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The tammar wallaby genome and transcriptome

A cross-journal collection of articles from the tammar wallaby genome and transcriptome sequencing project.

Collection published: 10 August 2011

Last updated: 17 October 2012

The tammar wallaby (Macropus eugenii) is a kangaroo species native to islands lying near the coasts of Western and South Australia, as well as to small pockets of the mainland. The tammar is considered to be a model marsupial organism, and its value lies chiefly in the study of mammalian evolution, development and immunity. In a collection of articles published by BioMed Central, including a lead article in Genome Biology, the Australian-led, international Tammar Wallaby Genome Sequencing Consortium present the tammar wallaby genome and transcriptome sequences. These landmark datasets constitute the first kangaroo genome sequence and are enriched by a number of exciting biological findings that have only been made possible by the novel availability of sequencing data.

Left: a tammar wallaby. Right: newborn tammar in its mother’s pouch.

		Research article Unique small RNA signatures uncovered in the tammar wallaby genome James Lindsay, Dawn M Carone, Judy Brown, Laura Hall, Sohaib Qureshi, Sarah E Mitchell, Nicholas Jannetty, Greg Hannon, Marilyn Renfree, Andrew Pask, Michael O’Neill, Rachel O’Neill BMC Genomics 2012, 13:559 (17 October 2012) Abstract \| Full text \| PDF \| PubMed
		Research Selected imprinting of INS in the marsupial Jessica M Stringer, Shunsuke Suzuki, Andrew J Pask, Geoff Shaw, Marilyn B Renfree Epigenetics & Chromatin 2012, 5:14 (28 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary INS, the gene encoding insulin, is imprinted in the mammary gland, suggesting a role for genomic imprinting during lactation which may be as critical for post-natal growth in mammals as imprinting in the placenta is pre-natally.
		Research article The mammary gland-specific marsupial ELP and eutherian CTI share a common ancestral gene Elizabeth A Pharo, Alison A De Leo, Marilyn B Renfree, Peter C Thomson, Christophe M Lefèvre, Kevin R Nicholas BMC Evolutionary Biology 2012, 12:80 (8 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article HOXA13 and HOXD13 expression during development of the syndactylous digits in the marsupial Macropus eugenii Keng Yih Chew, Hongshi Yu, Andrew J Pask, Geoffrey Shaw, Marilyn B Renfree BMC Developmental Biology 2012, 12:2 (11 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article A novel MSMB-related microprotein in the postovulatory egg coats of marsupials Stephen Frankenberg, Jane Fenelon, Bonnie Dopheide, Geoff Shaw, Marilyn B Renfree BMC Evolutionary Biology 2011, 11:373 (30 December 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Desert hedgehog is a mammal-specific gene expressed during testicular and ovarian development in a marsupial William A O'Hara, Walid J Azar, Richard R Behringer, Marilyn B Renfree, Andrew J Pask BMC Developmental Biology 2011, 11:72 (1 December 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Differential roles of TGIF family genes in mammalian reproduction Yanqiu Hu, Hongshi Yu, Geoff Shaw, Marilyn B Renfree, Andrew J Pask BMC Developmental Biology 2011, 11:58 (29 September 2011) Abstract \| Full text \| PDF \| PubMed
		Research Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, Hongshi Yu, Kirsty R Short, Hannah V Siddle, Stephen R Frankenberg, Keng Chew, Brandon R Menzies, Jessica M Stringer, Shunsuke Suzuki, Timothy A Hore, Margaret L Delbridge et al. Genome Biology 2011, 12:R81 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology
		Research article A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii) Chenwei Wang, Lee Webley, Ke-jun Wei, Matthew J Wakefield, Hardip R Patel, Janine E Deakin, Amber Alsop, Jennifer A Marshall Graves, Desmond W Cooper, Frank W Nicholas, Kyall R Zenger BMC Genetics 2011, 12:72 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The second-generation anchored genetic linkage map of the tammar wallaby genome has been constructed based on a total of 148 loci, and is a significant step towards complete genome coverage.
		Database Immunome database for marsupials and monotremes Emily SW Wong, Anthony T Papenfuss, Katherine Belov BMC Immunology 2011, 12:48 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Immunome Database for Marsupials and Monotremes is a comprehensive simple-to-use database of all known marsupial and monotreme immune genes which provides a catalogue of available genomic and transcriptomic datasets and a tool for evolutionary analyses into mammalian immunity.
		Research article A first-generation integrated tammar wallaby map and its use in creating a tammar wallaby first-generation virtual genome map Chenwei Wang, Janine E Deakin, Willem Rens, Kyall R Zenger, Katherine Belov, Jennifer A Marshall Graves, Frank W Nicholas BMC Genomics 2011, 12:422 (19 August 2011) Abstract \| Full text \| PDF \| PubMed
		Research article The tammar wallaby major histocompatibility complex shows evidence of past genomic instability Hannah V Siddle, Janine E Deakin, Penny Coggill, Laurens G Wilming, Jennifer Harrow, Jim Kaufman, Stephan Beck, Katherine Belov BMC Genomics 2011, 12:421 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The wallaby major histocompatibility complex of genes (MHC) has undergone genomic remodeling that includes gene duplication and reorganization of gene clusters since the American and Australian marsupials last shared a common ancestor.
		Research article Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby Emily SW Wong, Anthony T Papenfuss, Andreas Heger, Arthur L Hsu, Chris P Ponting, Robert D Miller, Jane C Fenelon, Marilyn B Renfree, Richard A Gibbs, Katherine Belov BMC Genomics 2011, 12:420 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptome analysis of the thoracic and the cervical thymuses of the tammar wallaby shows that both are functionally equivalent and have comparable patterns of gene expression suggesting an identical role in T-cell development.
		Research article Identification of two distinct genes at the vertebrate TRPC2 locus and their characterisation in a marsupial and a monotreme Stephen Frankenberg, Nanette Y Schneider, Terrence P Fletcher, Geoffrey Shaw, Marilyn B Renfree BMC Molecular Biology 2011, 12:39 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The tammar wallaby transient receptor potential channel, subfamily C, member 2 (TRPC2) locus, previously defined as a single gene in mouse, in fact consists of two distinct genes and this arrangement is conserved in all known vertebrates.
		Research article Characterisation of marsupial PHLDA2 reveals eutherian specific acquisition of imprinting Shunsuke Suzuki, Geoffrey Shaw, Tomoko Kaneko-Ishino, Fumitoshi Ishino, Marilyn B Renfree BMC Evolutionary Biology 2011, 11:244 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The marsupial orthologue of the mammalian PHLDA2 gene, expressed in the less-well developed placenta of the tammar wallaby, is not imprinted suggesting that acquisition of genomic imprinting in this gene occurred specifically in eutherians after marsupial divergence.
		Research Placental expression of pituitary hormones is an ancestral feature of therian mammals Brandon R Menzies, Andrew J Pask, Marilyn B Renfree EvoDevo 2011, 2:16 (19 August 2011) Abstract \| Full text \| PDF \| PubMed
		Research highlight Sequencing skippy: the genome sequence of an Australian kangaroo, Macropus eugenii Elizabeth P Murchison, David J Adams Genome Biology 2011, 12:123 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Sanger Institute's David Adams finds our kangaroo genome sequence article to be a fascinating window on mammalian evolution
		Research article ATRX has a critical and conserved role in mammalian sexual differentiation Kim Huyhn, Marilyn B Renfree, Jennifer A Graves, Andrew J Pask BMC Developmental Biology 2011, 11:39 (14 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic Shafagh Al Nadaf, Paul D Waters, Edda Koina, Janine E Deakin, Kristen S Jordan, Jennifer AM Graves Genome Biology 2010, 11:R122 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Incomplete escape from X inactivation in marsupials is revealed by a map of gene expression from the tammar wallaby X chromosome.

		Research article Unique small RNA signatures uncovered in the tammar wallaby genome James Lindsay, Dawn M Carone, Judy Brown, Laura Hall, Sohaib Qureshi, Sarah E Mitchell, Nicholas Jannetty, Greg Hannon, Marilyn Renfree, Andrew Pask, Michael O’Neill, Rachel O’Neill BMC Genomics 2012, 13:559 (17 October 2012) Abstract \| Full text \| PDF \| PubMed
		Research Selected imprinting of INS in the marsupial Jessica M Stringer, Shunsuke Suzuki, Andrew J Pask, Geoff Shaw, Marilyn B Renfree Epigenetics & Chromatin 2012, 5:14 (28 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary INS, the gene encoding insulin, is imprinted in the mammary gland, suggesting a role for genomic imprinting during lactation which may be as critical for post-natal growth in mammals as imprinting in the placenta is pre-natally.
		Research article The mammary gland-specific marsupial ELP and eutherian CTI share a common ancestral gene Elizabeth A Pharo, Alison A De Leo, Marilyn B Renfree, Peter C Thomson, Christophe M Lefèvre, Kevin R Nicholas BMC Evolutionary Biology 2012, 12:80 (8 June 2012) Abstract \| Full text \| PDF \| PubMed
		Research article HOXA13 and HOXD13 expression during development of the syndactylous digits in the marsupial Macropus eugenii Keng Yih Chew, Hongshi Yu, Andrew J Pask, Geoffrey Shaw, Marilyn B Renfree BMC Developmental Biology 2012, 12:2 (11 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article A novel MSMB-related microprotein in the postovulatory egg coats of marsupials Stephen Frankenberg, Jane Fenelon, Bonnie Dopheide, Geoff Shaw, Marilyn B Renfree BMC Evolutionary Biology 2011, 11:373 (30 December 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Desert hedgehog is a mammal-specific gene expressed during testicular and ovarian development in a marsupial William A O'Hara, Walid J Azar, Richard R Behringer, Marilyn B Renfree, Andrew J Pask BMC Developmental Biology 2011, 11:72 (1 December 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Differential roles of TGIF family genes in mammalian reproduction Yanqiu Hu, Hongshi Yu, Geoff Shaw, Marilyn B Renfree, Andrew J Pask BMC Developmental Biology 2011, 11:58 (29 September 2011) Abstract \| Full text \| PDF \| PubMed
		Research Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, Hongshi Yu, Kirsty R Short, Hannah V Siddle, Stephen R Frankenberg, Keng Chew, Brandon R Menzies, Jessica M Stringer, Shunsuke Suzuki, Timothy A Hore, Margaret L Delbridge et al. Genome Biology 2011, 12:R81 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology
		Research article A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii) Chenwei Wang, Lee Webley, Ke-jun Wei, Matthew J Wakefield, Hardip R Patel, Janine E Deakin, Amber Alsop, Jennifer A Marshall Graves, Desmond W Cooper, Frank W Nicholas, Kyall R Zenger BMC Genetics 2011, 12:72 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The second-generation anchored genetic linkage map of the tammar wallaby genome has been constructed based on a total of 148 loci, and is a significant step towards complete genome coverage.
		Database Immunome database for marsupials and monotremes Emily SW Wong, Anthony T Papenfuss, Katherine Belov BMC Immunology 2011, 12:48 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Immunome Database for Marsupials and Monotremes is a comprehensive simple-to-use database of all known marsupial and monotreme immune genes which provides a catalogue of available genomic and transcriptomic datasets and a tool for evolutionary analyses into mammalian immunity.
		Research article A first-generation integrated tammar wallaby map and its use in creating a tammar wallaby first-generation virtual genome map Chenwei Wang, Janine E Deakin, Willem Rens, Kyall R Zenger, Katherine Belov, Jennifer A Marshall Graves, Frank W Nicholas BMC Genomics 2011, 12:422 (19 August 2011) Abstract \| Full text \| PDF \| PubMed
		Research article The tammar wallaby major histocompatibility complex shows evidence of past genomic instability Hannah V Siddle, Janine E Deakin, Penny Coggill, Laurens G Wilming, Jennifer Harrow, Jim Kaufman, Stephan Beck, Katherine Belov BMC Genomics 2011, 12:421 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The wallaby major histocompatibility complex of genes (MHC) has undergone genomic remodeling that includes gene duplication and reorganization of gene clusters since the American and Australian marsupials last shared a common ancestor.
		Research article Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby Emily SW Wong, Anthony T Papenfuss, Andreas Heger, Arthur L Hsu, Chris P Ponting, Robert D Miller, Jane C Fenelon, Marilyn B Renfree, Richard A Gibbs, Katherine Belov BMC Genomics 2011, 12:420 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptome analysis of the thoracic and the cervical thymuses of the tammar wallaby shows that both are functionally equivalent and have comparable patterns of gene expression suggesting an identical role in T-cell development.
		Research article Identification of two distinct genes at the vertebrate TRPC2 locus and their characterisation in a marsupial and a monotreme Stephen Frankenberg, Nanette Y Schneider, Terrence P Fletcher, Geoffrey Shaw, Marilyn B Renfree BMC Molecular Biology 2011, 12:39 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The tammar wallaby transient receptor potential channel, subfamily C, member 2 (TRPC2) locus, previously defined as a single gene in mouse, in fact consists of two distinct genes and this arrangement is conserved in all known vertebrates.
		Research article Characterisation of marsupial PHLDA2 reveals eutherian specific acquisition of imprinting Shunsuke Suzuki, Geoffrey Shaw, Tomoko Kaneko-Ishino, Fumitoshi Ishino, Marilyn B Renfree BMC Evolutionary Biology 2011, 11:244 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The marsupial orthologue of the mammalian PHLDA2 gene, expressed in the less-well developed placenta of the tammar wallaby, is not imprinted suggesting that acquisition of genomic imprinting in this gene occurred specifically in eutherians after marsupial divergence.
		Research Placental expression of pituitary hormones is an ancestral feature of therian mammals Brandon R Menzies, Andrew J Pask, Marilyn B Renfree EvoDevo 2011, 2:16 (19 August 2011) Abstract \| Full text \| PDF \| PubMed
		Research highlight Sequencing skippy: the genome sequence of an Australian kangaroo, Macropus eugenii Elizabeth P Murchison, David J Adams Genome Biology 2011, 12:123 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Sanger Institute's David Adams finds our kangaroo genome sequence article to be a fascinating window on mammalian evolution
		Research article ATRX has a critical and conserved role in mammalian sexual differentiation Kim Huyhn, Marilyn B Renfree, Jennifer A Graves, Andrew J Pask BMC Developmental Biology 2011, 11:39 (14 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic Shafagh Al Nadaf, Paul D Waters, Edda Koina, Janine E Deakin, Kristen S Jordan, Jennifer AM Graves Genome Biology 2010, 11:R122 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Incomplete escape from X inactivation in marsupials is revealed by a map of gene expression from the tammar wallaby X chromosome.