Cargando…
A genetic map of Xenopus tropicalis
We present a genetic map for Xenopus tropicalis, consisting of 2886 Simple Sequence Length Polymorphism (SSLP) markers. Using a bioinformatics-based strategy, we identified unique SSLPs within the X. tropicalis genome. Scaffolds from X. tropicalis genome assembly 2.0 (JGI) were scanned for Simple Se...
Autores principales: | , , , , , , , , , , , , , , , , , , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2011
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098391/ https://www.ncbi.nlm.nih.gov/pubmed/21458440 http://dx.doi.org/10.1016/j.ydbio.2011.03.022 |
_version_ | 1782203968071401472 |
---|---|
author | Wells, Dan E. Gutierrez, Laura Xu, Zhenkang Krylov, Vladimir Macha, Jaroslav Blankenburg, Kerstin P. Hitchens, Matthew Bellot, Larry J. Spivey, Mary Stemple, Derek L. Kowis, Andria Ye, Yuan Pasternak, Shiran Owen, Jenetta Tran, Thu Slavikova, Renata Tumova, Lucie Tlapakova, Tereza Seifertova, Eva Scherer, Steven E. Sater, Amy K. |
author_facet | Wells, Dan E. Gutierrez, Laura Xu, Zhenkang Krylov, Vladimir Macha, Jaroslav Blankenburg, Kerstin P. Hitchens, Matthew Bellot, Larry J. Spivey, Mary Stemple, Derek L. Kowis, Andria Ye, Yuan Pasternak, Shiran Owen, Jenetta Tran, Thu Slavikova, Renata Tumova, Lucie Tlapakova, Tereza Seifertova, Eva Scherer, Steven E. Sater, Amy K. |
author_sort | Wells, Dan E. |
collection | PubMed |
description | We present a genetic map for Xenopus tropicalis, consisting of 2886 Simple Sequence Length Polymorphism (SSLP) markers. Using a bioinformatics-based strategy, we identified unique SSLPs within the X. tropicalis genome. Scaffolds from X. tropicalis genome assembly 2.0 (JGI) were scanned for Simple Sequence Repeats (SSRs); unique SSRs were then tested for amplification and polymorphisms using DNA from inbred Nigerian and Ivory Coast individuals. Thus identified, the SSLPs were genotyped against a mapping cross panel of DNA samples from 190 F2 individuals. Nearly 4000 SSLPs were genotyped, yielding a 2886-marker genetic map consisting of 10 major linkage groups between 73 and 132 cM in length, and 4 smaller linkage groups between 7 and 40 cM. The total effective size of the map is 1658 cM, and the average intermarker distance for each linkage group ranged from 0.27 to 0.75 cM. Fluorescence In Situ Hybridization (FISH) was carried out using probes for genes located on mapped scaffolds to assign linkage groups to chromosomes. Comparisons of this map with the X. tropicalis genome Assembly 4.1 (JGI) indicate that the map provides representation of a minimum of 66% of the X. tropicalis genome, incorporating 758 of the approximately 1300 scaffolds over 100,000 bp. The genetic map and SSLP marker database constitute an essential resource for genetic and genomic analyses in X. tropicalis. |
format | Text |
id | pubmed-3098391 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-30983912011-07-12 A genetic map of Xenopus tropicalis Wells, Dan E. Gutierrez, Laura Xu, Zhenkang Krylov, Vladimir Macha, Jaroslav Blankenburg, Kerstin P. Hitchens, Matthew Bellot, Larry J. Spivey, Mary Stemple, Derek L. Kowis, Andria Ye, Yuan Pasternak, Shiran Owen, Jenetta Tran, Thu Slavikova, Renata Tumova, Lucie Tlapakova, Tereza Seifertova, Eva Scherer, Steven E. Sater, Amy K. Dev Biol Resource We present a genetic map for Xenopus tropicalis, consisting of 2886 Simple Sequence Length Polymorphism (SSLP) markers. Using a bioinformatics-based strategy, we identified unique SSLPs within the X. tropicalis genome. Scaffolds from X. tropicalis genome assembly 2.0 (JGI) were scanned for Simple Sequence Repeats (SSRs); unique SSRs were then tested for amplification and polymorphisms using DNA from inbred Nigerian and Ivory Coast individuals. Thus identified, the SSLPs were genotyped against a mapping cross panel of DNA samples from 190 F2 individuals. Nearly 4000 SSLPs were genotyped, yielding a 2886-marker genetic map consisting of 10 major linkage groups between 73 and 132 cM in length, and 4 smaller linkage groups between 7 and 40 cM. The total effective size of the map is 1658 cM, and the average intermarker distance for each linkage group ranged from 0.27 to 0.75 cM. Fluorescence In Situ Hybridization (FISH) was carried out using probes for genes located on mapped scaffolds to assign linkage groups to chromosomes. Comparisons of this map with the X. tropicalis genome Assembly 4.1 (JGI) indicate that the map provides representation of a minimum of 66% of the X. tropicalis genome, incorporating 758 of the approximately 1300 scaffolds over 100,000 bp. The genetic map and SSLP marker database constitute an essential resource for genetic and genomic analyses in X. tropicalis. Elsevier 2011-06-01 /pmc/articles/PMC3098391/ /pubmed/21458440 http://dx.doi.org/10.1016/j.ydbio.2011.03.022 Text en © 2011 Elsevier Inc. https://creativecommons.org/licenses/by/3.0/ Open Access under CC BY 3.0 (https://creativecommons.org/licenses/by/3.0/) license |
spellingShingle | Resource Wells, Dan E. Gutierrez, Laura Xu, Zhenkang Krylov, Vladimir Macha, Jaroslav Blankenburg, Kerstin P. Hitchens, Matthew Bellot, Larry J. Spivey, Mary Stemple, Derek L. Kowis, Andria Ye, Yuan Pasternak, Shiran Owen, Jenetta Tran, Thu Slavikova, Renata Tumova, Lucie Tlapakova, Tereza Seifertova, Eva Scherer, Steven E. Sater, Amy K. A genetic map of Xenopus tropicalis |
title | A genetic map of Xenopus tropicalis |
title_full | A genetic map of Xenopus tropicalis |
title_fullStr | A genetic map of Xenopus tropicalis |
title_full_unstemmed | A genetic map of Xenopus tropicalis |
title_short | A genetic map of Xenopus tropicalis |
title_sort | genetic map of xenopus tropicalis |
topic | Resource |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098391/ https://www.ncbi.nlm.nih.gov/pubmed/21458440 http://dx.doi.org/10.1016/j.ydbio.2011.03.022 |
work_keys_str_mv | AT wellsdane ageneticmapofxenopustropicalis AT gutierrezlaura ageneticmapofxenopustropicalis AT xuzhenkang ageneticmapofxenopustropicalis AT krylovvladimir ageneticmapofxenopustropicalis AT machajaroslav ageneticmapofxenopustropicalis AT blankenburgkerstinp ageneticmapofxenopustropicalis AT hitchensmatthew ageneticmapofxenopustropicalis AT bellotlarryj ageneticmapofxenopustropicalis AT spiveymary ageneticmapofxenopustropicalis AT stemplederekl ageneticmapofxenopustropicalis AT kowisandria ageneticmapofxenopustropicalis AT yeyuan ageneticmapofxenopustropicalis AT pasternakshiran ageneticmapofxenopustropicalis AT owenjenetta ageneticmapofxenopustropicalis AT tranthu ageneticmapofxenopustropicalis AT slavikovarenata ageneticmapofxenopustropicalis AT tumovalucie ageneticmapofxenopustropicalis AT tlapakovatereza ageneticmapofxenopustropicalis AT seifertovaeva ageneticmapofxenopustropicalis AT schererstevene ageneticmapofxenopustropicalis AT sateramyk ageneticmapofxenopustropicalis AT wellsdane geneticmapofxenopustropicalis AT gutierrezlaura geneticmapofxenopustropicalis AT xuzhenkang geneticmapofxenopustropicalis AT krylovvladimir geneticmapofxenopustropicalis AT machajaroslav geneticmapofxenopustropicalis AT blankenburgkerstinp geneticmapofxenopustropicalis AT hitchensmatthew geneticmapofxenopustropicalis AT bellotlarryj geneticmapofxenopustropicalis AT spiveymary geneticmapofxenopustropicalis AT stemplederekl geneticmapofxenopustropicalis AT kowisandria geneticmapofxenopustropicalis AT yeyuan geneticmapofxenopustropicalis AT pasternakshiran geneticmapofxenopustropicalis AT owenjenetta geneticmapofxenopustropicalis AT tranthu geneticmapofxenopustropicalis AT slavikovarenata geneticmapofxenopustropicalis AT tumovalucie geneticmapofxenopustropicalis AT tlapakovatereza geneticmapofxenopustropicalis AT seifertovaeva geneticmapofxenopustropicalis AT schererstevene geneticmapofxenopustropicalis AT sateramyk geneticmapofxenopustropicalis |