Progress 01/01/13 to 12/31/13
Outputs
Target Audience: Researchers Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Dr. Jiang Yu was hired as a post-doctoral fellow on the project. By the last year of the project, Dr. Yu was the key contact for analyses and updates on the reference genome sequence. He is now a research scientist at the Beijing Genomics Institute (BGI). How have the results been disseminated to communities of interest? Outcomes of this project have been disseminated through the International Sheep Genomics Consortium (ISGC), which includes investigators from across the world who are engaged in research on livestock genomics. The ISGC achieved communication in a variety of ways, including bi-weekly conference calls, as well as face-to-face workshops at the annual Plant and Animal Genome (PAG) meeting and the bi-annual meetings of the International Society of Animal Genetics (ISAG). Presentations on the reference genome sequence and assembly were made by the principle investigators each year at the PAG and ISAG meetings. A list-server with over 75 consortium participants ensured communication through emails of key decisions, results and outcomes. Presentations were also made at the annual American Sheep Industry (ASI) meetings and an article on the reference genome assembly was included in the 2013 ASI magazine. In this way, US sheep producers were made aware of the research activities within the project. A manuscript describing the whole genome assembly (Oar v3.1), the RH map, and the linkage map is in preparation. Highlights of differences between the genome structure of sheep, cattle and goats are included in the manuscript. The analysis of about a terabite of data on the transcriptome is also included. Variation of alleles, allelic imbalance and copy number variation have been included in the manuscript as points of interest. Biological stories include reproduction, digestive tract enzymes, evolution of the rumen, lipid metabolism and evolution of wool. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
In 2010, sequence data were generated at two sequencing facilities (Beijing Genomics Institute and the Roslin Institute) from DNA of a Texel ewe and a Texel ram, respectively. The first step of the reference sequence assembly involved de novo assembly of 75X reads from the Texel ewe into contigs and scaffolds. Once that was completed, sequences from both animals were used for gap filling. Version 2.0 of the ovine whole genome reference sequence (Oar v2.0) was publicly released in February, 2011 and Oar v3.1 was released in October, 2012 through NCBI GenBank. The ovine whole genome reference sequence is being used by researchers worldwide to explore genetic regions of interest. These regions likely contain genes and regulatory sequences that influence phenotypes in sheep. Thus, the reference assembly is contributing to improvement in the efficiency of research targeted towards sheep production as well as the use of sheep as a biomedical model. The reference genome assembly is now being annotated by Ensembl using an RNA dataset produced by Roslin Institute. In this way, genes and genetic regulation elements will be identified within the assembly. The RNA dataset produced by Roslin Institute is the largest transcriptome analysis of any species in Ensembl, including man. The next version of the assembly (Oar v4.0) will include the annotation and its release is expected by late 2015. Updated patches for some regions will likely be released before then. Kim Worley (BCM-HGSC) received funding from USDA/AFRI to fill gaps in the sheep assembly. Using technology and analyses developed within the project. About 89% of the gaps that existed within the assembly have been closed. This has resulted in a contig N50 of over 500 kb (previously at 41.7 kb). However, there was only a minor shift in scaffold N50 (from 100.1Mb to 101.2Mb).
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Dong, Y.M., Cockett, N., 3. c. (2013). A reference genome of the domestic goat (Capra hircus) generated by Illumina sequencing and whole genome mapping. Nature Biotechnology, 31, 135-41.
- Type:
Other
Status:
Published
Year Published:
2012
Citation:
Jiang, Y., Xie, M., Dalrymple, B.P., Kijas, J., Talbot, R., Archibald, A., Maddox, J.F., Faraut, T., Cockett, N. (2012). The domestic sheep reference genome assembly (pp. P1019). Cairns: Proc. 33rd International Society of Animal Genetics.
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Progress 01/01/10 to 12/31/13
Outputs
Target Audience: Researchers Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Dr. Jiang Yu was hired as a post-doctoral fellow on the project. By the last year of the project, Dr. Yu was the key contact for analyses and updates on the reference genome sequence. He is now a research scientist at the Beijing Genomics Institute (BGI). How have the results been disseminated to communities of interest? Outcomes of this project have been disseminated through the International Sheep Genomics Consortium (ISGC), which includes investigators from across the world who are engaged in research on livestock genomics. The ISGC achieved communication in a variety of ways, including bi-weekly conference calls, as well as face-to-face workshops at the annual Plant and Animal Genome (PAG) meeting and the bi-annual meetings of the International Society of Animal Genetics (ISAG). Presentations on the reference genome sequence and assembly were made by the principle investigators each year at the PAG and ISAG meetings. A list-server with over 75 consortium participants ensured communication through emails of key decisions, results and outcomes. Presentations were also made at the annual American Sheep Industry (ASI) meetings and an article on the reference genome assembly was included in the 2013 ASI magazine. In this way, US sheep producers were made aware of the research activities within the project. A manuscript describing the whole genome assembly (Oar v3.1), the RH map, and the linkage map is in preparation. Highlights of differences between the genome structure of sheep, cattle and goats are included in the manuscript. The analysis of about a terabite of data on the transcriptome is also included. Variation of alleles, allelic imbalance and copy number variation have been included in the manuscript as points of interest. Biological stories include reproduction, digestive tract enzymes, evolution of the rumen, lipid metabolism and evolution of wool. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
In 2010, sequence data were generated at two sequencing facilities (Beijing Genomics Institute and the Roslin Institute) from DNA of a Texel ewe and a Texel ram, respectively. The first step of the reference sequence assembly involved de novo assembly of 75X reads from the Texel ewe into contigs and scaffolds. Once that was completed, sequences from both animals were used for gap filling. Version 2.0 of the ovine whole genome reference sequence (Oar v2.0) was publicly released in February, 2011 and Oar v3.1 was released in October, 2012 through NCBI GenBank. The ovine whole genome reference sequence is being used by researchers worldwide to explore genetic regions of interest. These regions likely contain genes and regulatory sequences that influence phenotypes in sheep. Thus, the reference assembly is contributing to improvement in the efficiency of research targeted towards sheep production as well as the use of sheep as a biomedical model. The reference genome assembly is now being annotated by Ensembl using an RNA dataset produced by Roslin Institute. In this way, genes and genetic regulation elements will be identified within the assembly. The RNA dataset produced by Roslin Institute is the largest transcriptome analysis of any species in Ensembl, including man. The next version of the assembly (Oar v4.0) will include the annotation and its release is expected by late 2015. Updated patches for some regions will likely be released before then. Kim Worley (BCM-HGSC) received funding from USDA/AFRI to fill gaps in the sheep assembly. Using technology and analyses developed within the project. About 89% of the gaps that existed within the assembly have been closed. This has resulted in a contig N50 of over 500 kb (previously at 41.7 kb). However, there was only a minor shift in scaffold N50 (from 100.1Mb to 101.2Mb).
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Dong, Y.M., Cockett, N., 3. c. (2013). A reference genome of the domestic goat (Capra hircus) generated by Illumina sequencing and whole genome mapping. Nature Biotechnology, 31, 135-41.
- Type:
Other
Status:
Published
Year Published:
2012
Citation:
Jiang, Y., Xie, M., Dalrymple, B.P., Kijas, J., Talbot, R., Archibald, A., Maddox, J.F., Faraut, T., Cockett, N. (2012). The domestic sheep reference genome assembly (pp. P1019). Cairns: Proc. 33rd International Society of Animal Genetics.
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Progress 01/01/12 to 12/31/12
Outputs
Target Audience: Researchers Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Dr. Jiang Yu was hired as a post-doctoral fellow on the project. By the last year of the project, Dr. Yu was the key contact for analyses and updates on the reference genome sequence. He is now a research scientist at the Beijing Genomics Institute (BGI). How have the results been disseminated to communities of interest? Outcomes of this project have been disseminated through the International Sheep Genomics Consortium (ISGC), which includes investigators from across the world who are engaged in research on livestock genomics. The ISGC achieved communication in a variety of ways, including bi-weekly conference calls, as well as face-to-face workshops at the annual Plant and Animal Genome (PAG) meeting and the bi-annual meetings of the International Society of Animal Genetics (ISAG). Presentations on the reference genome sequence and assembly were made by the principle investigators each year at the PAG and ISAG meetings. A list-server with over 75 consortium participants ensured communication through emails of key decisions, results and outcomes. Presentations were also made at the annual American Sheep Industry (ASI) meetings and an article on the reference genome assembly was included in the 2013 ASI magazine. In this way, US sheep producers were made aware of the research activities within the project. A manuscript describing the whole genome assembly (Oar v3.1), the RH map, and the linkage map is in preparation. Highlights of differences between the genome structure of sheep, cattle and goats are included in the manuscript. The analysis of about a terabite of data on the transcriptome is also included. Variation of alleles, allelic imbalance and copy number variation have been included in the manuscript as points of interest. Biological stories include reproduction, digestive tract enzymes, evolution of the rumen, lipid metabolism and evolution of wool. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
In 2010, sequence data were generated at two sequencing facilities (Beijing Genomics Institute and the Roslin Institute) from DNA of a Texel ewe and a Texel ram, respectively. The first step of the reference sequence assembly involved de novo assembly of 75X reads from the Texel ewe into contigs and scaffolds. Once that was completed, sequences from both animals were used for gap filling. Version 2.0 of the ovine whole genome reference sequence (Oar v2.0) was publicly released in February, 2011 and Oar v3.1 was released in October, 2012 through NCBI GenBank. The ovine whole genome reference sequence is being used by researchers worldwide to explore genetic regions of interest. These regions likely contain genes and regulatory sequences that influence phenotypes in sheep. Thus, the reference assembly is contributing to improvement in the efficiency of research targeted towards sheep production as well as the use of sheep as a biomedical model. The reference genome assembly is now being annotated by Ensembl using an RNA dataset produced by Roslin Institute. In this way, genes and genetic regulation elements will be identified within the assembly. The RNA dataset produced by Roslin Institute is the largest transcriptome analysis of any species in Ensembl, including man. The next version of the assembly (Oar v4.0) will include the annotation and its release is expected by late 2015. Updated patches for some regions will likely be released before then. Kim Worley (BCM-HGSC) received funding from USDA/AFRI to fill gaps in the sheep assembly. Using technology and analyses developed within the project. About 89% of the gaps that existed within the assembly have been closed. This has resulted in a contig N50 of over 500 kb (previously at 41.7 kb). However, there was only a minor shift in scaffold N50 (from 100.1Mb to 101.2Mb).
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Dong, Y.M., Cockett, N., 3. c. (2013). A reference genome of the domestic goat (Capra hircus) generated by Illumina sequencing and whole genome mapping. Nature Biotechnology, 31, 135-41. 170,
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Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: "An ongoing project of the ISGC is development of a whole genome reference assembly. In 2010, sequence data were generated at two sequencing facilities (Beijing Genomics Institute and the Roslin Institute) from DNA of a Texel ewe and a Texel ram, respectively. The first step of the reference sequence assembly involved de novo assembly of 75X reads from the Texel ewe into contigs and scaffolds. Once that was completed, sequences from both animals were used for gap filling. Version 2.0 of the ovine whole-genome reference sequence (Oar v2.0) was publicly released in February, 2011 and Oar v3.1 was released in October, 2012 through NCBI GenBank. Several improvements to the assembly have been added in the past few months and include tracks for SNPs and annotations. These additions will improve accessibility for people searching the genome sequence. Chromosome assemblies can be found at http://www.ncbi.nlm.nih.gov/assembly/GCA_000298735.1/ and the full assembly can be found at http://www.livestockgenomics.csiro.au/cgi-bin/gbrowse/oarv3.1/." PARTICIPANTS: Utah State University (USA), CSIRO Livestock Industries (Australia), AgResearch (New Zealand), The Roslin Institute (UK), and Baylor College of Medicine-Human Genome Sequencing Center (USA). TARGET AUDIENCES: Researchers PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
In the last year, the ovine whole genome reference sequence has been used by researchers to explore genetic regions of interest. These regions likely contain genes and regulatory sequences that influence phenotypes in sheep. Thus, the reference assembly is contributing to improvement in the efficiency of sheep production as well as the use of sheep as a biomedical model.
Publications
- Dong, Y.M., Cockett, N., & 3. c., (2012). A reference genome of the domestic goat (Capra hircus) generated by Illumina sequencing and whole genome mapping: Nature Biotechnology, doi:10.1038/nbt.2478. (Published).
- Jiang, Y., Xie, M., Dalrymple, B.P., Kijas, J., Talbot, R., Archibald, A., Maddox, J.F., Faraut, T., & Cockett, N., 2012. The domestic sheep reference genome assembly. Proc. 33rd International Society of Animal Genetics, Cairns, Australia (PP1019). (Published).
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Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: Members of the International Sheep Genomics Consortium (ISGC) have continued to refine the ovine genome assembly. A new version of the assembly (Oarv3.0) will be released within the next few months. Comparison of contig positions on the sequence scaffolds with locations in the genetic and RH maps have led to improvements in resolution of the assembly. This version will have fewer intra- and inter-scaffold gaps and unmapped sequences than Oarv2.0. In addition, scaffolds and super-scaffolds will cover larger regions. PARTICIPANTS: Utah State University (USA), CSIRO Livestock Industries (Australia), AgResearch (New Zealand), University of Melbourne (Australia), University of Sydney (Australia), University of New England (Australia), Research Institute of the Biology for Farm Animals (Germany), The Roslin Institute (UK), and Baylor College of Medicine-Human Genome Sequencing Center (USA). TARGET AUDIENCES: Researchers PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The ovine whole genome reference sequence has been used by several researchers to explore genetic regions of interest. These regions likely contain genes and regulatory sequences that influence phenotypes in sheep. Thus, the reference assembly is a tool that advances studies in genomics research.
Publications
- No publications reported this period
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