SNPs and Hox gene mapping in <it>Ciona intestinalis</it>
<p>Abstract</p> <p>Background</p> <p>The tunicate <it>Ciona intestinalis </it>(Enterogona, Ascidiacea), a major model system for evolutionary and developmental genetics of chordates, harbours two cryptic species. To assess the degree of intra- and inter-spec...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2008-01-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/9/39 |
| _version_ | 1819175500386402304 |
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| author | Biffali Elio Andreakis Nikos Borra Marco Caputi Luigi Sordino Paolo |
| author_facet | Biffali Elio Andreakis Nikos Borra Marco Caputi Luigi Sordino Paolo |
| author_sort | Biffali Elio |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The tunicate <it>Ciona intestinalis </it>(Enterogona, Ascidiacea), a major model system for evolutionary and developmental genetics of chordates, harbours two cryptic species. To assess the degree of intra- and inter-specific genetic variability, we report the identification and analysis of <it>C. intestinalis </it>SNP (Single Nucleotide Polymorphism) markers. A SNP subset was used to determine the genetic distance between <it>Hox-5 </it>and <it>-10 </it>genes.</p> <p>Results</p> <p>DNA fragments were amplified from 12 regions of <it>C. intestinalis </it>sp. A. In total, 128 SNPs and 32 one bp indels have been identified within 8 Kb DNA. SNPs in coding regions cause 4 synonymous and 12 non-synonymous substitutions. The highest SNP frequency was detected in the <it>Hox5 </it>and <it>Hox10 </it>intragenic regions. In <it>C. intestinalis</it>, these two genes have lost their archetypal topology within the cluster, such that <it>Hox10 </it>is located between <it>Hox4 </it>and <it>Hox5</it>. A subset of the above primers was used to perform successful amplification in <it>C. intestinalis </it>sp. B. In this cryptic species, 62 SNPs were identified within 3614 bp: 41 in non-coding and 21 in coding regions. The genetic distance of the <it>Hox-5 </it>and <it>-10 </it>loci, computed combining a classical backcross approach with the application of SNP markers, was found to be 8.4 cM (Haldane's function). Based on the physical distance, 1 cM corresponds to 39.5 Kb. Linkage disequilibrium between the aforementioned loci was calculated in the backcross generation.</p> <p>Conclusion</p> <p>SNPs here described allow analysis and comparisons within and between <it>C. intestinalis </it>cryptic species. We provide the first reliable computation of genetic distance in this important model chordate. This latter result represents an important platform for future studies on Hox genes showing deviations from the archetypal topology.</p> |
| first_indexed | 2024-12-22T20:55:51Z |
| format | Article |
| id | doaj.art-53d2a01d170d4ebeaad614d20a9860d0 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-22T20:55:51Z |
| publishDate | 2008-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-53d2a01d170d4ebeaad614d20a9860d02022-12-21T18:12:57ZengBMCBMC Genomics1471-21642008-01-01913910.1186/1471-2164-9-39SNPs and Hox gene mapping in <it>Ciona intestinalis</it>Biffali ElioAndreakis NikosBorra MarcoCaputi LuigiSordino Paolo<p>Abstract</p> <p>Background</p> <p>The tunicate <it>Ciona intestinalis </it>(Enterogona, Ascidiacea), a major model system for evolutionary and developmental genetics of chordates, harbours two cryptic species. To assess the degree of intra- and inter-specific genetic variability, we report the identification and analysis of <it>C. intestinalis </it>SNP (Single Nucleotide Polymorphism) markers. A SNP subset was used to determine the genetic distance between <it>Hox-5 </it>and <it>-10 </it>genes.</p> <p>Results</p> <p>DNA fragments were amplified from 12 regions of <it>C. intestinalis </it>sp. A. In total, 128 SNPs and 32 one bp indels have been identified within 8 Kb DNA. SNPs in coding regions cause 4 synonymous and 12 non-synonymous substitutions. The highest SNP frequency was detected in the <it>Hox5 </it>and <it>Hox10 </it>intragenic regions. In <it>C. intestinalis</it>, these two genes have lost their archetypal topology within the cluster, such that <it>Hox10 </it>is located between <it>Hox4 </it>and <it>Hox5</it>. A subset of the above primers was used to perform successful amplification in <it>C. intestinalis </it>sp. B. In this cryptic species, 62 SNPs were identified within 3614 bp: 41 in non-coding and 21 in coding regions. The genetic distance of the <it>Hox-5 </it>and <it>-10 </it>loci, computed combining a classical backcross approach with the application of SNP markers, was found to be 8.4 cM (Haldane's function). Based on the physical distance, 1 cM corresponds to 39.5 Kb. Linkage disequilibrium between the aforementioned loci was calculated in the backcross generation.</p> <p>Conclusion</p> <p>SNPs here described allow analysis and comparisons within and between <it>C. intestinalis </it>cryptic species. We provide the first reliable computation of genetic distance in this important model chordate. This latter result represents an important platform for future studies on Hox genes showing deviations from the archetypal topology.</p>http://www.biomedcentral.com/1471-2164/9/39 |
| spellingShingle | Biffali Elio Andreakis Nikos Borra Marco Caputi Luigi Sordino Paolo SNPs and Hox gene mapping in <it>Ciona intestinalis</it> BMC Genomics |
| title | SNPs and Hox gene mapping in <it>Ciona intestinalis</it> |
| title_full | SNPs and Hox gene mapping in <it>Ciona intestinalis</it> |
| title_fullStr | SNPs and Hox gene mapping in <it>Ciona intestinalis</it> |
| title_full_unstemmed | SNPs and Hox gene mapping in <it>Ciona intestinalis</it> |
| title_short | SNPs and Hox gene mapping in <it>Ciona intestinalis</it> |
| title_sort | snps and hox gene mapping in it ciona intestinalis it |
| url | http://www.biomedcentral.com/1471-2164/9/39 |
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