A BAC-based physical map of the Drosophila buzzatii genome

被引：17

作者：

González, J

Nefedov, M

Bosdet, I

Casals, F

Calvete, O

Delprat, A

Shin, H

Chiu, R

Mathewson, C

Wye, N

Hoskins, RA

Schein, JE

de Jong, P

Ruiz, A ^{[1
]}

机构：

[1] Univ Autonoma Barcelona, Dept Genet & Microbiol, Bellaterra 08193, Barcelona, Spain

[2] Childrens Hosp, Oakland Res Inst, Oakland, CA 94609 USA

[3] British Columbia Canc Res Ctr, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada

[4] Lawrence Berkeley Lab, Berkeley, CA 94720 USA

来源：

GENOME RESEARCH | 2005年 / 15卷 / 06期

关键词：

D O I：

10.1101/gr.3263105

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Large-insert genomic libraries facilitate cloning of large genomic regions, allow the construction of clone-based physical maps, and provide useful resources for sequencing entire genomes. Drosophila buzzatii is a representative species of the repleta group in the Drosophila subgenus, which is being widely used as a model in Studies of genome evolution, ecological adaptation, and speciation. We constructed a Bacterial Artificial Chromosome (BAC) genomic library of D. buzzatii using the shuttle vector pTARBAC2.1. The library comprises 18,353 clones with an average insert size of 152 kb and an similar to 18x expected representation of the A buzzatii euchromatic genome. We screened the entire library with six euchromatic gene probes and estimated the actual genome representation to be similar to 23x. In addition, we fingerprinted by restriction digestion and agarose gel electrophoresis a sample of 9555 clones, and assembled them using FingerPrint Contigs (FPC) software and manual editing into 345 contigs (mean of 26 clones per contig) and 670 singletons. Finally, we anchored 181 large contigs (containing 7788 clones) to the D. buzzatii salivary gland polytene chromosomes by in Situ hybridization of 427 representative clones. The BAC library and a database with all the information regarding the high coverage BAC-based physical map described in this paper are available to the research community.

引用

页码：885 / +

页数：6

共 37 条

[1] The genome sequence of Drosophila melanogaster [J].

Adams, MD ;

Celniker, SE ;

Holt, RA ;

Evans, CA ;

Gocayne, JD ;

Amanatides, PG ;

Scherer, SE ;

Li, PW ;

Hoskins, RA ;

Galle, RF ;

George, RA ;

Lewis, SE ;

Richards, S ;

Ashburner, M ;

Henderson, SN ;

Sutton, GG ;

Wortman, JR ;

Yandell, MD ;

Zhang, Q ;

Chen, LX ;

Brandon, RC ;

Rogers, YHC ;

Blazej, RG ;

Champe, M ;

Pfeiffer, BD ;

Wan, KH ;

Doyle, C ;

Baxter, EG ;

Helt, G ;

Nelson, CR ;

Miklos, GLG ;

Abril, JF ;

Agbayani, A ;

An, HJ ;

Andrews-Pfannkoch, C ;

Baldwin, D ;

Ballew, RM ;

Basu, A ;

Baxendale, J ;

Bayraktaroglu, L ;

Beasley, EM ;

Beeson, KY ;

Benos, PV ;

Berman, BP ;

Bhandari, D ;

Bolshakov, S ;

Borkova, D ;

Botchan, MR ;

Bouck, J ;

Brokstein, P .

SCIENCE, 2000, 287 (5461) :2185-2195

[2]

[Anonymous], GENOME BIOL

[3]

Barker J. S. F., 1982, CACTUS YEAST DROSOPH

[4]

Barker J.S.F., 1990, ECOLOGICAL EVOLUTION

[5]

Betrán E, 1998, EVOLUTION, V52, P144, DOI 10.2307/2410929

[6] The Foldback-like transposon Galileo is involved in the generation of two different natural chromosomal inversions of Drosophila buzzatii [J].

Casals, F ;

Cáceres, M ;

Ruiz, A .

MOLECULAR BIOLOGY AND EVOLUTION, 2003, 20 (05) :674-685

[7] The Drosophila melanogaster genome [J].

Celniker, SE ;

Rubin, GM .

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, 2003, 4 :89-117

[8]

Crow J. F., 1942, University of Texas Publications, Vno. 4228, P53

[9] Internet Contig Explorer (iCE) - A tool for visualizing clone fingerprint maps [J].

Fjell, CD ;

Bosdet, I ;

Schein, JE ;

Jones, SJM ;

Marra, MA .

GENOME RESEARCH, 2003, 13 (06) :1244-1249

[10] A modular, positive selection bacterial artificial chromosome vector with multiple cloning sites [J].

Frengen, E ;

Weichenhan, D ;

Zhao, BH ;

Osoegawa, K ;

van Geel, M ;

de Jong, PJ .

GENOMICS, 1999, 58 (03) :250-253

← 1 2 3 4 →