A comparative analysis of the complete mitochondrial genome of the Eurasian otter Lutra lutra (Carnivora; Mustelidae)

Department of Molecular and Environmental Bioscience, Graduate School, Hanyang University, Seoul, 133-791, South Korea.
Molecular Biology Reports (Impact Factor: 2.02). 09/2009; 37(4):1943-55. DOI: 10.1007/s11033-009-9641-0
Source: PubMed


Otter populations are declining throughout the world and most otter species are considered endangered. Molecular methods are suitable tools for population genetic research on endangered species. In the present study, we analyzed the complete mitochondrial genome (mitogenome) sequence of the Eurasian otter Lutra lutra. The mitochondrial DNA sequence of the Eurasian otter is 16,505 bp in length and consists of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region (CR). The CR sequence of otters from Europe and Asia showed nearly identical numbers and nucleotide sequences of minisatellites. Phylogenetic analysis of Mustelidae mitogenomes, including individual genes, revealed that Lutrinae and Mustelinae form a clade, and that L. lutra and Enhydra lutris are sister taxa within the Lutrinae. Phylogenetic analyses revealed that of the 13 mitochondrial protein-coding genes, ND5 is the most reliable marker for analysis of phylogenetic relationships within the Mustelidae.

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Available from: Jae-Seong Lee, Apr 17, 2014
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    • "To our knowledge, this is the only wetland species that has been reported to be affected by this barrier. In addition, threats that may exist to otters between the Danube and Tisza Rivers include habitat loss via removal of vegetation along the small watercourses, reduction in food resources due to drainage of wetlands, and human disturbances (Lanszki et al. 2009b; Dövényi 2010). The shallow but significant genetic subdivision found in the present study may represent a long-term pattern of 2 subpopulations evolving within river basins, but connected by gene flow, or could be the result of decreasing genetic connectivity between 1 historically large, genetically interconnected population inhabiting both river basins. "
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    ABSTRACT: The Eurasian otter (Lutra lutra) is widely distributed in Europe and has been down-listed from Vulnerable to Near Threatened on the IUCN Red List in 2004 following successful conservation interventions. River otter recoveries were driven by active and passive protection of wetlands and a decrease in environmental pollutants. In Hungary, although otter populations have been stable in recent decades, there is little information available regarding genetic diversity, population genetic or phylogeographic structure, and potential barriers affecting gene flow. This study, therefore, aimed to determine genetic diversity and structure across the range of this species in Hungary. To achieve this, we analyzed 255 tissue samples collected since 2002, mainly from road-kill incidents, in various regions of Hungary. We found a relatively high level of genetic diversity in Hungarian otter populations (expected heterozygosity: 0.69–0.74; mean number of alleles per locus: 6.8–7.7). At a regional level, we identified 2 distinct genetic clusters corresponding to 2 river basins (Danube and Tisza). We also identified isolation by distance and patterns of genetic differentiation that appear to reflect population divergence of otters that are spatially restricted to one of these 2 river basins. Our results show the strong influence of river networks on population structure and genetic divergence in otters and provide a framework for the development of conservation management plans for otters in Hungary.
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    • "The complete mitochondrial genomes not only provide more information than single genes, but also show genome-level characteristics which are valuable for better understanding genome evolution and phylogeny (Lei et al., 2010). Up to now, the complete mitochondrial genomes have been reported in many aquatic organisms, including Penaeus monodon (Wilson et al., 2000), Portunus trituberculatus (Yamauchi et al., 2003), Eriocheir sinensis (Sun et al., 2005), Fenneropenaeus chinensis (Shen et al., 2007), Apostichopus japonicas (Shen et al., 2009), Radix balthica (Feldmeyer et al., 2010), Lutra lutra (Ki et al., 2010), Miichthys miiuy (Cheng et al., 2010), Charybdis japonica (Liu and Cui, 2010) and Collichthys lucidus (Cheng et al., 2012a). Due to its haploid nature, limited recombination, maternal inheritance and rapid evolutionary rate, the mitochondrial DNA has now been widely used for studying population genetics (Brown et al., 2011; Lee et al., 2010; Ma et al., 2011a), phylogeography and phylogeny (Keskin and Can, 2009; Gvozdik et al., 2010; Xu et al., 2009), and species identification (Feng et al., 2011; Ma et al., 2012a). "
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    ABSTRACT: The complete mitochondrial genome is of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In the present study, we determined the complete mitochondrial genome DNA sequence of the mud crab (Scylla paramamosain) by 454 deep sequencing and sanger sequencing approaches. The complete genome DNA was 15, 824 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). Of 37 genes, twenty-three were encoded by the heavy strand (H-strand), while the other ones were encoded by light strand (L-strand). The gene order in the mitochondrial genome was largely identical to those obtained in most arthropods, although the relative position of gene tRNA(His) differed from other arthropods. Among 13 protein-coding genes, three (ATPase subunits 6 (ATP6), NADH dehydrogenase subunits 1 (ND1) and ND3) started with a rare start codon ATT, whereas, one gene cytochrome c oxidase subunit I (COI) ended with the incomplete stop codon TA. All 22 tRNAs could fold into a typical clover-leaf secondary structure, with the gene sizes ranging from 63 to 73 bp. The phylogenetic analysis based on 12 concatenated protein-coding genes showed that the molecular genetic relationship of 19 species of 11 genera was identical to the traditional taxonomy.
    Gene 02/2013; 519(1). DOI:10.1016/j.gene.2013.01.028 · 2.14 Impact Factor
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    • "The equine mtDNA has an approximate length of 16,660 bp and consists of a coding region which contains 37 genes and a non-coding region called the D-loop region of approximately 1,192 bp (Wolstenholme, 1992; Boore, 1999; Bowling et al., 2000). The mtDNA sequences have been widely used to study taxonomy, phylogeny, genetic structure and biological identity (Peng et al., 2007; Ji et al., 2008; Ki et al., 2010). D-loop mtDNA is an important tool to study equine diversity, phylogenetic relationships and origins, such as the Mongolian horse (Lei et al., 2009), Cheju horse (Yang et al., 2002), Debao pony (Jiang et al., 2011), Japanese horse (Kakoi et al., 2007), Tibetan horse (Xu et al., 2007), Przewalskii’s wild horse (Ishida et al., 1995) and donkey (Lei et al., 2005). "
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    ABSTRACT: In order to protect the genetic resource of native horse breeds, the genetic diversity of mitochondrial DNA (mtDNA) D-loop of three native horse breeds in western China were investigated. Forty-three 600 bp mtDNA D-loop sequences were analyzed by PCR and sequencing techniques, 33 unique haplotypes with 70 polymorphic sites were detected in these horses, which account for 11.67% of 600 bp sequence analyzed, showing the abundant genetic diversity of the three native horse breeds in western China. The Neighbour-Joining (NJ) phylogenetic tree based on 247 bp of 43 D-loop sequences demonstrated the presence of seven major lineages (A to G), indicating that the three native horse breeds in western China originated from multiple maternal origins. Consistent with the front, the NJ phylogenetic tree based on 600 bp of mtDNA D-loop sequences of 43 Chinese western native horses and 81 sequences of six horse breeds from GenBank indicated that the three horse breeds had distributed into the seven major lineages (A to G). The structure of the phylogenic tree is often blurred because the variation in a short segment of the mitochondrial genome is often accompanied by high levels of recurrent mutations. Consequently, longer D-loop sequences are helpful in achieving a higher level of molecular resolution in horses.
    Asian Australasian Journal of Animal Sciences 07/2012; 25(7):921-6. DOI:10.5713/ajas.2011.11483 · 0.54 Impact Factor
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