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RESEARCH ARTICLE
Contents Vol 45(8)

Harnessing the bovine genome sequence for the Australian cattle and sheep industries

B. P. Dalrymple
+ Author Affiliations
- Author Affiliations

CSIRO Livestock Industries, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, Qld 4067, Australia. Email: Brian.Dalrymple@csiro.au

Australian Journal of Experimental Agriculture 45(8) 1011-1016 https://doi.org/10.1071/EA05043
Submitted: 9 February 2005  Accepted: 2 June 2005   Published: 26 August 2005

Abstract

Genomics is an emerging science and the release of the human and mouse genomes has significantly altered our picture of the information content of mammalian genomes. A smaller number of protein coding genes, and a larger number of genes that do not appear to encode protein products, the so-called non-coding RNAs (ncRNAs), have been identified. The first 2 drafts of the bovine genome sequence have been released, and work to utilise the framework of the bovine genome to facilitate ovine genomics is underway. In anticipation of the requirement for a detailed analysis of the ruminant genomes, their transcriptomes, interactomes, regulomes and similar, we have been developing the informatics platform for the analysis and integration of genome sequences and expression data for cattle and sheep. This resource will enable us to utilise the ruminant datasets and integrate them with equivalent data from other mammals for the advancement of animal scientific research for applications in the cattle and sheep industries in Australia.


Acknowledgments

The members of the CSIRO Livestock Industries Bioinformatics group; Toni Reverter-Gomez, Wes Barris and Sean McWilliam, without whom this would not have been possible. Rachel Hawken, the power behind IBISS. Ross Tellam for driving the involvement of CSIRO Livestock Industries in the International Bovine BAC Mapping Consortium and the Bovine Genome Project. Shaun Coffey and Peter Willadsen for their support throughout the project.


The partners in the Bovine Genome Sequencing Project are: the National Human Genome Research Institute (USA); CSIRO (Australia); the US Department of Agriculture; the State of Texas; Genome Canada; New Zealand’s Agritech Investments Ltd, Dairy Insight Inc. and AgResearch Ltd; the Kleberg Foundation (USA); and the National, Texas and South Dakota Beef Check-off Funds (USA). The sequencing and assembly of the bovine genome began in December 2003 and is being undertaken at the Baylor College of Medicine’s Human Genome Sequencing Center (USA) and the British Columbia Cancer Agency (Vancouver, Canada).


References


Ambros V (2004) The functions of animal microRNAs. Nature 431, 350–355.
| Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Barendse W (2005) The transition from quantitative trait loci to diagnostic test in cattle and other livestock. Australian Journal of Experimental Agriculture 45, 831–836. open url image1

Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D (2004) Ultraconserved elements in the human genome. Science 304, 1321–1325.
| Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM (2003) Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299, 1391–1394.
| Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Chen N, Lawson D, Bradnam K, Harris TW, Stein LD (2004) WormBase as an integrated platform for the C. elegans ORFeome. Genome Research 14, 2155–2161.
| Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S , et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308, 1149–1154.
| Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Eddy SR (2005) A model of the statistical power of comparative genome sequence analysis. PLoS Biology 3, e10.
| Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Emes RD, Beatson SA, Ponting CP, Goodstadt L (2004) Evolution and comparative genomics of odorant- and pheromone-associated genes in rodents. Genome Research 14, 591–602.
| Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Fields C, Adams MD, White O, Venter JC (1994) How many genes in the human genome? Nature Genetics 7, 345–346.
| Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Research 33, D121–D124.
| Crossref | PubMed |
open url image1

Hawken RJ, Barris WC, McWilliam SM, Dalrymple BP (2004) An interactive bovine in silico SNP database (IBISS). Mammalian Genome 15, 819–827.
| Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y , et al. (2005) Ensembl 2005. Nucleic Acids Research 33, D447–D453.
| Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409, 860–921.
| Crossref | GoogleScholarGoogle Scholar | open url image1

International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431, 931–945.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S , et al. (2004) Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Research 14, 331–342.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916–919.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Kirkness EF, Bafna V, Halpern AL, Levy S, Remington K , et al. (2003) The dog genome: survey sequencing and comparative analysis. Science 301, 1898–1903.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Lewis SE (2004) Gene ontology: looking backwards and forwards. Genome Biology 6, 103.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Maglott D, Ostell J, Pruitt KD, Tatusova T (2005) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Research 33, D54–D58.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Mattick JS (2003) Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. BioEssays 25, 930–939.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Miller W, Makova KD, Nekrutenko A, Hardison RC (2004) Comparative genomics. Annual Review of Genomics and Human Genetics 5, 15–56.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Modrek B, Lee C (2002) A genomic view of alternative splicing. Nature Genetics 30, 13–19.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562.
| Crossref | GoogleScholarGoogle Scholar | open url image1

The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I and II Team (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563–573.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Pruitt KD, Tatusova T, Maglott DR (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research 33, D501–D504.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Rat Genome Sequencing Project Consortium (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428, 493–521.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Reverter A, McWilliam SM, Barris W, Dalrymple BP (2005a) A rapid method for computationally inferring transcriptome coverage and microarray sensitivity. Bioinformatics 21, 80–89.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Reverter A, Barris W, McWilliam S, Byrne KA, Wang YH, Tan SH, Hudson N, Dalrymple BP (2005b) Validation of alternative methods of data normalization in gene co-expression studies. Bioinformatics 21, 1112–1120.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Reverter A, Barris W, Moreno-Sánchez N, McWilliam S, Wang YH, Harper GS, Lehnert SA, Dalrymple BP (2005c) Construction of gene interaction and regulatory networks in bovine skeletal muscle from expression data. Australian Journal of Experimental Agriculture 45, 821–829. open url image1

Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD (2004) Computational prediction of human metabolic pathways from the complete human genome. Genome Biology 6, R2.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Stein LD, Mungall C, Shu S, Caudy M, Mangone M , et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Research 12, 1599–1610.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Taylor JS, Raes J (2004) Duplication and divergence: the evolution of new genes and old ideas. Annual Review of Genetics 38, 615–643.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Woodley L, Valcarcel J (2002) Regulation of alternative pre-mRNA splicing. Briefings in Functional Genomics and Proteomics 1, 266–277. open url image1

Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK , et al. (2005) Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biology 3, e7.
| Crossref | GoogleScholarGoogle Scholar | open url image1