Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Broad Institute Genome Sequencing Platform; Tarjei S Mikkelsen; Matthew J Wakefield; Bronwen Aken; Chris T Amemiya; Jean L Chang; Shannon Duke; Manuel Garber; Andrew J Gentles; Leo Goodstadt; Andreas Heger; Jerzy Jurka; Michael Kamal; Evan Mauceli; Stephen M J Searle; Ted Sharpe; Michelle L Baker; Mark A Batzer; Panayiotis V Benos; Katherine Belov; Michele Clamp; April Cook; James Cuff; Radhika Das; Lance Davidow; Janine E Deakin; Melissa J Fazzari; Jacob L Glass; Manfred Grabherr; John M Greally; Wanjun Gu; Timothy A Hore; Gavin A Huttley; Michael Kleber; Randy L Jirtle; Edda Koina; Jeannie T Lee; Shaun Mahony; Marco A Marra; Robert D Miller; Robert D Nicholls; Mayumi Oda; Anthony T Papenfuss; Zuly E Parra; David D Pollock; David A Ray; Jacqueline E Schein; Terence P Speed; Katherine Thompson; John L VandeBerg; Chris P Ponting

doi:10.1038/nature05805

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Broad Institute Genome Sequencing Platform, Tarjei S Mikkelsen, Matthew J Wakefield, Bronwen Aken, Chris T Amemiya, Jean L Chang, Shannon Duke, Manuel Garber, Andrew J Gentles, Leo Goodstadt, Andreas Heger, Jerzy Jurka, Michael Kamal, Evan Mauceli, Stephen M J Searle, Ted Sharpe, Michelle L Baker, Mark A Batzer, Panayiotis V Benos, Katherine BelovMichele Clamp, April Cook, James Cuff, Radhika Das, Lance Davidow, Janine E Deakin, Melissa J Fazzari, Jacob L Glass, Manfred Grabherr, John M Greally, Wanjun Gu, Timothy A Hore, Gavin A Huttley, Michael Kleber, Randy L Jirtle, Edda Koina, Jeannie T Lee, Shaun Mahony, Marco A Marra, Robert D Miller, Robert D Nicholls, Mayumi Oda, Anthony T Papenfuss, Zuly E Parra, David D Pollock, David A Ray, Jacqueline E Schein, Terence P Speed, Katherine Thompson, John L VandeBerg, Chris P Ponting

Research output: Contribution to journal › Article › peer-review

Abstract

We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

Original language	English
Pages (from-to)	167-77
Number of pages	11
Journal	Nature
Volume	447
Issue number	7141
DOIs	https://doi.org/10.1038/nature05805
Publication status	Published - 10 May 2007

Keywords

Animals
Base Composition
Conserved Sequence
DNA Transposable Elements
Evolution, Molecular
Genome
Genomics
Humans
Opossums
Polymorphism, Single Nucleotide
Protein Biosynthesis
Synteny
X Chromosome Inactivation

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Broad Institute Genome Sequencing Platform, Mikkelsen, T. S., Wakefield, M. J., Aken, B., Amemiya, C. T., Chang, J. L., Duke, S., Garber, M., Gentles, A. J., Goodstadt, L., Heger, A., Jurka, J., Kamal, M., Mauceli, E., Searle, S. M. J., Sharpe, T., Baker, M. L., Batzer, M. A., Benos, P. V., ... Ponting, C. P. (2007). Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature, 447(7141), 167-77. https://doi.org/10.1038/nature05805

@article{8f038406228c444f88e0d859586fa357,

title = "Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences",

abstract = "We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.",

keywords = "Animals, Base Composition, Conserved Sequence, DNA Transposable Elements, Evolution, Molecular, Genome, Genomics, Humans, Opossums, Polymorphism, Single Nucleotide, Protein Biosynthesis, Synteny, X Chromosome Inactivation",

author = "{Broad Institute Genome Sequencing Platform} and Mikkelsen, {Tarjei S} and Wakefield, {Matthew J} and Bronwen Aken and Amemiya, {Chris T} and Chang, {Jean L} and Shannon Duke and Manuel Garber and Gentles, {Andrew J} and Leo Goodstadt and Andreas Heger and Jerzy Jurka and Michael Kamal and Evan Mauceli and Searle, {Stephen M J} and Ted Sharpe and Baker, {Michelle L} and Batzer, {Mark A} and Benos, {Panayiotis V} and Katherine Belov and Michele Clamp and April Cook and James Cuff and Radhika Das and Lance Davidow and Deakin, {Janine E} and Fazzari, {Melissa J} and Glass, {Jacob L} and Manfred Grabherr and Greally, {John M} and Wanjun Gu and Hore, {Timothy A} and Huttley, {Gavin A} and Michael Kleber and Jirtle, {Randy L} and Edda Koina and Lee, {Jeannie T} and Shaun Mahony and Marra, {Marco A} and Miller, {Robert D} and Nicholls, {Robert D} and Mayumi Oda and Papenfuss, {Anthony T} and Parra, {Zuly E} and Pollock, {David D} and Ray, {David A} and Schein, {Jacqueline E} and Speed, {Terence P} and Katherine Thompson and VandeBerg, {John L} and Ponting, {Chris P}",

year = "2007",

month = may,

day = "10",

doi = "10.1038/nature05805",

language = "English",

volume = "447",

pages = "167--77",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "7141",

}

Broad Institute Genome Sequencing Platform, Mikkelsen, TS, Wakefield, MJ, Aken, B, Amemiya, CT, Chang, JL, Duke, S, Garber, M, Gentles, AJ, Goodstadt, L, Heger, A, Jurka, J, Kamal, M, Mauceli, E, Searle, SMJ, Sharpe, T, Baker, ML, Batzer, MA, Benos, PV, Belov, K, Clamp, M, Cook, A, Cuff, J, Das, R, Davidow, L, Deakin, JE, Fazzari, MJ, Glass, JL, Grabherr, M, Greally, JM, Gu, W, Hore, TA, Huttley, GA, Kleber, M, Jirtle, RL, Koina, E, Lee, JT, Mahony, S, Marra, MA, Miller, RD, Nicholls, RD, Oda, M, Papenfuss, AT, Parra, ZE, Pollock, DD, Ray, DA, Schein, JE, Speed, TP, Thompson, K, VandeBerg, JL & Ponting, CP 2007, 'Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences', Nature, vol. 447, no. 7141, pp. 167-77. https://doi.org/10.1038/nature05805

TY - JOUR

T1 - Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

AU - Broad Institute Genome Sequencing Platform

AU - Mikkelsen, Tarjei S

AU - Wakefield, Matthew J

AU - Aken, Bronwen

AU - Amemiya, Chris T

AU - Chang, Jean L

AU - Duke, Shannon

AU - Garber, Manuel

AU - Gentles, Andrew J

AU - Goodstadt, Leo

AU - Heger, Andreas

AU - Jurka, Jerzy

AU - Kamal, Michael

AU - Mauceli, Evan

AU - Searle, Stephen M J

AU - Sharpe, Ted

AU - Baker, Michelle L

AU - Batzer, Mark A

AU - Benos, Panayiotis V

AU - Belov, Katherine

AU - Clamp, Michele

AU - Cook, April

AU - Cuff, James

AU - Das, Radhika

AU - Davidow, Lance

AU - Deakin, Janine E

AU - Fazzari, Melissa J

AU - Glass, Jacob L

AU - Grabherr, Manfred

AU - Greally, John M

AU - Gu, Wanjun

AU - Hore, Timothy A

AU - Huttley, Gavin A

AU - Kleber, Michael

AU - Jirtle, Randy L

AU - Koina, Edda

AU - Lee, Jeannie T

AU - Mahony, Shaun

AU - Marra, Marco A

AU - Miller, Robert D

AU - Nicholls, Robert D

AU - Oda, Mayumi

AU - Papenfuss, Anthony T

AU - Parra, Zuly E

AU - Pollock, David D

AU - Ray, David A

AU - Schein, Jacqueline E

AU - Speed, Terence P

AU - Thompson, Katherine

AU - VandeBerg, John L

AU - Ponting, Chris P

PY - 2007/5/10

Y1 - 2007/5/10

N2 - We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

AB - We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

KW - Animals

KW - Base Composition

KW - Conserved Sequence

KW - DNA Transposable Elements

KW - Evolution, Molecular

KW - Genome

KW - Genomics

KW - Humans

KW - Opossums

KW - Polymorphism, Single Nucleotide

KW - Protein Biosynthesis

KW - Synteny

KW - X Chromosome Inactivation

U2 - 10.1038/nature05805

DO - 10.1038/nature05805

M3 - Article

C2 - 17495919

VL - 447

SP - 167

EP - 177

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7141

ER -

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Abstract

Keywords

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