ArticleBMC genomics2007
Simple sequence repeats in zebra finch (Taeniopygia guttata) expressed sequence tags: a new resource for evolutionary genetic studies of passerines.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 61 citations in OpenAlex.
- Variation in fine-scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird.Ecology and evolution · 2017Article
- Heterozygosity is linked to the costs of immunity in nestling great tits (Parus major).Ecology and evolution · 2013Article
- Inbreeding causes early death in a passerine bird.Nature communications · 2012Article
- Internal incubation and early hatching in brood parasitic birds.Proceedings. Biological sciences · 2011Article
- Article
- Identification and analysis of immune-related transcriptome in Asian seabass Lates calcarifer.BMC genomics · 2010Article
- A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata).BMC genomics · 2010Article
- A bacterial artificial chromosome library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in gene isolation and genome characterization.BMC genomics · 2009Article
- A simple and efficient method for isolating polymorphic microsatellites from cDNA.BMC genomics · 2009Article
- Large-scale identification of polymorphic microsatellites using an in silico approach.BMC bioinformatics · 2008Article
- A linkage map of the zebra finch Taeniopygia guttata provides new insights into avian genome evolution.Genetics · 2008Article
- The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution.BMC genomics · 2008Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundPasserines (perching birds) are widely studied across many biological disciplines including ecology, population biology, neurobiology, behavioural ecology and evolutionary biology. However, understanding the molecular basis of relevant traits is hampered by the paucity of passerine genomics tools. Efforts to address this problem are underway, and the zebra finch (Taeniopygia guttata) will be the first passerine to have its genome sequenced. Here we describe a bioinformatic analysis of zebra finch expressed sequence tag (EST) Genbank entries.
resultsA total of 48,862 ESTs were downloaded from GenBank and assembled into contigs, representing an estimated 17,404 unique sequences. The unique sequence set contained 638 simple sequence repeats (SSRs) or microsatellites of length > or =20 bp and purity > or =90% and 144 simple sequence repeats of length > or =30 bp. A chromosomal location for the majority of SSRs was predicted by BLASTing against assembly 2.1 of the chicken genome sequence. The relative exonic location (5' untranslated region, coding region or 3' untranslated region) was predicted for 218 of the SSRs, by BLAST search against the ENSEMBL chicken peptide database. Ten loci were examined for polymorphism in two zebra finch populations and two populations of a distantly related passerine, the house sparrow Passer domesticus. Linkage was confirmed for four loci that were predicted to reside on the passerine homologue of chicken chromosome 7.
conclusionWe show that SSRs are abundant within zebra finch ESTs, and that their genomic location can be predicted from sequence similarity with the assembled chicken genome sequence. We demonstrate that a useful proportion of zebra finch EST-SSRs are likely to be polymorphic, and that they can be used to build a linkage map. Finally, we show that many zebra finch EST-SSRs are likely to be useful in evolutionary genetic studies of other passerines.
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