A BAC library for grape and strategies for the development of a physical framework for the grape genome

J. P. Tomkins; D. G. Peterson; T. J. Yang; D. Main; Effie M. Ablett; Robert, J. Henry; L. Slade Lee; Timothy A. Holton; Daniel LE Waters; R. A. Wing

A BAC library for grape and strategies for the development of a physical framework for the grape genome

J. P. Tomkins, D. G. Peterson, T. J. Yang, D. Main, Effie M. Ablett, Robert, J. Henry, L. Slade Lee, Timothy A. Holton, Daniel LE Waters, R. A. Wing

Research output: Other contribution to conference › Other › peer-review

Abstract

We have constructed a grape BAC library using the cultivar Syrah. The library contains 55,296 clones stored in 144 384-well microtiter plates. A random sampling of 381 BACs indicated an average insert size of 144 kb with a range of 30 to 355 kb, and less than 4% of the clones do not contain inserts. Eighty-nine percent of BAC clones in the library have an average insert size greater than 100 kb. Based on a genome size of 483 Mb, library coverage is 16.5 haploid genome equivalents. Screening the BAC library colony filters with cpDNA sequences showed that contamination of the genomic library with chloroplast clones was low (1.5%). Library screening of an 11X coverage (2 BAC colony filters) with 12 cDNA probes corresponding to flavonoid and stilbene biosynthesis genes resulted in an average of 13 hits per probe (range = 1 to 27). ). To gain a glimpse into the grape genome and evaluate the library for sequence-tagged connector (STC) development, 768 BAC clones were end sequenced in both forward and reverse directions. The STCs were queried against the SWISS-PROT database and significant hits were sorted according to putative function. Potential applications of this library towards the development of a physical framework for the grape genome will also be discussed.

Original language	English
Publication status	Published - 2002
Event	Plant, Animal and Microbe Genomes X Conference - San Diego, United States Duration: 12 Jan 2002 → …

Conference

Conference	Plant, Animal and Microbe Genomes X Conference
Country/Territory	United States
City	San Diego
Period	12/01/02 → …

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http://epubs.scu.edu.au/cpcg_pubs/399/Licence: Unspecified

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Tomkins, J. P., Peterson, D. G., Yang, T. J., Main, D., Ablett, E. M., Henry, R. J., Lee, L. S., Holton, T. A., Waters, D. LE., & Wing, R. A. (2002). A BAC library for grape and strategies for the development of a physical framework for the grape genome. Plant, Animal and Microbe Genomes X Conference, San Diego, California, United States. http://epubs.scu.edu.au/cpcg_pubs/399/

@conference{501cc3b1a00243ed9dd3e6bff88197da,

title = "A BAC library for grape and strategies for the development of a physical framework for the grape genome",

abstract = "We have constructed a grape BAC library using the cultivar Syrah. The library contains 55,296 clones stored in 144 384-well microtiter plates. A random sampling of 381 BACs indicated an average insert size of 144 kb with a range of 30 to 355 kb, and less than 4% of the clones do not contain inserts. Eighty-nine percent of BAC clones in the library have an average insert size greater than 100 kb. Based on a genome size of 483 Mb, library coverage is 16.5 haploid genome equivalents. Screening the BAC library colony filters with cpDNA sequences showed that contamination of the genomic library with chloroplast clones was low (1.5%). Library screening of an 11X coverage (2 BAC colony filters) with 12 cDNA probes corresponding to flavonoid and stilbene biosynthesis genes resulted in an average of 13 hits per probe (range = 1 to 27). ). To gain a glimpse into the grape genome and evaluate the library for sequence-tagged connector (STC) development, 768 BAC clones were end sequenced in both forward and reverse directions. The STCs were queried against the SWISS-PROT database and significant hits were sorted according to putative function. Potential applications of this library towards the development of a physical framework for the grape genome will also be discussed.",

author = "Tomkins, {J. P.} and Peterson, {D. G.} and Yang, {T. J.} and D. Main and Ablett, {Effie M.} and Henry, {Robert, J.} and Lee, {L. Slade} and Holton, {Timothy A.} and Waters, {Daniel LE} and Wing, {R. A.}",

year = "2002",

language = "English",

note = "Plant, Animal and Microbe Genomes X Conference ; Conference date: 12-01-2002",

}

TY - CONF

T1 - A BAC library for grape and strategies for the development of a physical framework for the grape genome

AU - Tomkins, J. P.

AU - Peterson, D. G.

AU - Yang, T. J.

AU - Main, D.

AU - Ablett, Effie M.

AU - Henry, Robert, J.

AU - Lee, L. Slade

AU - Holton, Timothy A.

AU - Waters, Daniel LE

AU - Wing, R. A.

PY - 2002

Y1 - 2002

N2 - We have constructed a grape BAC library using the cultivar Syrah. The library contains 55,296 clones stored in 144 384-well microtiter plates. A random sampling of 381 BACs indicated an average insert size of 144 kb with a range of 30 to 355 kb, and less than 4% of the clones do not contain inserts. Eighty-nine percent of BAC clones in the library have an average insert size greater than 100 kb. Based on a genome size of 483 Mb, library coverage is 16.5 haploid genome equivalents. Screening the BAC library colony filters with cpDNA sequences showed that contamination of the genomic library with chloroplast clones was low (1.5%). Library screening of an 11X coverage (2 BAC colony filters) with 12 cDNA probes corresponding to flavonoid and stilbene biosynthesis genes resulted in an average of 13 hits per probe (range = 1 to 27). ). To gain a glimpse into the grape genome and evaluate the library for sequence-tagged connector (STC) development, 768 BAC clones were end sequenced in both forward and reverse directions. The STCs were queried against the SWISS-PROT database and significant hits were sorted according to putative function. Potential applications of this library towards the development of a physical framework for the grape genome will also be discussed.

AB - We have constructed a grape BAC library using the cultivar Syrah. The library contains 55,296 clones stored in 144 384-well microtiter plates. A random sampling of 381 BACs indicated an average insert size of 144 kb with a range of 30 to 355 kb, and less than 4% of the clones do not contain inserts. Eighty-nine percent of BAC clones in the library have an average insert size greater than 100 kb. Based on a genome size of 483 Mb, library coverage is 16.5 haploid genome equivalents. Screening the BAC library colony filters with cpDNA sequences showed that contamination of the genomic library with chloroplast clones was low (1.5%). Library screening of an 11X coverage (2 BAC colony filters) with 12 cDNA probes corresponding to flavonoid and stilbene biosynthesis genes resulted in an average of 13 hits per probe (range = 1 to 27). ). To gain a glimpse into the grape genome and evaluate the library for sequence-tagged connector (STC) development, 768 BAC clones were end sequenced in both forward and reverse directions. The STCs were queried against the SWISS-PROT database and significant hits were sorted according to putative function. Potential applications of this library towards the development of a physical framework for the grape genome will also be discussed.

M3 - Other

T2 - Plant, Animal and Microbe Genomes X Conference

Y2 - 12 January 2002

ER -

A BAC library for grape and strategies for the development of a physical framework for the grape genome

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