Role of fluorescence in situ hybridization in sequencing the tomato genome

S. M. Stack, S. M. Royer, L. A. Shearer, S. B. Chang, J. J. Giovannoni, D. H. Westfall, R. A. White, L. K. Anderson

研究成果: Review article

25 引文 (Scopus)

摘要

The tomato (Solanum lycopersicum L.) genome is being sequenced by a consortium of laboratories in 10 countries. Seventy-seven percent of the tomato genome (DNA) is located in repeat-rich, gene-poor, pericentric heterochromatin, while 23% of the genome is located in repeat-poor, gene-rich, distal euchromatin. It is estimated that approximately 90% of tomato's nuclear genes can be characterized by limiting the sequencing effort to euchromatin while avoiding the problems involved in sequencing the repetitive DNA in heterochromatin. Sequencing is being performed on tomato nuclear DNA cloned into bacterial artificial chromosome (BAC) vectors. Fluorescence in situ hybridization (FISH) is used to help direct the sequencing effort by cytologically demonstrating the location of selected BACs on tomato chromosomes. While mitotic metaphase chromosomes are too short and compact for this purpose, long pachytene chromosomes are ideal. BACs localized in euchromatin can be used confidently as anchors for the assembly of BAC contigs that extend through the euchromatic length of each chromosome arm. Another important role for FISH is identification of BACs near telomeres and near borders with pericentric heterochromatin to indicate that sequencing should not extend much further. This role of FISH is enhanced by our ability to estimate base pair distances between localized BACs and these chromosomal features. Finally, it is noteworthy that when BAC-FISH is combined with chromosomal in situ suppression (CISS) hybridization to block repeats and localize single/low copy sequences, the great majority of BACs localize to single sites. This observation is consistent with tomato being an ancient diploid.

原文English
頁(從 - 到)339-350
頁數12
期刊Cytogenetic and Genome Research
124
發行號3-4
DOIs
出版狀態Published - 2009 六月 1

指紋

Lycopersicon esculentum
Fluorescence In Situ Hybridization
Genome
Euchromatin
Bacterial Artificial Chromosomes
Heterochromatin
Chromosomes
Genes
DNA
Telomere
Metaphase
Diploidy
DNA Sequence Analysis
Base Pairing
In Situ Hybridization

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

引用此文

Stack, S. M., Royer, S. M., Shearer, L. A., Chang, S. B., Giovannoni, J. J., Westfall, D. H., ... Anderson, L. K. (2009). Role of fluorescence in situ hybridization in sequencing the tomato genome. Cytogenetic and Genome Research, 124(3-4), 339-350. https://doi.org/10.1159/000218137
Stack, S. M. ; Royer, S. M. ; Shearer, L. A. ; Chang, S. B. ; Giovannoni, J. J. ; Westfall, D. H. ; White, R. A. ; Anderson, L. K. / Role of fluorescence in situ hybridization in sequencing the tomato genome. 於: Cytogenetic and Genome Research. 2009 ; 卷 124, 編號 3-4. 頁 339-350.
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Stack, SM, Royer, SM, Shearer, LA, Chang, SB, Giovannoni, JJ, Westfall, DH, White, RA & Anderson, LK 2009, 'Role of fluorescence in situ hybridization in sequencing the tomato genome', Cytogenetic and Genome Research, 卷 124, 編號 3-4, 頁 339-350. https://doi.org/10.1159/000218137

Role of fluorescence in situ hybridization in sequencing the tomato genome. / Stack, S. M.; Royer, S. M.; Shearer, L. A.; Chang, S. B.; Giovannoni, J. J.; Westfall, D. H.; White, R. A.; Anderson, L. K.

於: Cytogenetic and Genome Research, 卷 124, 編號 3-4, 01.06.2009, p. 339-350.

研究成果: Review article

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AU - Stack, S. M.

AU - Royer, S. M.

AU - Shearer, L. A.

AU - Chang, S. B.

AU - Giovannoni, J. J.

AU - Westfall, D. H.

AU - White, R. A.

AU - Anderson, L. K.

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