt genomes for any of Toxocara species is available. RESULTS: The sizes of the entire mt genome are 14,322 bp for T. canis, 14029 bp for T. cati and 14266 bp for T. malaysiensis, respectively. These circular genomes are amongst the largest reported to date for all secernentean nematodes. Their relatively large sizes relate mainly to an increased length in the AT-rich region. The mt genomes of the three Toxocara species all encode 12 proteins, two ribosomal RNAs and 22 transfer RNA genes, but lack the ATP synthetase subunit 8 gene, which is consistent with all other species of Nematode studied to date, with the exception of Trichinella spiralis. All genes are transcribed in the same direction and have a nucleotide composition high in A and T, but low in G and C. The contents of A+T of the complete genomes are 68.57% for T. canis, 69.95% for T. cati and 68.86% for T. malaysiensis, among which the A+T for T. canis is the lowest among all nematodes studied to date. The AT bias had a significant effect on both the codon usage pattern and amino acid composition of proteins. The mt genome structures for three Toxocara species, including genes and non-coding regions, are in the same order as for Ascaris suum and Anisakis simplex, but differ from Ancylostoma duodenale, Necator americanus and Caenorhabditis elegans only in the location of the AT-rich region, whereas there are substantial differences when compared with Onchocerca volvulus,Dirofiliria immitis and Strongyloides stercoralis. Phylogenetic analyses based on concatenated amino acid sequences of 12 protein-coding genes revealed that the newly described species T. malaysiensis was more closely related to T. cati than to T. canis, consistent with results of a previous study using sequences of nuclear internal transcribed spacers as genetic markers. CONCLUSION: The present study determined the complete mt genome sequences for three roundworms of human and animal health significance, which provides mtDNA evidence for the validity of T. malaysiensis and also provides a foundation for studying the systematics, population genetics and ecology of these and other nematodes of socio-economic importance.

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SSR repeat dynamics in mitochondrial genomes of five domestic animal species.

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SSR repeat dynamics in mitochondrial genomes of five domestic animal species.

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