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Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms

A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, “Heinz 1706.” By referring to the “Heinz 1706” physical map and by el...

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Autores principales: Asamizu, Erika, Shirasawa, Kenta, Hirakawa, Hideki, Sato, Shusei, Tabata, Satoshi, Yano, Kentaro, Ariizumi, Tohru, Shibata, Daisuke, Ezura, Hiroshi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514829/
https://www.ncbi.nlm.nih.gov/pubmed/23227037
http://dx.doi.org/10.1155/2012/437026
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author Asamizu, Erika
Shirasawa, Kenta
Hirakawa, Hideki
Sato, Shusei
Tabata, Satoshi
Yano, Kentaro
Ariizumi, Tohru
Shibata, Daisuke
Ezura, Hiroshi
author_facet Asamizu, Erika
Shirasawa, Kenta
Hirakawa, Hideki
Sato, Shusei
Tabata, Satoshi
Yano, Kentaro
Ariizumi, Tohru
Shibata, Daisuke
Ezura, Hiroshi
author_sort Asamizu, Erika
collection PubMed
description A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, “Heinz 1706.” By referring to the “Heinz 1706” physical map and by eliminating redundant or nonsignificant hits, 28,804 “unique pair ends” and 8,263 “unique ends” were selected to construct hypothetical BAC contigs. The total physical length of the BAC contigs was 495, 833, 423 bp, covering 65.3% of the entire genome. The average coverage of euchromatin and heterochromatin was 58.9% and 67.3%, respectively. From this analysis, two possible genome rearrangements were identified: one in chromosome 2 (inversion) and the other in chromosome 3 (inversion and translocation). Polymorphisms (SNPs and Indels) between the two cultivars were identified from the BLAST alignments. As a result, 171,792 polymorphisms were mapped on 12 chromosomes. Among these, 30,930 polymorphisms were found in euchromatin (1 per 3,565 bp) and 140,862 were found in heterochromatin (1 per 2,737 bp). The average polymorphism density in the genome was 1 polymorphism per 2,886 bp. To facilitate the use of these data in Micro-Tom research, the BAC contig and polymorphism information are available in the TOMATOMICS database.
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spelling pubmed-35148292012-12-07 Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms Asamizu, Erika Shirasawa, Kenta Hirakawa, Hideki Sato, Shusei Tabata, Satoshi Yano, Kentaro Ariizumi, Tohru Shibata, Daisuke Ezura, Hiroshi Int J Plant Genomics Research Article A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, “Heinz 1706.” By referring to the “Heinz 1706” physical map and by eliminating redundant or nonsignificant hits, 28,804 “unique pair ends” and 8,263 “unique ends” were selected to construct hypothetical BAC contigs. The total physical length of the BAC contigs was 495, 833, 423 bp, covering 65.3% of the entire genome. The average coverage of euchromatin and heterochromatin was 58.9% and 67.3%, respectively. From this analysis, two possible genome rearrangements were identified: one in chromosome 2 (inversion) and the other in chromosome 3 (inversion and translocation). Polymorphisms (SNPs and Indels) between the two cultivars were identified from the BLAST alignments. As a result, 171,792 polymorphisms were mapped on 12 chromosomes. Among these, 30,930 polymorphisms were found in euchromatin (1 per 3,565 bp) and 140,862 were found in heterochromatin (1 per 2,737 bp). The average polymorphism density in the genome was 1 polymorphism per 2,886 bp. To facilitate the use of these data in Micro-Tom research, the BAC contig and polymorphism information are available in the TOMATOMICS database. Hindawi Publishing Corporation 2012 2012-11-27 /pmc/articles/PMC3514829/ /pubmed/23227037 http://dx.doi.org/10.1155/2012/437026 Text en Copyright © 2012 Erika Asamizu et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Asamizu, Erika
Shirasawa, Kenta
Hirakawa, Hideki
Sato, Shusei
Tabata, Satoshi
Yano, Kentaro
Ariizumi, Tohru
Shibata, Daisuke
Ezura, Hiroshi
Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms
title Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms
title_full Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms
title_fullStr Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms
title_full_unstemmed Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms
title_short Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms
title_sort mapping of micro-tom bac-end sequences to the reference tomato genome reveals possible genome rearrangements and polymorphisms
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514829/
https://www.ncbi.nlm.nih.gov/pubmed/23227037
http://dx.doi.org/10.1155/2012/437026
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