ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, Poecilia reticulata View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2007-12

AUTHORS

Christine Dreyer, Margarete Hoffmann, Christa Lanz, Eva-Maria Willing, Markus Riester, Norman Warthmann, Andrea Sprecher, Namita Tripathi, Stefan R Henz, Detlef Weigel

ABSTRACT

BACKGROUND: The guppy, Poecilia reticulata, is a well-known model organism for studying inheritance and variation of male ornamental traits as well as adaptation to different river habitats. However, genomic resources for studying this important model were not previously widely available. RESULTS: With the aim of generating molecular markers for genetic mapping of the guppy, cDNA libraries were constructed from embryos and different adult organs to generate expressed sequence tags (ESTs). About 18,000 ESTs were annotated according to BLASTN and BLASTX results and the sequence information from the 3' UTRs was exploited to generate PCR primers for re-sequencing of genomic DNA from different wild type strains. By comparison of EST-linked genomic sequences from at least four different ecotypes, about 1,700 polymorphisms were identified, representing about 400 distinct genes. Two interconnected MySQL databases were built to organize the ESTs and markers, respectively. A robust phylogeny of the guppy was reconstructed, based on 10 different nuclear genes. CONCLUSION: Our EST and marker databases provide useful tools for genetic mapping and phylogenetic studies of the guppy. More... »

PAGES

269

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2164-8-269

DOI

http://dx.doi.org/10.1186/1471-2164-8-269

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1034427525

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/17686157


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Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-8-269'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-8-269'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-8-269'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-8-269'


 

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