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Title: The Release 6 reference sequence of the Drosophila melanogaster genome

Abstract

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellitemore » blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.« less

Authors:
 [1];  [2];  [1];  [1];  [1];  [1];  [1];  [3];  [3];  [3];  [4];  [4];  [5];  [5];  [5];  [6];  [6];  [7];  [7];  [7] more »;  [4];  [8];  [5];  [6];  [9];  [3];  [2];  [1] « less
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
  3. Howard Hughes Medical Inst., Ashburn, VA (United States). Janelia Farm Research Campus
  4. BC Cancer Agency, Vancouver, BC (Canada)
  5. Sapienza Univ. of Rome (Italy)
  6. Autonomous Univ. of Madrid (Spain)
  7. Russian Academy of Sciences (RAS), Moscow (Russian Federation)
  8. Federal Univ. of Rio de Janeiro (Brazil)
  9. Russian Academy of Sciences (RAS), Moscow (Russian Federation); Novosibirsk State Univ. (Russian Federation)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1257379
Grant/Contract Number:  
AC02- 05CH11231; AC0376SF00098; 13-04-40137; 12-04-00874-a; BFU2011-30295-C02-01; R01 GM064590
Resource Type:
Accepted Manuscript
Journal Name:
Genome Research
Additional Journal Information:
Journal Volume: 25; Journal Issue: 3; Journal ID: ISSN 1088-9051
Publisher:
Cold Spring Harbor Laboratory Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Hoskins, Roger A., Carlson, Joseph W., Wan, Kenneth H., Park, Soo, Mendez, Ivonne, Galle, Samuel E., Booth, Benjamin W., Pfeiffer, Barret D., George, Reed A., Svirskas, Robert, Krzywinski, Martin, Schein, Jacqueline, Accardo, Maria Carmela, Damia, Elisabetta, Messina, Giovanni, Méndez-Lago, María, de Pablos, Beatriz, Demakova, Olga V., Andreyeva, Evgeniya N., Boldyreva, Lidiya V., Marra, Marco, Carvalho, A. Bernardo, Dimitri, Patrizio, Villasante, Alfredo, Zhimulev, Igor F., Rubin, Gerald M., Karpen, Gary H., and Celniker, Susan E. The Release 6 reference sequence of the Drosophila melanogaster genome. United States: N. p., 2015. Web. doi:10.1101/gr.185579.114.
Hoskins, Roger A., Carlson, Joseph W., Wan, Kenneth H., Park, Soo, Mendez, Ivonne, Galle, Samuel E., Booth, Benjamin W., Pfeiffer, Barret D., George, Reed A., Svirskas, Robert, Krzywinski, Martin, Schein, Jacqueline, Accardo, Maria Carmela, Damia, Elisabetta, Messina, Giovanni, Méndez-Lago, María, de Pablos, Beatriz, Demakova, Olga V., Andreyeva, Evgeniya N., Boldyreva, Lidiya V., Marra, Marco, Carvalho, A. Bernardo, Dimitri, Patrizio, Villasante, Alfredo, Zhimulev, Igor F., Rubin, Gerald M., Karpen, Gary H., & Celniker, Susan E. The Release 6 reference sequence of the Drosophila melanogaster genome. United States. doi:10.1101/gr.185579.114.
Hoskins, Roger A., Carlson, Joseph W., Wan, Kenneth H., Park, Soo, Mendez, Ivonne, Galle, Samuel E., Booth, Benjamin W., Pfeiffer, Barret D., George, Reed A., Svirskas, Robert, Krzywinski, Martin, Schein, Jacqueline, Accardo, Maria Carmela, Damia, Elisabetta, Messina, Giovanni, Méndez-Lago, María, de Pablos, Beatriz, Demakova, Olga V., Andreyeva, Evgeniya N., Boldyreva, Lidiya V., Marra, Marco, Carvalho, A. Bernardo, Dimitri, Patrizio, Villasante, Alfredo, Zhimulev, Igor F., Rubin, Gerald M., Karpen, Gary H., and Celniker, Susan E. Wed . "The Release 6 reference sequence of the Drosophila melanogaster genome". United States. doi:10.1101/gr.185579.114. https://www.osti.gov/servlets/purl/1257379.
@article{osti_1257379,
title = {The Release 6 reference sequence of the Drosophila melanogaster genome},
author = {Hoskins, Roger A. and Carlson, Joseph W. and Wan, Kenneth H. and Park, Soo and Mendez, Ivonne and Galle, Samuel E. and Booth, Benjamin W. and Pfeiffer, Barret D. and George, Reed A. and Svirskas, Robert and Krzywinski, Martin and Schein, Jacqueline and Accardo, Maria Carmela and Damia, Elisabetta and Messina, Giovanni and Méndez-Lago, María and de Pablos, Beatriz and Demakova, Olga V. and Andreyeva, Evgeniya N. and Boldyreva, Lidiya V. and Marra, Marco and Carvalho, A. Bernardo and Dimitri, Patrizio and Villasante, Alfredo and Zhimulev, Igor F. and Rubin, Gerald M. and Karpen, Gary H. and Celniker, Susan E.},
abstractNote = {Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.},
doi = {10.1101/gr.185579.114},
journal = {Genome Research},
number = 3,
volume = 25,
place = {United States},
year = {2015},
month = {1}
}

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