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1.  Analyses of pig genomes provide insight into porcine demography and evolution 
Groenen, Martien A. M. | Archibald, Alan L. | Uenishi, Hirohide | Tuggle, Christopher K. | Takeuchi, Yasuhiro | Rothschild, Max F. | Rogel-Gaillard, Claire | Park, Chankyu | Milan, Denis | Megens, Hendrik-Jan | Li, Shengting | Larkin, Denis M. | Kim, Heebal | Frantz, Laurent A. F. | Caccamo, Mario | Ahn, Hyeonju | Aken, Bronwen L. | Anselmo, Anna | Anthon, Christian | Auvil, Loretta | Badaoui, Bouabid | Beattie, Craig W. | Bendixen, Christian | Berman, Daniel | Blecha, Frank | Blomberg, Jonas | Bolund, Lars | Bosse, Mirte | Botti, Sara | Bujie, Zhan | Bystrom, Megan | Capitanu, Boris | Silva, Denise Carvalho | Chardon, Patrick | Chen, Celine | Cheng, Ryan | Choi, Sang-Haeng | Chow, William | Clark, Richard C. | Clee, Christopher | Crooijmans, Richard P. M. A. | Dawson, Harry D. | Dehais, Patrice | De Sapio, Fioravante | Dibbits, Bert | Drou, Nizar | Du, Zhi-Qiang | Eversole, Kellye | Fadista, João | Fairley, Susan | Faraut, Thomas | Faulkner, Geoffrey J. | Fowler, Katie E. | Fredholm, Merete | Fritz, Eric | Gilbert, James G. R. | Giuffra, Elisabetta | Gorodkin, Jan | Griffin, Darren K. | Harrow, Jennifer L. | Hayward, Alexander | Howe, Kerstin | Hu, Zhi-Liang | Humphray, Sean J. | Hunt, Toby | Hornshøj, Henrik | Jeon, Jin-Tae | Jern, Patric | Jones, Matthew | Jurka, Jerzy | Kanamori, Hiroyuki | Kapetanovic, Ronan | Kim, Jaebum | Kim, Jae-Hwan | Kim, Kyu-Won | Kim, Tae-Hun | Larson, Greger | Lee, Kyooyeol | Lee, Kyung-Tai | Leggett, Richard | Lewin, Harris A. | Li, Yingrui | Liu, Wansheng | Loveland, Jane E. | Lu, Yao | Lunney, Joan K. | Ma, Jian | Madsen, Ole | Mann, Katherine | Matthews, Lucy | McLaren, Stuart | Morozumi, Takeya | Murtaugh, Michael P. | Narayan, Jitendra | Nguyen, Dinh Truong | Ni, Peixiang | Oh, Song-Jung | Onteru, Suneel | Panitz, Frank | Park, Eung-Woo | Park, Hong-Seog | Pascal, Geraldine | Paudel, Yogesh | Perez-Enciso, Miguel | Ramirez-Gonzalez, Ricardo | Reecy, James M. | Zas, Sandra Rodriguez | Rohrer, Gary A. | Rund, Lauretta | Sang, Yongming | Schachtschneider, Kyle | Schraiber, Joshua G. | Schwartz, John | Scobie, Linda | Scott, Carol | Searle, Stephen | Servin, Bertrand | Southey, Bruce R. | Sperber, Goran | Stadler, Peter | Sweedler, Jonathan V. | Tafer, Hakim | Thomsen, Bo | Wali, Rashmi | Wang, Jian | Wang, Jun | White, Simon | Xu, Xun | Yerle, Martine | Zhang, Guojie | Zhang, Jianguo | Zhang, Jie | Zhao, Shuhong | Rogers, Jane | Churcher, Carol | Schook, Lawrence B.
Nature  2012;491(7424):393-398.
For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
doi:10.1038/nature11622
PMCID: PMC3566564  PMID: 23151582
2.  Tracking and coordinating an international curation effort for the CCDS Project 
The Consensus Coding Sequence (CCDS) collaboration involves curators at multiple centers with a goal of producing a conservative set of high quality, protein-coding region annotations for the human and mouse reference genome assemblies. The CCDS data set reflects a ‘gold standard’ definition of best supported protein annotations, and corresponding genes, which pass a standard series of quality assurance checks and are supported by manual curation. This data set supports use of genome annotation information by human and mouse researchers for effective experimental design, analysis and interpretation. The CCDS project consists of analysis of automated whole-genome annotation builds to identify identical CDS annotations, quality assurance testing and manual curation support. Identical CDS annotations are tracked with a CCDS identifier (ID) and any future change to the annotated CDS structure must be agreed upon by the collaborating members. CCDS curation guidelines were developed to address some aspects of curation in order to improve initial annotation consistency and to reduce time spent in discussing proposed annotation updates. Here, we present the current status of the CCDS database and details on our procedures to track and coordinate our efforts. We also present the relevant background and reasoning behind the curation standards that we have developed for CCDS database treatment of transcripts that are nonsense-mediated decay (NMD) candidates, for transcripts containing upstream open reading frames, for identifying the most likely translation start codons and for the annotation of readthrough transcripts. Examples are provided to illustrate the application of these guidelines.
Database URL: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi
doi:10.1093/database/bas008
PMCID: PMC3308164  PMID: 22434842
3.  Community gene annotation in practice 
Manual annotation of genomic data is extremely valuable to produce an accurate reference gene set but is expensive compared with automatic methods and so has been limited to model organisms. Annotation tools that have been developed at the Wellcome Trust Sanger Institute (WTSI, http://www.sanger.ac.uk/.) are being used to fill that gap, as they can be used remotely and so open up viable community annotation collaborations. We introduce the ‘Blessed’ annotator and ‘Gatekeeper’ approach to Community Annotation using the Otterlace/ZMap genome annotation tool. We also describe the strategies adopted for annotation consistency, quality control and viewing of the annotation.
Database URL: http://vega.sanger.ac.uk/index.html
doi:10.1093/database/bas009
PMCID: PMC3308165  PMID: 22434843

Results 1-3 (3)