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

Dreyer C, Hoffmann M, Lanz C, Willing EM, Riester M, Warthmann N, Sprecher A, Tripathi N, Henz SR, Weigel D - BMC Genomics (2007)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany. christine.dreyer@tuebingen.mpg.de

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.

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Related in: MedlinePlus

Classification of deduced gene products represented in the guppy EST library. Annotations of the best hits found by BLASTX searches against public databases were parsed and classified according to molecular function or biological process. The group of others includes about 3000 ESTs with hits whose E-value was not better than 10-5 Red: number of different ESTs, blue: number of total ESTs.
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Figure 1: Classification of deduced gene products represented in the guppy EST library. Annotations of the best hits found by BLASTX searches against public databases were parsed and classified according to molecular function or biological process. The group of others includes about 3000 ESTs with hits whose E-value was not better than 10-5 Red: number of different ESTs, blue: number of total ESTs.

Mentions: The results of the BLASTX searches were parsed for annotation according to GO criteria [16], describing molecular function or biological processes, provided that the E-value of the best hit was lower than 10-5 (Fig. 1). Most of the proteins encoded by non-redundant annotated guppy ESTs have binding (17%) or catalytic (13%) activity or are structural proteins (13%). This distribution resembles that described for the Fundulus heteroclitus EST database [17], although the guppy database contains relatively more ESTs derived from retina, testis, and muscle. Among enzymes and structural proteins, muscle proteins are the most abundant, because somite tissue prevails in advanced embryos, the predominant source of our EST libraries (Table 1). Sequences without significant best BLAST hits or with hits to genes that lacked informative annotation, e.g. from genomic surveys or non-annotated EST products, are listed as unknown in Table 2. About 25% of the guppy cDNAs in our database is annotated as unknown.


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

Dreyer C, Hoffmann M, Lanz C, Willing EM, Riester M, Warthmann N, Sprecher A, Tripathi N, Henz SR, Weigel D - BMC Genomics (2007)

Classification of deduced gene products represented in the guppy EST library. Annotations of the best hits found by BLASTX searches against public databases were parsed and classified according to molecular function or biological process. The group of others includes about 3000 ESTs with hits whose E-value was not better than 10-5 Red: number of different ESTs, blue: number of total ESTs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1994688&req=5

Figure 1: Classification of deduced gene products represented in the guppy EST library. Annotations of the best hits found by BLASTX searches against public databases were parsed and classified according to molecular function or biological process. The group of others includes about 3000 ESTs with hits whose E-value was not better than 10-5 Red: number of different ESTs, blue: number of total ESTs.
Mentions: The results of the BLASTX searches were parsed for annotation according to GO criteria [16], describing molecular function or biological processes, provided that the E-value of the best hit was lower than 10-5 (Fig. 1). Most of the proteins encoded by non-redundant annotated guppy ESTs have binding (17%) or catalytic (13%) activity or are structural proteins (13%). This distribution resembles that described for the Fundulus heteroclitus EST database [17], although the guppy database contains relatively more ESTs derived from retina, testis, and muscle. Among enzymes and structural proteins, muscle proteins are the most abundant, because somite tissue prevails in advanced embryos, the predominant source of our EST libraries (Table 1). Sequences without significant best BLAST hits or with hits to genes that lacked informative annotation, e.g. from genomic surveys or non-annotated EST products, are listed as unknown in Table 2. About 25% of the guppy cDNAs in our database is annotated as unknown.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany. christine.dreyer@tuebingen.mpg.de

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.

Show MeSH
Related in: MedlinePlus