Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms
Joint Authors
Shibata, Daisuke
Sato, Shusei
Ezura, Hiroshi
Ariizumi, Tohru
Asamizu, Erika
Yano, Kentaro
Tabata, Satoshi
Hirakawa, Hideki
Shirasawa, Kenta
Source
International Journal of Plant Genomics
Issue
Vol. 2012, Issue 2012 (31 Dec. 2012), pp.1-8, 8 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2012-11-27
Country of Publication
Egypt
No. of Pages
8
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Asamizu, Erika& Shirasawa, Kenta& Hirakawa, Hideki& Sato, Shusei& Tabata, Satoshi& Yano, Kentaro…[et al.]. 2012. Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms. International Journal of Plant Genomics،Vol. 2012, no. 2012, pp.1-8.
https://search.emarefa.net/detail/BIM-472209
Modern Language Association (MLA)
Asamizu, Erika…[et al.]. Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms. International Journal of Plant Genomics No. 2012 (2012), pp.1-8.
https://search.emarefa.net/detail/BIM-472209
American Medical Association (AMA)
Asamizu, Erika& Shirasawa, Kenta& Hirakawa, Hideki& Sato, Shusei& Tabata, Satoshi& Yano, Kentaro…[et al.]. Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms. International Journal of Plant Genomics. 2012. Vol. 2012, no. 2012, pp.1-8.
https://search.emarefa.net/detail/BIM-472209
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-472209