Progress 04/01/17 to 03/31/21
Outputs
Target Audience:The annotation of the ovine genome reference assembly delivers genomicresources for studying the sheep and comparativegenomic biologythrough online databases, including those supported by the International FAANG Consortium. This resource is relevant and useful to the entire scientific research community, extension educators and the general public. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This International collaboration has allowed the investigators to present data, meet and gather together for meaningful discussions such that they can learn from others in International Sheep Genome Consortium (ISGC), Functional Annotation of Animal Genome (FAANG) consortium and Animal Genomics community. In addition, Post-doctoral fellows, graduate and even undergraduate students have been encouraged to train and participate in this work. These opportunities occurred through workshops held prior to the International Plant and Animal Genome meetings in San Diego with joint ISGC, FAANG consortium meetings (2019 and 2020). Graduate Student training in performing methylation and chromatin immune precipitation assay followed by sequencing analyses. These outcomes were delivered as graduate students talks. These talks allowed information to be shared with other graduate students expanding these learning opportunities to other students and faculty. How have the results been disseminated to communities of interest?Theese results have been disseminated through invited talks and published manuscripts. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
1. Characterize the complexity of the ovine transcriptome and the regulatory signals that control the expression of the transcriptome using assays for coding and non-coding transcript isoforms and alternative splicing, promoters and cis-acting regulatory elements, histone modifications, DNA methylation and open chromatin across a wide range of sheep tissues. 2. Annotate the most current ovine reference genome assembly so that all transcriptome and regulatory features are included and available for analysis. Towards the goal of providing transcriptomic data for gene annotation of the new reference genome, RNA, specifically mRNA and miRNA has been extracted for approximately 30 tissues and sequenced by Dr. Kim Worley at Baylor College of Medicine. Long read Iso-sequencing has also been completed for the cerebellum, ovary, lung, alveolar macrophages, and the atrium of the rumen. Messenger RNA sequence data for an additional 30 tissues has been generated by Dr. Tim Smith of the Animal Research station at the Meat and Animal Research Center. Furthermore, mRNA for 58 tissues have been extracted and delivered to Alan Archibald and Emily Clark at the Roslin Institute, for CAGE assay and sequencing. These data have been analyzed and the manuscript has been published. DNA for these same tissues (54 tissues) have been sent to Shannon Clark at AgResearch and DNA methylation sequencing and analyses has been performed. Chromatin immune precipitation is complete for 44 tissues and library construction for sequencing by Dr. Tim Smith has been completed. Furthermore, ATAC followed by sequencing has been performed for 35 tissues. The final manuscript that describes the utility all of these data together is in progress. To improve the utility of these data the ovine reference genome has been updated to ARS-UI_rambv2.0. Importantly, these data were used towards an enhancing the annotation of thissheep reference genome.
Publications
- Type:
Journal Articles
Status:
Accepted
Year Published:
2021
Citation:
J. W. Thorne, B. M. Murdoch, B. A. Freking, R. R. Redden, T. W. Murphy, J. B. Taylor and H. D. Blackburn. Evolution of the sheep industry and genetic research in the United States: Opportunities for convergence in the 21st century. Animal Genetics. (2021) May 06.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2021
Citation:
Davenport KM, Massa AT, Bhattarai S, McKay SD, Mousel MR, Herndon MK, White SN, Cockett NE, Smith TPL, Murdoch BM. Characterizing Genetic Regulatory Elements in Ovine Tissues. Frontiers in Genetics (2021).
- Type:
Journal Articles
Status:
Accepted
Year Published:
2021
Citation:
Massa AT, Mousel MR, Herndon MK, Herndon DR, Murdoch BM, White SN. Genome-wide histone modifications and CTCF enrichment predict gene expression in sheep macrophages. Frontiers in Genetics (2021) Jan 07
- Type:
Journal Articles
Status:
Accepted
Year Published:
2020
Citation:
Salavati M, Caulton A, Clark R, Gazova I, Smith TPL. Worley KC, Cockett NE, Archabald AL, Clarke SM, Murdoch BM, Clark EL. on behalf of the Ovine FAANG Project Consortium. Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0). Frontiers in Genetics (2020) Oct 23.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2021
Citation:
1. Suraj Bhattarai1, Kimberly M. Davenport2, Alisha T. Massa3, Michelle R. Mousel4,5, Maria K. Herndon3, Stephen N. White3,4,6, Noelle Cockett7, Timothy P.L. Smith8, Brenda M. Murdoch2,6 and Stephanie D. McKay1* on behalf of The Ovine FAANG Project Consortium. Whole genome bisulfite sequencing reveals tissue specific DNA methylation profiles in Sheep. International Sheep Genome Consortium. June 8-10, 2021.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2021
Citation:
Kimberly M. Davenport1, Alisha T. Massa2, Michelle R. Mousel3,4, Maria K. Herndon2, Stephen N. White2,3,5, Mazdak Salavati6, Emily Clark6, Alan Archibald6, Suraj Bhattarai7, Stephanie D. McKay7, Kim C. Worley8, Brian Dalrymple9, James Kijas10, Alex Caulton11, Shannon Clarke11, Rudiger Brauning11, Tracy Hadfield12, Noelle E. Cockett12, Timothy P.L. Smith13, and Brenda M. Murdoch1,5 on behalf of The Ovine FAANG Project Consortium. Functional annotation of the reference Rambouillet sheep genome International Sheep Genome Consortium. June 8-10, 2021
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2021
Citation:
Kimberly M. Davenport*, Shavahn C. Loux*, Derek M. Bickhart, Kim C. Worley, Brad A. Freking, Brian L. Vander Ley, Shwetha C. Murali, Steven G. Schroeder, Noelle Cockett, Michael P. Heaton, Shannon Clarke, Thomas W. Murphy, Theodore S. Kalbfleisch, Brenda M. Murdoch, Timothy P.L. Smith, and Benjamin D. Rosen. High-quality ovine reference genome assemblies. International Sheep Genome Consortium. June 8-10, 2021
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2021
Citation:
Brenda M. Murdoch, Noelle Cockett, Tracy Hadfield, Michelle Mousel, Stephen White, Emily Clark, Mazdak Salavati, Shannon Clarke, Andrew Hess, Rudiger Brauning, Darren Hagen, Theodore S. Kalbfleisch, Michael Heaton, Derek Bickhart, Benjamin Rosen, Timothy P.L. Smith Constructing the Ovine Pan-genome. International Sheep Genome Consortium. June 8-10, 2021.
- Type:
Other
Status:
Accepted
Year Published:
2020
Citation:
Murdoch BM The functional annotation of the sheep and cattle genomes. Lecture in ANSC691 Current Topics in Genomics, Instructor Luiz Brito Nov 10th, 2020.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2021
Citation:
Kimberly M Davenport, Derek M. Bickhart, Kim C. Worley, Shwetha C. Murali, Noelle E. Cockett, Michael P. Heaton, Timothy P.L. Smith, Brenda M. Murdoch, Benjamin D. Rosen. An improved ovine reference genome assembly to facilitate in depth functional annotation of the sheep genome. GigaScience
- Type:
Journal Articles
Status:
Accepted
Year Published:
2021
Citation:
MR Mousel, SN White, MK Herndon, DR Herndon, JB Taylor, GM Becker, and B.M. Murdoch. Genes involved in immune, gene translation and chromatin organization pathways associated with Mycoplasma ovipneumoniae presence in nasal secretions of domestic sheep. PLoS One (2021).
|
Progress 04/01/19 to 03/31/20
Outputs
Target Audience:The annotation of the ovine genome reference assembly delivers tools and resources for studying the ovine genome through online databases, including those supported by the International FAANG Consortium. This resource is relevant and useful to the entire scientific research community, extension educators and the general public. Changes/Problems:While the reference genome assembly Oar_rambouillet_v1.0 is vastly better in comparison the Oar_3.1 or Oar_4.0, recent advances to the algorithms use to assemble genome have now made it possible to make great improvements to sheep reference genome. Because all of the assays described in this grant rely and build on this reference information the sheep genomics community (most of which are involved in this project) thought it imperative to improve to the current reference genome. As a result, all of the analysis pipelines we be rerun with the new assembly (Oar_rambouillet_v2.0) upon completion. Lastly, the emergenceof a worldwide pandemic has hampered our ability to move forward some of the remaining data generation and lab work. Although we anticipate with added precaution, we will be able to proceed it may be at a much slower pace.? What opportunities for training and professional development has the project provided?This International collaboration has allowed the investigators to present preliminary data, meet and gather together for meaningful discussions such that they can learn from others in International Sheep Genome Consortium (ISGC), Functional Annotation of Animal Genome (FAANG) consortium and Animal Genomics community. In addition, Post-doctoral fellows, graduate and even undergraduate students have been encouraged to train and participate in this work. These opportunities occurred through workshops held prior to the International Plant and Animal Genome meetings in San Diego with joint ISGC, FAANG consortium meetings (2019 and 2020). Graduate Student training in performing chromatin immune precipitation assay followed by sequencing analyses. The outcome of this was delivered in a talk for her graduate student seminar entitled "Hitting the Mark: Characterizing Histone Modifications and Genetic Regulatory Elements in Sheep." This talk allowed this information to be shared with other graduate students enhancing the learning opportunity to 40 other students and faculty. Furthermore, this graduate student was invited to speak in the Epigenomic workshop at the International Plant and Animal Genomes conference. Davenport KM, Massa AT, Mousel MR, Herndon MK, White SN, Bhattarai S, McKay S, Smith T.P.L, Carnahan JK, Cockett N, Murdoch BM. Hitting the Mark: Characterizing Four Histone Modifications in Ovine Liver and Spleen. The 28th International Plant and Animal Genome Conference. San Diego Ca Jan 14th, 2020. Furthermore, a graduate student is being trained to understand the methylome. Alex Caulton, Rudiger Brauning, Shannon Clarke and the Ovine FAANG Project. Characterisation of the ovine methylome and its utility as a molecular phenotype to predict stress traits. MapNet lightening talk, University of Otago. How have the results been disseminated to communities of interest?These results have been disseminated thus far through invited talks: Murdoch BM, White SN, Mousel MR, Massa A, Worley KC, Archibald AL, Clark EL, Dalrymple B, Kijas JW, Clarke SM, Brauning R, Smith TPL, Hadfield T, Cockett N. Update of the Ovine FAANG Update. The FAANG Workshop. The 28th International Plant and Animal Genome Conference. San Diego Ca Jan 10th, 2020. Clark E, Salavati M, Caulton AJ, Clark R, Gazova I, Smith TPL, Worley KC, Cockett N, Archibald AL, Clarke SM, Murdoch B. The Ovine FAANG Project: A High-Resolution Atlas of Transcription Start Sites in the New Rambouillet Ovine Reference Genome. The 28th International Plant and Animal Genome Conference. San Diego Ca Jan 11th, 2020. Murdoch BM, White SN, Mousel MR, Massa A, Worley KC, Archibald AL, Clark EL, Dalrymple B, Kijas JW, Clarke SM, Brauning R, Smith TPL, Hadfield T, Cockett N. Update of the Ovine FAANG Update. The International Sheep Genomics Consortium. The 28th International Plant and Animal Genome Conference San Diego Ca Jan 13th, 2020. Davenport KM, Massa AT, Mousel MR, Herndon MK, White SN, Bhattarai S, McKay S, Smith T.P.L, Carnahan JK, Cockett N, Murdoch BM. Hitting the Mark: Characterizing Four Histone Modifications in Ovine Liver and Spleen. The 28th International Plant and Animal Genome Conference. San Diego Ca Jan 14th, 2020. Murdoch B. Epigenetics: how nutrition and maternal environment impact offspring. The 123rd US Animal Health Association Annual Meeting, Rhode Island Providence October 29, 2019. Murdoch B. GWAS: how it works, limitations, and new developments. The 123rd US Animal Health Association Annual Meeting, Rhode Island Providence October 29, 2019. Murdoch B. Flock54: A new, targeted marker panel for the sheep industry. 37th International Society for Animal Genetics. Lleida, Spain. July 11, 2019. Murdoch B. Cost effective and informative genotyping by sequencing using Agriseq targeted sequencing for genotyping in the livestock. 37th International Society for Animal Genetics. Lleida Spain July 8, 2019. Murdoch B. Functional Annotation of the Animal Genome: FAANG. Midwestern Section American Society of Animal Science, Omaha Nebraska March 11th, 2019. Emily L. Clark, Mazdak Salavati, Alexandra J. Caulton, Richard Clark, Iveta Gazova, Tim P.L. Smith, Kim C. Worley, Noelle E. Cockett, Alan L. Archibald, Shannon Clarke, Brenda Murdoch and The Ovine FAANG Project. The Ovine FAANG Project: A High-Resolution Atlas of Transcription Start Sites in the new Rambouillet Ovine Reference Genome. FAANG-Europe workshop on Functional Annotation of Animal Genomes. Furthermore, abstracts have been presented in poster format: Cendejas PM, Davenport KM, Becker GM, Mousel MR, Massa AT, White SN, Murdoch BM. Chromatin immunoprecipitation of histone modifications: an approach to understanding gene regulation in sheep. Western Section American Society of Animal Science, Boise Idaho, June 10-13, 2019. Cendejas PM, Davenport KM, Becker GM, Mousel MR, Massa AT, White SN, Murdoch BM. Chromatin immunoprecipitation of histone modifications: an approach to understanding gene regulation in sheep. University of Idaho undergraduate research symposium, April 29, 2019. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period we will work to complete the chromatin immune-precipitation sequencing and analyses with Oar_rambouillet_v2.0. We will submit the raw sequencing data and the assembled transcript data to international database for public access. We are in the process of preparing the manuscripts for both the CAGE assay sequencing data and ChIP sequencing data. DNA methylation and ATAC sequencing assay is in the final stages of the data analyses and manuscript preparation for these will commence.
Impacts
What was accomplished under these goals?
Towards the goal of providing transcriptomic data for gene annotation of the new reference genome, RNA, specifically mRNA and miRNA has been extracted for approximately 30 tissues and sequenced by Dr. Kim Worley at Baylor College of Medicine. Long read Iso-sequencing has also been completed for the cerebellum, ovary, lung, alveolar macrophages, and the atrium of the rumen. Messenger RNA sequence data for an additional 30 tissues has been generated by Dr. Tim Smith of the Animal Research station at the Meat and Animal Research Center. Furthermore, mRNA for 58 tissues have been extracted and delivered to Alan Archibald and Emily Clark at the Roslin Institute, for CAGE assay and sequencing. Sequencing libraries have been prepared for 56 tissues and these libraries have been sequenced, check for quality and analyzed. Specifically, an adapted pipeline analysis for CAGE that uses TagDust2 for clean-up and trimming, Bowtie2 for mapping, CAGEr for normalization and clustering, and finally the Integrative Genome Viewer (IGV) for visualization. By using this pipeline, we have been able to map genome wide TSS for Benz2616, a key first step in understanding transcript regulation and diversity. These data have been analyzed and the manuscript is in preparation. Chromatin immunoprecipitation pilot projects to test antibodies on sheep and improve the ChIP-Seq protocol for multiple tissues are complete and analyses had been performed and a manuscript regarding this is in progress. Regarding the BENZ2616 tissues, chromatin immunoprecipitation has been completed for 44 tissues with all 4 antibodies; H3K4me3, H3K4me1, H3K27ac and H3K27me3, and library construction for sequencing is currently underway. It is important to note that, given recent advances of algorithms for assembling genomes, there is a concerted effort (which includes some members of the grant as well as Dr. B. Rosen) to make improvements to the current genome assembly. It is anticipated that this will increase number of mappable reads for all of the assay being analyzed. Lastly, DNA for (54 tissues) of these same tissues have been sent to Shannon Clark in New Zealand for DNA methylation assays and analyses. Leveraging of the Ovine FAANG project for new proposals A large funding bid for cattle in the European Union (H2020 SFS-30 FAANG Agri-Aqua Labs: Dr Emily Clark co-applicant and Brenda Murdoch a member of the advisory board) entitled "BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle". The BovReg consortium will provide a comprehensive map of functionally active genomic features in cattle and how their (epi)genetic variation in beef and dairy breeds translates into phenotypes. This constitutes key knowledge for biology-driven genomic prediction needed by scientific and industry livestock communities. The ovine FAANG project was used as a template for tissue selection for the functional genomics assays for BovReg and we will perform comparative analysis between sheep and cattle using the parallel CAGE and RNA-Seq datasets. Professor Alan Archibald and Dr Emily Clark, with colleagues at the European Bioinformatics Institute (EBI), submitted and received a Bioinformatics and Biological Resources Fund Application to the Biotechnology and Biological Sciences Research Council entitled - "Ensembl - adding value to animal genomes through high quality annotation". The application covered the maintenance and continued development of the Ensembl genome portal for farmed and domesticated animals. We leveraged the Benz2616 assembly as one of the examples of a highly contiguous assembly with high quality functional annotation which could be added to the Ensembl genome portal using this funding.
Publications
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Clark E, Salavati M, Caulton AJ, Clark R, Gazova I, Smith TPL, Worley KC, Cockett N, Archibald AL, Clarke SM, Murdoch B. The Ovine FAANG Project: A High-Resolution Atlas of Transcription Start Sites in the New Rambouillet Ovine Reference Genome. The 28th International Plant and Animal Genome Conference. San Diego Ca Jan 11th, 2020.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Murdoch BM, White SN, Mousel MR, Massa A, Worley KC, Archibald AL, Clark EL, Dalrymple B, Kijas JW, Clarke SM, Brauning R, Smith TPL, Hadfield T, Cockett N. Update of the Ovine FAANG Update. The International Sheep Genomics Consortium. The 28th International Plant and Animal Genome Conference San Diego Ca Jan 13th, 2020.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Davenport KM, Massa AT, Mousel MR, Herndon MK, White SN, Bhattarai S, McKay S, Smith T.P.L, Carnahan JK, Cockett N, Murdoch BM. Hitting the Mark: Characterizing Four Histone Modifications in Ovine Liver and Spleen. The 28th International Plant and Animal Genome Conference. San Diego Ca Jan 14th, 2020.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Murdoch B. Epigenetics: how nutrition and maternal environment impact offspring. The 123rd US Animal Health Association Annual Meeting, Rhode Island Providence October 29, 2019.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Murdoch B. GWAS: how it works, limitations, and new developments. The 123rd US Animal Health Association Annual Meeting, Rhode Island Providence October 29, 2019. Murdoch B. Flock54: A new, targeted marker panel for the sheep industry. 37th International Society for Animal Genetics. Lleida, Spain. July 11, 2019.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Murdoch B. Cost effective and informative genotyping by sequencing using Agriseq targeted sequencing for genotyping in the livestock. 37th International Society for Animal Genetics. Lleida Spain July 8, 2019.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Murdoch B. Functional Annotation of the Animal Genome: FAANG. Midwestern Section American Society of Animal Science, Omaha Nebraska March 11th, 2019.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Emily L. Clark, Mazdak Salavati, Alexandra J. Caulton, Richard Clark, Iveta Gazova, Tim P.L. Smith, Kim C. Worley, Noelle E. Cockett, Alan L. Archibald, Shannon Clarke, Brenda Murdoch and The Ovine FAANG Project. The Ovine FAANG Project: A High-Resolution Atlas of Transcription Start Sites in the new Rambouillet Ovine Reference Genome. FAANG-Europe workshop on Functional Annotation of Animal Genomes.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Murdoch BM, White SN, Mousel MR, Massa A, Worley KC, Archibald AL, Clark EL, Dalrymple B, Kijas JW, Clarke SM, Brauning R, Smith TPL, Hadfield T, Cockett N. Update of the Ovine FAANG Update. The FAANG Workshop. The 28th International Plant and Animal Genome Conference. San Diego Ca Jan 10th, 2020.
|
Progress 04/01/18 to 03/31/19
Outputs
Target Audience:The annotation of the ovine genome reference assembly delivers tools and resources for studying the ovine genome through online databases, including those supported by the International FAANG Consortium. This resource is relevant and useful to the scientific research community, extension educators and the general public. Changes/Problems:We experienced some delays in performing the ChIP Seq assay as this is a technically challenging methodology and each tissue requires slight modification to the protocol. Additionally, the ATAC Seq assay has presented methodological challenges and although typically performs better with fresh tissues we are making progress on the frozen tissues What opportunities for training and professional development has the project provided?This International collaboration has allowed the investigators to present preliminary data, meet and gather together for meaningful discussions such that they can learn from others in International Sheep Genome Consortium (ISGC), Functional Annotation of Animal Genome (FAANG) consortium and Animal Genomics community. In addition, Post-doctoral fellows, graduate and even undergraduate students have been encouraged to train and participate in this work. These opportunities occurred at the International Plant and Animal Genome meetings in San Diego with joint ISGC, FAANG consortium meetings (2018 and 2019). McKay S. and Murdoch B. Chromatin Immuno-Precipitation Sequencing workshop. 7th International Symposium on Animal Functional Genomics and Functional Annotation of Animal Genomes Workshop. Adelaide, Australia, November 12-15, 2018. McKay S. and Murdoch B. Transcriptomics Sequencing workshop. 7th International Symposium on Animal Functional Genomics and Functional Annotation of Animal Genomes Workshop. Adelaide, Australia, November 12-15, 2018. Graduate Student Alex Caulton at the University of Otago, New Zealand presented a lightning talk entitled "Characterisation of the ovine methylome and its utility as a molecular phenotype to predict stress traits." 2018. Graduate Student Alex Caulton at the University of Otago, New Zealand presented a poster entitled "Tissue specific characterisation of the ovine methylome" at the 7th International Symposium on Animal Functional Genomics and Functional Annotation of Animal Genomes Workshop. Adelaide, Australia, November 12-15, 2018. Undergraduate Directed Research Study AVS499 and presentations at the University of Idaho and Western Section Of the American Society of Animal Science, Cendejas PM, Davenport KM, Becker GM, Mousel MR, Massa AT, White SN, Murdoch BM. Chromatin immunoprecipitation of histone modifications: an approach to understanding gene regulation in sheep. University of Idaho undergraduate research symposium, April 29, 2019. How have the results been disseminated to communities of interest?These results have beenpredominantly disseminated thus far through invited talks: 1) Murdoch B. Functional Annotation of the Animal Genome: FAANG. Midwestern Section American Society of Animal Science, Omaha Nebraska March 11th, 2019. 2) Murdoch B, White S, Mousel M, Massa A, Worley, K, Archibald A, Clark E, Dalrymple B, Kijas J, Clarke S, Brauning R, Smith TPL, Hadfield T, Cockett N. The Ovine FAANG Project Update. International Sheep Genome Consortium. January 14th, 2019. 3) Murdoch B, White S, Mousel M, Massa A, Worley, K, Archibald A, Clark E, Dalrymple B, Kijas J, Clarke S, Brauning R, Smith TPL, Hadfield T, Cockett N. The Ovine FAANG Project: What's newe? FAANG Consortium San Diego Ca, Jan 11 2019. 4) Murdoch BM. The Ovine FAANG Project. 7th International Symposium on Animal Functional Genomics and Functional Annotation of Animal Genomes Workshop. Adelaide, Australia, November 12-15, 2018. 5) The Ovine FAANG Project. Murdoch BM, White SN, Mousel MR, Massa AT, Worley KC, Archibald AL, Clark EL, Dalrymple B, Kijas J, Clarke S, Brauning R, Smith TPL, Hadfield T, Cockett N. International Sheep Genomics Consortium. Jan 15, 2018. 6) Developing the functional annotation of the sheep genome. Murdoch BM, White SN, Mousel MR, Massa AT, Worley KC, Archibald AL, Clark EL, Dalrymple B, Kijas J, Clarke S, Brauning R, Smith TPL, Hadfield T, Cockett N. FAANG Consortium. Jan 12, 2018. Furthermore, abstracts have been presented in poster format: 1) Murdoch B, White S, Mousel M, Massa A, Worley, K, Archibald A, Clark E, Dalrymple B, Kijas J, Clarke S, Brauning R, Smith TPL, Hadfield T, Cockett N. The Ovine FAANG Project: What's newe? FAANG Consortium San Diego Ca, Jan 11 2019. 2) Liu Y, Harris RA, Qin X, Richards S, Rogers J, Han Y, Vee V, Meng Q, Heaton MP, Smith TPL, Dalrymple B, White SN, Clark EL,Kijas JW, Cockett N, Murdoch BM, Muzny DM, Worley KC. Rambouillet sheep transcriptome annotation resources. The 27th International Plant and Animal Genome Conference. San Diego Ca Jan 12-16th, 2019. 3) Massa AT, Mousel MR, Murdoch BM, White S. ChIP-Seq genome-wide identification of regulatory elements in sheep alveolar macrophages. International Plant & Animal Genomes XXVI Conference, San Diego, CA (2018) Jan 13-17. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, we will work to complete the transcriptome sequencing and analyses. We will submit the raw sequencing data and the assembled transcript data to the international database for public access. The CAGE assay sequencing data and ChIP sequencing data will be analyzed and we are in the process of preparing the manuscripts. DNA methylation and ATAC sequencing assay will proceed and the data analyses for these assays will commence soon after. Some project members will continue to deliver data, analyses updates at the 37th International Society for Animal Genetics Conference in Lleida Spain and the International Plant and Animal Genome in San Diego.
Impacts
What was accomplished under these goals?
Objective 1: Develop a deep and robust dataset of transcribed elements in the sheep genome. Transcript sequencing of the initial reference animal for mRNA is completed for 29 tissues and miRNA for 30 tissues in completed and have been deposited in NCBI https://www.ncbi.nlm.nih.gov/biosample?LinkName=bioproject_biosample_all&from_uid=414087. Long read Iso Seq has been completed for 7 tissues and is in the process of being submitted to NCBI. Furthermore, mRNA will be extracted and sequenced from 30 additional tissues to total 60 tissues. Objective 2: Develop a deep and robust dataset of transcription regulatory features of the sheep. To date, mRNA has been extracted from 60 tissues (the same tissues targeted for mRNA transcript data) and shipped to Roslin Institute for CAGE assay and sequencing. Sequencing libraries have been prepared for 56 tissues and sequencing libraries for 40 of these libraries have been sequenced, assessed for quality control and preliminary analysis has been performed on this dataset. More specifically, the adapted pipeline analysis for CAGE uses TagDust2 for clean-up and trimming, Bowtie2 for mapping, CAGEr for normalization and clustering, and finally the Integrative Genome Viewer (IGV) for visualization. By using this pipeline we are able to map genome-wide TSS for Benz2616, a key first step in understanding transcript regulation and diversity. Chromatin immunoprecipitation pilot projects to test antibodies on sheep and improve the ChIP-Seq protocol for multiple tissues are complete as well as some preliminary analyses. Regarding the BENZ2616 tissues, chromatin immunoprecipitation has been completed for 42 tissues with all 4 antibodies; H3K4me3, H3K4me1, H3K27ac and H3K27me3, and library construction for sequencing is currently underway. DNA for these same tissues (54 tissues to date) from Benz2616 have been delivered to Shannon Clark in New Zealand for DNA methylation assays and analyses. Whole genome bisulfite sequencing (WGBS) is planned for 12 tissues and reduced-representation bisulfite sequencing (RRBS) is planned for all 54 tissues.
Publications
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2019
Citation:
Murdoch B. Functional Annotation of the Animal Genome: FAANG. Midwestern Section American Society of Animal Science, Omaha Nebraska March 11th, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Murdoch B, White S, Mousel M, Massa A, Worley, K, Archibald A, Clark E, Dalrymple B, Kijas J, Clarke S, Brauning R, Smith TPL, Hadfield T, Cockett N. The Ovine FAANG Project Update. International Sheep Genome Consortium. January 14th, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Murdoch B, White S, Mousel M, Massa A, Worley, K, Archibald A, Clark E, Dalrymple B, Kijas J, Clarke S, Brauning R, Smith TPL, Hadfield T, Cockett N. The Ovine FAANG Project: Whats newe? FAANG Consortium San Diego Ca, Jan 11 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Murdoch BM. The Ovine FAANG Project. 7th International Symposium on Animal Functional Genomics and Functional Annotation of Animal Genomes Workshop. Adelaide, Australia, November 12-15, 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
The Ovine FAANG Project. Murdoch BM, White SN, Mousel MR, Massa AT, Worley KC, Archibald AL, Clark EL, Dalrymple B, Kijas J, Clarke S, Brauning R, Smith TPL, Hadfield T, Cockett N. International Sheep Genomics Consortium. Jan 15, 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Developing the functional annotation of the sheep genome. Murdoch BM, White SN, Mousel MR, Massa AT, Worley KC, Archibald AL, Clark EL, Dalrymple B, Kijas J, Clarke S, Brauning R, Smith TPL, Hadfield T, Cockett N. FAANG Consortium. Jan 12, 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Murdoch B, White S, Mousel M, Massa A, Worley, K, Archibald A, Clark E, Dalrymple B, Kijas J, Clarke S, Brauning R, Smith TPL, Hadfield T, Cockett N. The Ovine FAANG Project: Whats newe? FAANG Consortium San Diego Ca, Jan 11 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Liu Y, Harris RA, Qin X, Richards S, Rogers J, Han Y, Vee V, Meng Q, Heaton MP, Smith TPL, Dalrymple B, White SN, Clark EL,Kijas JW, Cockett N, Murdoch BM, Muzny DM, Worley KC. Rambouillet sheep transcriptome annotation resources. The 27th International Plant and Animal Genome Conference. San Diego Ca Jan 12-16th, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Massa AT, Mousel MR, Murdoch BM, White S. ChIP-Seq genome-wide identification of regulatory elements in sheep alveolar macrophages. International Plant & Animal Genomes XXVI Conference, San Diego, CA (2018) Jan 13-17.
|
Progress 04/01/17 to 03/31/18
Outputs
Target Audience:The annotation of the ovine genome reference assembly delivers tools and resources for studying the ovine genome through online databases, including those supported by the International FAANG Consortium. This resource is relevant and useful to the scientific research community and the general public. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This International collaboration has allowed the investigators to present preliminary data, meet and gather together for meaningful discussions such that they can learn from others in International Sheep Genome Consortium (ISGC), Functional Annotation of Animal Genome (FAANG) consortium and Animal Genomics community. In addition, Post-doctoral fellows, graduate and even undergraduate students have been encouraged to train and participate in this work. These opportunities occurred at the International Plant and Animal Genome meetings in San Diego with joint ISGC, FAANG consortium meetings (2017 and 2018) as well as the International Society of Animal Genomes meeting in Dublin Ireland (2017). How have the results been disseminated to communities of interest?These results have been disseminated thus far through invited talks: The Ovine FAANG Project. Murdoch BM, White SN, Mousel MR, Massa AT, Worley KC, Archibald AL, Clark EL, Dalrymple B, Kijas J, Clarke S, Brauning R, Smith TPL, Hadfield T, Cockett N. International Sheep Genomics Consortium. Jan 15, 2018. Developing the functional annotation of the sheep genome. Murdoch BM, White SN, Mousel MR, Massa AT, Worley KC, Archibald AL, Clark EL, Dalrymple B, Kijas J, Clarke S, Brauning R, Smith TPL, Hadfield T, Cockett N. FAANG Consortium. Jan 12, 2018. Rambouillet Sheep Genomic Resources. Liu Y, Harris RA., Qin X, Richards S, Rogers J, Han Y, Vee V, Wang M, Meng Q, Heaton MP, Smith T.P.L., Dalrymple B, White SN, Murdoch BM, Kijas JW, Cockett N, Muzny DM, Gibbs R, Worley K. International Plant & Animal Genomes XXV Conference, January 14, 2017. Gene regulation in Sheep Alveolar Macrophages: Genome-Wide Identification of Active Enhancers. Massa A, Mousel M, Murdoch BM, White S. 36th International Society of Animal Genetic Conference, Dublin July 20, 2017. Update on the Rambouillet Assembly, the 5.0 Reference, and plans for FAANG RNA Sequencing. Liu Y, Harris RA, Qin X, Richards S, Rogers J, Han Y, Vee V, Wang M, Meng Q, Heaton MP, Smith TPL, Dalrymple B, White SN, Murdoch BM, Kijas JW, Cockett N, Muzny DM, Gibbs R, Worley K. International Plant & Animal Genomes XXV Conference, January 16, 2017. Genome-Wide Landscape of Active Enhancers in Sheep Alveolar Macrophages. Massa A, Mousel M, Murdoch BM, White S. International Plant & Animal Genomes XXV Conference, January 16, 2017. Furthermore, abstracts have been presented in poster format: Massa AT, Mousel MR, Murdoch BM, White S. ChIP-Seq genome-wide identification of regulatory elements in sheep alveolar macrophages. International Plant & Animal Genomes XXVI Conference, San Diego, CA (2018) Jan 13-17. Murdoch B, White S, Mousel M, Massa A, Worley K, Archibald A, Clark E, Dalrymple B, Kijas J, Clarke S, Brauning R, Smith T, Hadfield T, Cockett N. The Ovine Functional Annotation Project. 36th International Society of Animal Genetic Conference, Dublin, Ireland (2017) July 16-21. Liu Y, Harris RA, Qin X, Richards S, Rogers J, Han Y, Meng Q, Smith TP, Dalrymple BP, White SN, Murdoch BM, Kijas JW, Cockett N, Muzny DM, Worley KC. Rambouillet Sheep Genome and FAANG RNA Resources. 36th International Society of Animal Genetic Conference, Dublin, Ireland (2017) July 16-21. Massa A, Mousel M, Murdoch B, White S. Gene regulation in sheep alveolar macrophages: Genome-wide identification of active enhancers. 36th International Society of Animal Genetic Conference, Dublin, Ireland (2017) July 16-21. Liu Y, Harris RA, Qin X, Richards S, Rodger J, Han Y, Vee V, Meng Q, Heaton M, Smith TPL, Dalrymple B, White S, Murdoch B, Kijas J, Cockett N, Muzny D, Gibbs R, Worley KC. Rambouillet Sheep Genomic Resources. International Plant & Animal Genomes XXV Conference, San Diego, CA (2017) January 14-18. Massa A, Mousel M, Murdoch BM, White S. Genome-Wide Identification of Active Enhancers in Sheep Alveolar Macrophages. International Plant & Animal Genomes XXV Conference, San Diego, CA (2017) January 14-18. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period we will work to complete the transcriptome sequencing and analyses. We will submit the raw sequencing data and the assembled transcript data to international database for public access. The CAGE assay sequencing data should be coming through the pipeline and the DNA assays (DNA methylation, ChIP seq, ATAC seq) will begin. Some project members will join the training events during International Symposium on Animal Functional Genomics and FAANG conference in Adelaide Australia.
Impacts
What was accomplished under these goals?
Towards the goal of providing transcriptomic data for gene annotation of the new reference genome, RNA, specifically mRNA and miRNA has been extracted for approximately 30 tissues and sequenced by Dr. Kim Worley at Baylor College of Medicine. Long read Iso-sequencing has also been completed for the cerebellum, ovary, lung, alveolar macrophage, and the atrium of the rumen. Furthermore, mRNA has been extracted for 44 tissues by Dr. Timothy Smith and shipped to Emily Clark and Alan Archibald at the Roslin Institute for CAGE sequencing.
Publications
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2017
Citation:
1.The Ovine FAANG Project. Murdoch BM, White SN, Mousel MR, Massa AT, Worley KC, Archibald AL, Clark EL, Dalrymple B, Kijas J, Clarke S, Brauning R, Smith TPL, Hadfield T, Cockett N. International Sheep Genomics Consortium. Jan 15, 2018.
2.Developing the functional annotation of the sheep genome. Murdoch BM, White SN, Mousel MR, Massa AT, Worley KC, Archibald AL, Clark EL, Dalrymple B, Kijas J, Clarke S, Brauning R, Smith TPL, Hadfield T, Cockett N. FAANG Consortium. Jan 12, 2018.
3.Rambouillet Sheep Genomic Resources. Liu Y, Harris RA., Qin X, Richards S, Rogers J, Han Y, Vee V, Wang M, Meng Q, Heaton MP, Smith T.P.L., Dalrymple B, White SN, Murdoch BM, Kijas JW, Cockett N, Muzny DM, Gibbs R, Worley K. Plant & Animal Genomes XXV Conference, January 14, 2017.
4.Gene regulation in Sheep Alveolar Macrophages: Genome-Wide Identification of Active Enhancers. Massa A, Mousel M, Murdoch BM, White S. 36th International Society of Animal Genetic Conference, Dublin July 20, 2017.
5.Update on the Rambouillet Assembly, the 5.0 Reference, and plans for FAANG RNA Sequencing. Liu Y, Harris RA, Qin X, Richards S, Rogers J, Han Y, Vee V, Wang M, Meng Q, Heaton MP, Smith TPL, Dalrymple B, White SN, Murdoch BM, Kijas JW, Cockett N, Muzny DM, Gibbs R, Worley K. Plant & Animal Genomes XXV Conference, January 16, 2017.
6.Genome-Wide Landscape of Active Enhancers in Sheep Alveolar Macrophages. Massa A, Mousel M, Murdoch BM, White S. Plant & Animal Genomes XXV Conference, January 16, 2017.
- Type:
Book Chapters
Status:
Published
Year Published:
2017
Citation:
Noelle E. Cockett, Brian Dalrymple, James Kijas, Brenda Murdoch, Kim C. Worley. Mapping the sheep genome, Chapter 5, Achieving sustainable production of sheep Burleigh Dodds Series in Agricultural Science (Book 22), Edited by Prof J.P.C. Greyling, Burleigh Dodds Science Publishing September 15, 2017
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