Circumventing Heterozygosity: Sequencing the Amplified Genome of a Single Haploid Drosophila melanogaster Embryo

被引:39
作者
Langley, Charles H. [1 ]
Crepeau, Marc [1 ]
Cardeno, Charis [1 ]
Corbett-Detig, Russell [1 ]
Stevens, Kristian [1 ]
机构
[1] Univ Calif Davis, Dept Ecol & Evolut, Davis, CA 95616 USA
基金
美国国家卫生研究院;
关键词
PATERNAL EFFECT GENE; AMPLIFICATION; TELOMERES; CLONING; CELLS;
D O I
10.1534/genetics.111.127530
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Heterozygosity is a major challenge to efficient, high-quality genomic assembly and to the full genomic survey of polymorphism and divergence. In Drosophila melanogaster lines derived from equatorial populations are particularly resistant to inbreeding, thus imposing a major barrier to the determination and analyses of genomic variation in natural populations of this model organism. Here we present a simple genome sequencing protocol based on the whole-genome amplification of the gynogenetically derived haploid genome of a progeny of females mated to males homozygous for the recessive male sterile mutation, ms(3)K81. A single "lane" of paired-end sequences (2 x 76 bp) provides a good syntenic assembly with > 95% high-quality coverage (more than five reads). The amplification of the genomic DNA moderately inflates the variation in coverage across the euchromatic portion of the genome. It also increases the frequency of chimeric clones. But the low frequency and random genomic distribution of the chimeric clones limits their impact on the final assemblies. This method provides a solid path forward for population genomic sequencing and offers applications to many other systems in which small amounts of genomic DNA have unique experimental relevance.
引用
收藏
页码:239 / U21
页数:11
相关论文
共 24 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]   Accurate whole human genome sequencing using reversible terminator chemistry [J].
Bentley, David R. ;
Balasubramanian, Shankar ;
Swerdlow, Harold P. ;
Smith, Geoffrey P. ;
Milton, John ;
Brown, Clive G. ;
Hall, Kevin P. ;
Evers, Dirk J. ;
Barnes, Colin L. ;
Bignell, Helen R. ;
Boutell, Jonathan M. ;
Bryant, Jason ;
Carter, Richard J. ;
Cheetham, R. Keira ;
Cox, Anthony J. ;
Ellis, Darren J. ;
Flatbush, Michael R. ;
Gormley, Niall A. ;
Humphray, Sean J. ;
Irving, Leslie J. ;
Karbelashvili, Mirian S. ;
Kirk, Scott M. ;
Li, Heng ;
Liu, Xiaohai ;
Maisinger, Klaus S. ;
Murray, Lisa J. ;
Obradovic, Bojan ;
Ost, Tobias ;
Parkinson, Michael L. ;
Pratt, Mark R. ;
Rasolonjatovo, Isabelle M. J. ;
Reed, Mark T. ;
Rigatti, Roberto ;
Rodighiero, Chiara ;
Ross, Mark T. ;
Sabot, Andrea ;
Sankar, Subramanian V. ;
Scally, Aylwyn ;
Schroth, Gary P. ;
Smith, Mark E. ;
Smith, Vincent P. ;
Spiridou, Anastassia ;
Torrance, Peta E. ;
Tzonev, Svilen S. ;
Vermaas, Eric H. ;
Walter, Klaudia ;
Wu, Xiaolin ;
Zhang, Lu ;
Alam, Mohammed D. ;
Anastasi, Carole .
NATURE, 2008, 456 (7218) :53-59
[3]   CLONING OF DNA-SEQUENCES FROM THE WHITE LOCUS OF DROSOPHILA-MELANOGASTER BY A NOVEL AND GENERAL-METHOD [J].
BINGHAM, PM ;
LEVIS, R ;
RUBIN, GM .
CELL, 1981, 25 (03) :693-704
[4]   Identification of EMS-Induced Mutations in Drosophila melanogaster by Whole-Genome Sequencing [J].
Blumenstiel, Justin P. ;
Noll, Aaron C. ;
Griffiths, Jennifer A. ;
Perera, Anoja G. ;
Walton, Kendra N. ;
Gilliland, William D. ;
Hawley, R. Scott ;
Staehling-Hampton, Karen .
GENETICS, 2009, 182 (01) :25-32
[5]   Comprehensive human genome amplification using multiple displacement amplification [J].
Dean, FB ;
Hosono, S ;
Fang, LH ;
Wu, XH ;
Faruqi, AF ;
Bray-Ward, P ;
Sun, ZY ;
Zong, QL ;
Du, YF ;
Du, J ;
Driscoll, M ;
Song, WM ;
Kingsmore, SF ;
Egholm, M ;
Lasken, RS .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (08) :5261-5266
[6]   Specialization of a Drosophila Capping Protein Essential for the Protection of Sperm Telomeres [J].
Dubruille, Raphaelle ;
Orsi, Guillermo A. ;
Delabaere, Laetitia ;
Cortier, Elisabeth ;
Couble, Pierre ;
Marais, Gabriel A. B. ;
Loppin, Benjamin .
CURRENT BIOLOGY, 2010, 20 (23) :2090-2099
[7]   The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease [J].
El-Sayed, NM ;
Myler, PJ ;
Bartholomeu, DC ;
Nilsson, D ;
Aggarwal, G ;
Tran, AN ;
Ghedin, E ;
Worthey, EA ;
Delcher, AL ;
Blandin, G ;
Westenberger, SJ ;
Caler, E ;
Cerqueira, GC ;
Branche, C ;
Haas, B ;
Anupama, A ;
Arner, E ;
Åslund, L ;
Attipoe, P ;
Bontempi, E ;
Bringaud, F ;
Burton, P ;
Cadag, E ;
Campbell, DA ;
Carrington, M ;
Crabtree, J ;
Darban, H ;
da Silveira, JF ;
de Jong, P ;
Edwards, K ;
Englund, PT ;
Fazelina, G ;
Feldblyum, T ;
Ferella, M ;
Frasch, AC ;
Gull, K ;
Horn, D ;
Hou, LH ;
Huang, YT ;
Kindlund, E ;
Ktingbeil, M ;
Kluge, S ;
Koo, H ;
Lacerda, D ;
Levin, MJ ;
Lorenzi, H ;
Louie, T ;
Machado, CR ;
McCulloch, R ;
McKenna, A .
SCIENCE, 2005, 309 (5733) :409-415
[8]  
Falconer D. S., 1989, Introduction to quantitative genetics.
[9]   The Drosophila grapes gene is related to checkpoint gene chk1/rad27 and is required for late syncytial division fidelity [J].
Fogarty, P ;
Campbell, SD ;
AbuShumays, R ;
deSaintPhalle, B ;
Yu, KR ;
Uy, GL ;
Goldberg, ML ;
Sullivan, W .
CURRENT BIOLOGY, 1997, 7 (06) :418-426
[10]   GYNOGENESIS IN DROSOPHILA-MELANOGASTER [J].
FUYAMA, Y .
JAPANESE JOURNAL OF GENETICS, 1984, 59 (01) :91-96