PCOGR: Phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms

Meereis, Florian; Kaufmann, Michael

doi:10.1186/1471-2105-5-150

Cited by 292 publications

(7 citation statements)

References 10 publications

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“…All new sequences were submitted to NCBI GenBank (accession numbers from GQ214060 to GQ214077). After analysing the entire fragment variability in MEGA 3.1 (Kumar et al 2004), we selected a short fragment of the first exon, which revealed high interspecific diagnostic polymorphism, thus showing great potential to easily and reliably identify all species. This region was also selected because lower intraspecific variation is likely to occur in exons, when compared to intronic regions or other non-coding fragments.…”

Section: Methodsmentioning

confidence: 99%

Species identification using a small nuclear gene fragment: application to sympatric wild carnivores from South-western Europe

et al. 2009

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Species identification is essential for noninvasive studies of elusive and rare animals, and for detecting illegal harvest or trade of wildlife species. However, most molecular tests identify only a limited number of species or require multiple laboratory steps to distinguish many taxa. Additionally, most protocols use mitochondrial DNA being, therefore, especially prone to problems such as nuclear insert copies, high intraspecific diversity or heteroplasmy. Here, we developed a molecular test based on the polymorphisms detected on a small nuclear gene fragment (221 bp of the IRBP -Interphotoreceptor Retinoid-Binding Protein-exon 1). This fragment revealed 51 variable sites (including 12 non-synonymous and 19 species-specific sites), which enabled the successful distinction of all 16 carnivore species native to Southwestern Europe. A SSCP (Single-Strand Conformational Polymorphism) gel electrophoresis technique was also optimized to allow the simple and inexpensive application of this molecular test. Sequences and SSCP profiles were consistent in identifying a total of 387 samples, including faeces (172) and hairs (17) collected non-invasively in the field. Due to its low cost, simplicity, and wide range of identifiable species, this test shows great promise to facilitate studies in molecular ecology, conservation genetics, and forensic analysis, as well as DNA bar-coding projects.

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Section: Methodsmentioning

confidence: 99%

Species identification using a small nuclear gene fragment: application to sympatric wild carnivores from South-western Europe

et al. 2009

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“…All haplotypes identified here have been deposited in GenBank (Accession numbers FJ596283-FJ596287). DNA sequences were aligned with the CLUSTALW algorithm implemented in MEGA 3.1 (Kumar et al 2004). MEGA was also used to identify identical haplotypes, to assess the presence and consistency of diagnostic sites between the two species, and to perform phylogenetic analyses.…”

Section: Methodsmentioning

confidence: 99%

Development and testing of an optimized method for DNA-based identification of jaguar (Panthera onca) and puma (Puma concolor) faecal samples for use in ecological and genetic studies

et al. 2009

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The elusive nature and endangered status of most carnivore species imply that efficient approaches for their non-invasive sampling are required to allow for genetic and ecological studies. Faecal samples are a major potential source of information, and reliable approaches are needed to foster their application in this field, particularly in areas where few studies have been conducted. A major obstacle to the reliable use of faecal samples is their uncertain species-level identification in the field, an issue that can be addressed with DNA-based assays. In this study we describe a sequence-based approach that efficiently distinguishes jaguar versus puma scats, and that presents several desirable properties: (1) considerably high amplification and sequencing rates; (2) multiple diagnostic sites reliably differentiating the two focal species; (3) high information content that allows for future application in other carnivores; (4) no evidence of amplification of prey DNA; and (5) no evidence of amplification of a nuclear mitochondrial DNA insertion known to occur in the jaguar. We demonstrate the reliability and usefulness of this approach by evaluating 55 field-collected samples from four locations in the highly fragmented Atlantic Forest biome of Brazil and Argentina, and document the presence of one or both of these endangered felids in each of these areas.

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“…The full length gene sequence of cyt b and a partial sequence of the 16S rDNA gene and the D-loop mitochondrial region were analyzed separately for genetic distance and character-based variations using the MEGA 3.1 computer package (Kumar et al 2004) and PAUP (version 4b10) (Swofford 1998), respectively. The obtained sequences were aligned using Clustal X (version 1.83) and phylogenetic distances were calculated according to Kimura (1980) or/and Jukes and Cantor (1969) methods.…”

Section: Sequencing and Data Analysismentioning

confidence: 99%

Genetic differentiation among Greek lake populations of Carassius gibelio and Cyprinus carpio carpio

et al. 2008

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The genetic structure of the Western Greece lake populations of Carassius gibelio and Cyprinus carpio carpio populations was characterized by using a PCR-based RFLP and sequencing analysis of mitochondrial rDNA genes and regions (16S rDNA, cytochrome b and D-loop). Our analysis was able to detect: (a) two haplotypes in C. c. carpio populations and two haplotypes in C. gibelio populations (b) a high nucleotide divergence between the two species and (c) two genetically distinct C. gibelio populations, one existing in the Amvrakia habitat (AMV1) with a second in Ozeros and Trichonida (OZE1 and TRI1) habitat. The present analysis indicates that genetic diversity observed was limited with a haplotype index between 0.0 and 55.6%, and a nucleotide diversity within and among populations between 0.0 and 1.27%. It also underlines a restricted mtDNA-based evaluation of the phylogenetic relationships among C. gibelio and C. c. carpio populations. In addition, the present study contributed knowledge on the genetic variation and structure of these populations which is absolutely necessary for any efficient fish management and/or conservation programme.

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PCOGR: Phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms

Cited by 292 publications

References 10 publications

Species identification using a small nuclear gene fragment: application to sympatric wild carnivores from South-western Europe

Species identification using a small nuclear gene fragment: application to sympatric wild carnivores from South-western Europe

Development and testing of an optimized method for DNA-based identification of jaguar (Panthera onca) and puma (Puma concolor) faecal samples for use in ecological and genetic studies

Genetic differentiation among Greek lake populations of Carassius gibelio and Cyprinus carpio carpio

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