Evolution of genes and genomes on the Drosophila phylogeny.: Drosophila 12 Genomes Consortium

Andrew G Clark; Michael B Eisen; Douglas R Smith; Casey M Bergman; Brian Oliver; Therese A Markow; Thomas C Kaufman; Manolis Kellis; William Gelbart; Venky N Iyer; Daniel A Pollard; Timothy B Sackton; Amanda M Larracuente; Nadia D Singh; Jose P Abad; Dawn N Abt; Boris Adryan; Montserrat Aguade; Hiroshi Akashi; Wyatt W Anderson; Charles F Aquadro; David H Ardell; Roman Arguello; Carlo G Artieri; Daniel A Barbash; Daniel Barker; Paolo Barsanti; Phil Batterham; Serafim Batzoglou; Dave Begun; Arjun Bhutkar; Enrico Blanco; Stephanie A Bosak; Robert K Bradley; Adrianne D Brand; Michael R Brent; Angela N Brooks; Randall H Brown; Roger K Butlin; Corrado Caggese; Brian R Calvi; A Bernardo de Carvalho; Anat Caspi; Sergio Castrezana; Susan E Celniker; Jean L Chang; Ana C L Garcia; Rasmus Nielsen; Jakob Skou Pedersen; Filipe Jorge Garrett Vieira; Drosophila 12 Genomes Consortium

doi:10.1038/nature06341

Evolution of genes and genomes on the Drosophila phylogeny. Drosophila 12 Genomes Consortium

Andrew G Clark, Michael B Eisen, Douglas R Smith, Casey M Bergman, Brian Oliver, Therese A Markow, Thomas C Kaufman, Manolis Kellis, William Gelbart, Venky N Iyer, Daniel A Pollard, Timothy B Sackton, Amanda M Larracuente, Nadia D Singh, Jose P Abad, Dawn N Abt, Boris Adryan, Montserrat Aguade, Hiroshi Akashi, Wyatt W AndersonCharles F Aquadro, David H Ardell, Roman Arguello, Carlo G Artieri, Daniel A Barbash, Daniel Barker, Paolo Barsanti, Phil Batterham, Serafim Batzoglou, Dave Begun, Arjun Bhutkar, Enrico Blanco, Stephanie A Bosak, Robert K Bradley, Adrianne D Brand, Michael R Brent, Angela N Brooks, Randall H Brown, Roger K Butlin, Corrado Caggese, Brian R Calvi, A Bernardo de Carvalho, Anat Caspi, Sergio Castrezana, Susan E Celniker, Jean L Chang, Ana C L Garcia, Rasmus Nielsen, Jakob Skou Pedersen, Filipe Jorge Garrett Vieira, Drosophila 12 Genomes Consortium

1361 Citations (Scopus)

Abstract

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Original language	English
Journal	Nature
Volume	450
Issue number	7167
Pages (from-to)	203-18
Number of pages	15
ISSN	0028-0836
DOIs	https://doi.org/10.1038/nature06341
Publication status	Published - 2007

Keywords

Faculty of Science
Animals
Codon
DNA
DNA Transposable Elements
Drosophila
Drosophila Proteins
Evolution, Molecular
Molecular
Gene Order
Genes, Insect
Genome, Insect
Genome, Mitochondrial
Genomics
Immunity
Multigene Family
Phylogeny
RNA, Untranslated
Reproduction
Sequence Alignment
Analysis, DNA
Synteny

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Clark, A. G., Eisen, M. B., Smith, D. R., Bergman, C. M., Oliver, B., Markow, T. A., Kaufman, T. C., Kellis, M., Gelbart, W., Iyer, V. N., Pollard, D. A., Sackton, T. B., Larracuente, A. M., Singh, N. D., Abad, J. P., Abt, D. N., Adryan, B., Aguade, M., Akashi, H., ... Drosophila 12 Genomes Consortium (2007). Evolution of genes and genomes on the Drosophila phylogeny. Drosophila 12 Genomes Consortium. Nature, 450(7167), 203-18. https://doi.org/10.1038/nature06341

Clark, AG, Eisen, MB, Smith, DR, Bergman, CM, Oliver, B, Markow, TA, Kaufman, TC, Kellis, M, Gelbart, W, Iyer, VN, Pollard, DA, Sackton, TB, Larracuente, AM, Singh, ND, Abad, JP, Abt, DN, Adryan, B, Aguade, M, Akashi, H, Anderson, WW, Aquadro, CF, Ardell, DH, Arguello, R, Artieri, CG, Barbash, DA, Barker, D, Barsanti, P, Batterham, P, Batzoglou, S, Begun, D, Bhutkar, A, Blanco, E, Bosak, SA, Bradley, RK, Brand, AD, Brent, MR, Brooks, AN, Brown, RH, Butlin, RK, Caggese, C, Calvi, BR, Bernardo de Carvalho, A, Caspi, A, Castrezana, S, Celniker, SE, Chang, JL, Garcia, ACL, Nielsen, R, Pedersen, JS, Garrett Vieira, FJ & Drosophila 12 Genomes Consortium 2007, 'Evolution of genes and genomes on the Drosophila phylogeny. Drosophila 12 Genomes Consortium', Nature, vol. 450, no. 7167, pp. 203-18. https://doi.org/10.1038/nature06341

@article{ac3886904dc311dd8d9f000ea68e967b,

title = "Evolution of genes and genomes on the Drosophila phylogeny.: Drosophila 12 Genomes Consortium",

abstract = "Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.",

keywords = "Faculty of Science, Animals, Codon, DNA, DNA Transposable Elements, Drosophila, Drosophila Proteins, Evolution, Molecular, Molecular, Gene Order, Genes, Insect, Genome, Insect, Genome, Mitochondrial, Genomics, Immunity, Multigene Family, Phylogeny, RNA, Untranslated, Reproduction, Sequence Alignment, Analysis, DNA, Synteny",

author = "Clark, {Andrew G} and Eisen, {Michael B} and Smith, {Douglas R} and Bergman, {Casey M} and Brian Oliver and Markow, {Therese A} and Kaufman, {Thomas C} and Manolis Kellis and William Gelbart and Iyer, {Venky N} and Pollard, {Daniel A} and Sackton, {Timothy B} and Larracuente, {Amanda M} and Singh, {Nadia D} and Abad, {Jose P} and Abt, {Dawn N} and Boris Adryan and Montserrat Aguade and Hiroshi Akashi and Anderson, {Wyatt W} and Aquadro, {Charles F} and Ardell, {David H} and Roman Arguello and Artieri, {Carlo G} and Barbash, {Daniel A} and Daniel Barker and Paolo Barsanti and Phil Batterham and Serafim Batzoglou and Dave Begun and Arjun Bhutkar and Enrico Blanco and Bosak, {Stephanie A} and Bradley, {Robert K} and Brand, {Adrianne D} and Brent, {Michael R} and Brooks, {Angela N} and Brown, {Randall H} and Butlin, {Roger K} and Corrado Caggese and Calvi, {Brian R} and {Bernardo de Carvalho}, A and Anat Caspi and Sergio Castrezana and Celniker, {Susan E} and Chang, {Jean L} and Garcia, {Ana C L} and Rasmus Nielsen and Pedersen, {Jakob Skou} and {Garrett Vieira}, {Filipe Jorge} and {Drosophila 12 Genomes Consortium}",

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doi = "10.1038/nature06341",

language = "English",

volume = "450",

pages = "203--18",

journal = "Nature",

issn = "0028-0836",

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number = "7167",

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T1 - Evolution of genes and genomes on the Drosophila phylogeny.

T2 - Drosophila 12 Genomes Consortium

AU - Clark, Andrew G

AU - Eisen, Michael B

AU - Smith, Douglas R

AU - Bergman, Casey M

AU - Oliver, Brian

AU - Markow, Therese A

AU - Kaufman, Thomas C

AU - Kellis, Manolis

AU - Gelbart, William

AU - Iyer, Venky N

AU - Pollard, Daniel A

AU - Sackton, Timothy B

AU - Larracuente, Amanda M

AU - Singh, Nadia D

AU - Abad, Jose P

AU - Abt, Dawn N

AU - Adryan, Boris

AU - Aguade, Montserrat

AU - Akashi, Hiroshi

AU - Anderson, Wyatt W

AU - Aquadro, Charles F

AU - Ardell, David H

AU - Arguello, Roman

AU - Artieri, Carlo G

AU - Barbash, Daniel A

AU - Barker, Daniel

AU - Barsanti, Paolo

AU - Batterham, Phil

AU - Batzoglou, Serafim

AU - Begun, Dave

AU - Bhutkar, Arjun

AU - Blanco, Enrico

AU - Bosak, Stephanie A

AU - Bradley, Robert K

AU - Brand, Adrianne D

AU - Brent, Michael R

AU - Brooks, Angela N

AU - Brown, Randall H

AU - Butlin, Roger K

AU - Caggese, Corrado

AU - Calvi, Brian R

AU - Bernardo de Carvalho, A

AU - Caspi, Anat

AU - Castrezana, Sergio

AU - Celniker, Susan E

AU - Chang, Jean L

AU - Garcia, Ana C L

AU - Nielsen, Rasmus

AU - Pedersen, Jakob Skou

AU - Garrett Vieira, Filipe Jorge

AU - Drosophila 12 Genomes Consortium

PY - 2007

Y1 - 2007

N2 - Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

AB - Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

KW - Faculty of Science

KW - Animals

KW - Codon

KW - DNA

KW - DNA Transposable Elements

KW - Drosophila

KW - Drosophila Proteins

KW - Evolution, Molecular

KW - Molecular

KW - Gene Order

KW - Genes, Insect

KW - Genome, Insect

KW - Genome, Mitochondrial

KW - Genomics

KW - Immunity

KW - Multigene Family

KW - Phylogeny

KW - RNA, Untranslated

KW - Reproduction

KW - Sequence Alignment

KW - Analysis, DNA

KW - Synteny

U2 - 10.1038/nature06341

DO - 10.1038/nature06341

M3 - Journal article

C2 - 17994087

SN - 0028-0836

VL - 450

SP - 203

EP - 218

JO - Nature

JF - Nature

IS - 7167

ER -

Evolution of genes and genomes on the Drosophila phylogeny. Drosophila 12 Genomes Consortium

Abstract

Keywords

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