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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...

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Autores principales: 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.
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
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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.
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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
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