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Title: Comparative genome sequencing of drosophila pseudoobscura: Chromosomal, gene and cis-element evolution

Abstract

The genome sequence of a second fruit fly, D. pseudoobscura, presents an opportunity for comparative analysis of a primary model organism D. melanogaster. The vast majority of Drosophila genes have remained on the same arm, but within each arm gene order has been extensively reshuffled leading to the identification of approximately 1300 syntenic blocks. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 35 My since divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome wide average consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than control sequences between the species but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a picture of repeat mediated chromosomal rearrangement, and high co-adaptation of both male genes and cis-regulatory sequences emerges as important themes ofmore » genome divergence between these species of Drosophila.« less

Authors:
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Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Director. Office of Science. Office of Biological and Environmental Research (US)
OSTI Identifier:
838187
Report Number(s):
LBNL-55260
R&D Project: LGFGAA; TRN: US200507%%583
DOE Contract Number:  
AC03-76SF00098
Resource Type:
Journal Article
Journal Name:
Science
Additional Journal Information:
Journal Volume: 15; Journal Issue: 1; Other Information: Submitted to Science: Volume 15, No.1; Journal Publication Date: 01/2005; PBD: 1 Apr 2004
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; AMINO ACID SEQUENCE; DROSOPHILA; GENES; MALES; PROTEINS; RECOMBINATION; TESTES

Citation Formats

Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, Thornton, Kevin, Todd, Melissa J., Chen, Rui, Meisel, Richard P., Couronne, Olivier, Hua, Sujun, Smith, Mark A., Bussemaker, Harmen J., van Batenburg, Marinus F., Howells, Sally L., Scherer, Steven E., Sodergren, Erica, Matthews, Beverly B., Crosby, Madeline A., Schroeder, Andrew J., Ortiz-Barrientos, Daniel, Rives, Catherine M., Metzker, Michael L., Muzny, Donna M., Scott, Graham, Steffen, David, Wheeler, David A., Worley, Kim C., Havlak, Paul, Durbin, K. James, Egan, Amy, Gill, Rachel, Hume, Jennifer, Morgan, Margaret B., Miner, George, Hamilton, Cerissa, Huang, Yanmei, Waldron, Lenee, Verduzco, Daniel, Blankenburg, Kerstin P., Dubchak, Inna, Noor, Mohamed A.F., Anderson, Wyatt, White, Kevin P., Clark, Andrew G., Schaeffer, Stephen W., Gelbart, William, Weinstock, George M., and Gibbs, Richard A. Comparative genome sequencing of drosophila pseudoobscura: Chromosomal, gene and cis-element evolution. United States: N. p., 2004. Web.
Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, Thornton, Kevin, Todd, Melissa J., Chen, Rui, Meisel, Richard P., Couronne, Olivier, Hua, Sujun, Smith, Mark A., Bussemaker, Harmen J., van Batenburg, Marinus F., Howells, Sally L., Scherer, Steven E., Sodergren, Erica, Matthews, Beverly B., Crosby, Madeline A., Schroeder, Andrew J., Ortiz-Barrientos, Daniel, Rives, Catherine M., Metzker, Michael L., Muzny, Donna M., Scott, Graham, Steffen, David, Wheeler, David A., Worley, Kim C., Havlak, Paul, Durbin, K. James, Egan, Amy, Gill, Rachel, Hume, Jennifer, Morgan, Margaret B., Miner, George, Hamilton, Cerissa, Huang, Yanmei, Waldron, Lenee, Verduzco, Daniel, Blankenburg, Kerstin P., Dubchak, Inna, Noor, Mohamed A.F., Anderson, Wyatt, White, Kevin P., Clark, Andrew G., Schaeffer, Stephen W., Gelbart, William, Weinstock, George M., & Gibbs, Richard A. Comparative genome sequencing of drosophila pseudoobscura: Chromosomal, gene and cis-element evolution. United States.
Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, Thornton, Kevin, Todd, Melissa J., Chen, Rui, Meisel, Richard P., Couronne, Olivier, Hua, Sujun, Smith, Mark A., Bussemaker, Harmen J., van Batenburg, Marinus F., Howells, Sally L., Scherer, Steven E., Sodergren, Erica, Matthews, Beverly B., Crosby, Madeline A., Schroeder, Andrew J., Ortiz-Barrientos, Daniel, Rives, Catherine M., Metzker, Michael L., Muzny, Donna M., Scott, Graham, Steffen, David, Wheeler, David A., Worley, Kim C., Havlak, Paul, Durbin, K. James, Egan, Amy, Gill, Rachel, Hume, Jennifer, Morgan, Margaret B., Miner, George, Hamilton, Cerissa, Huang, Yanmei, Waldron, Lenee, Verduzco, Daniel, Blankenburg, Kerstin P., Dubchak, Inna, Noor, Mohamed A.F., Anderson, Wyatt, White, Kevin P., Clark, Andrew G., Schaeffer, Stephen W., Gelbart, William, Weinstock, George M., and Gibbs, Richard A. Thu . "Comparative genome sequencing of drosophila pseudoobscura: Chromosomal, gene and cis-element evolution". United States. https://www.osti.gov/servlets/purl/838187.
@article{osti_838187,
title = {Comparative genome sequencing of drosophila pseudoobscura: Chromosomal, gene and cis-element evolution},
author = {Richards, Stephen and Liu, Yue and Bettencourt, Brian R. and Hradecky, Pavel and Letovsky, Stan and Nielsen, Rasmus and Thornton, Kevin and Todd, Melissa J. and Chen, Rui and Meisel, Richard P. and Couronne, Olivier and Hua, Sujun and Smith, Mark A. and Bussemaker, Harmen J. and van Batenburg, Marinus F. and Howells, Sally L. and Scherer, Steven E. and Sodergren, Erica and Matthews, Beverly B. and Crosby, Madeline A. and Schroeder, Andrew J. and Ortiz-Barrientos, Daniel and Rives, Catherine M. and Metzker, Michael L. and Muzny, Donna M. and Scott, Graham and Steffen, David and Wheeler, David A. and Worley, Kim C. and Havlak, Paul and Durbin, K. James and Egan, Amy and Gill, Rachel and Hume, Jennifer and Morgan, Margaret B. and Miner, George and Hamilton, Cerissa and Huang, Yanmei and Waldron, Lenee and Verduzco, Daniel and Blankenburg, Kerstin P. and Dubchak, Inna and Noor, Mohamed A.F. and Anderson, Wyatt and White, Kevin P. and Clark, Andrew G. and Schaeffer, Stephen W. and Gelbart, William and Weinstock, George M. and Gibbs, Richard A.},
abstractNote = {The genome sequence of a second fruit fly, D. pseudoobscura, presents an opportunity for comparative analysis of a primary model organism D. melanogaster. The vast majority of Drosophila genes have remained on the same arm, but within each arm gene order has been extensively reshuffled leading to the identification of approximately 1300 syntenic blocks. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 35 My since divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome wide average consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than control sequences between the species but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a picture of repeat mediated chromosomal rearrangement, and high co-adaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.},
doi = {},
journal = {Science},
number = 1,
volume = 15,
place = {United States},
year = {2004},
month = {4}
}