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Grimplet J, Van Hemert J, Carbonell-Bejerano P, Díaz-Riquelme J, Dickerson J, Fennell A, Pezzotti M, Martínez-Zapater JM. Comparative analysis of grapevine whole-genome gene predictions, functional annotation, categorization and integration of the predicted gene sequences. BMC Res Notes 2012; 5:213. [PMID: 22554261 PMCID: PMC3419625 DOI: 10.1186/1756-0500-5-213] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 05/03/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The first draft assembly and gene prediction of the grapevine genome (8X base coverage) was made available to the scientific community in 2007, and functional annotation was developed on this gene prediction. Since then additional Sanger sequences were added to the 8X sequences pool and a new version of the genomic sequence with superior base coverage (12X) was produced. RESULTS In order to more efficiently annotate the function of the genes predicted in the new assembly, it is important to build on as much of the previous work as possible, by transferring 8X annotation of the genome to the 12X version. The 8X and 12X assemblies and gene predictions of the grapevine genome were compared to answer the question, "Can we uniquely map 8X predicted genes to 12X predicted genes?" The results show that while the assemblies and gene structure predictions are too different to make a complete mapping between them, most genes (18,725) showed a one-to-one relationship between 8X predicted genes and the last version of 12X predicted genes. In addition, reshuffled genomic sequence structures appeared. These highlight regions of the genome where the gene predictions need to be taken with caution. Based on the new grapevine gene functional annotation and in-depth functional categorization, twenty eight new molecular networks have been created for VitisNet while the existing networks were updated. CONCLUSIONS The outcomes of this study provide a functional annotation of the 12X genes, an update of VitisNet, the system of the grapevine molecular networks, and a new functional categorization of genes. Data are available at the VitisNet website (http://www.sdstate.edu/ps/research/vitis/pathways.cfm).
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Affiliation(s)
- Jérôme Grimplet
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), CCT, C/Madre de Dios 51, Logroño, España.
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Derrien T, Vaysse A, André C, Hitte C. Annotation of the domestic dog genome sequence: finding the missing genes. Mamm Genome 2011; 23:124-31. [PMID: 22076420 DOI: 10.1007/s00335-011-9372-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 10/23/2011] [Indexed: 12/20/2022]
Abstract
There are over 350 genetically distinct breeds of domestic dog that present considerable variation in morphology, physiology, and disease susceptibility. The genome sequence of the domestic dog was assembled and released in 2005, providing an estimated 20,000 protein-coding genes that are a great asset to the scientific community that uses the dog system as a genetic biomedical model and for comparative and evolutionary studies. Although the canine gene set had been predicted using a combination of ab initio methods, homology studies, motif analysis, and similarity-based programs, it still requires a deep annotation of noncoding genes, alternative splicing, pseudogenes, regulatory regions, and gain and loss events. Such analyses could benefit from new sequencing technologies (RNA-Seq) to better exploit the advantages of the canine genetic system in tracking disease genes. Here, we review the catalog of canine protein-coding genes and the search for missing genes, and we propose rationales for an accurate identification of noncoding genes though next-generation sequencing.
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Affiliation(s)
- Thomas Derrien
- Institut de Génétique et Développement de Rennes, CNRS-UMR6061, Université de Rennes 1, 2 av Pr. Léon Bernard, 35043 Rennes, France
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Wang C, Deakin JE, Rens W, Zenger KR, Belov K, Marshall Graves JA, Nicholas FW. A first-generation integrated tammar wallaby map and its use in creating a tammar wallaby first-generation virtual genome map. BMC Genomics 2011; 12:422. [PMID: 21854555 PMCID: PMC3170641 DOI: 10.1186/1471-2164-12-422] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 08/19/2011] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The limited (2X) coverage of the tammar wallaby (Macropus eugenii) genome sequence dataset currently presents a challenge for assembly and anchoring onto chromosomes. To provide a framework for this assembly, it would be a great advantage to have a dense map of the tammar wallaby genome. However, only limited mapping data are available for this non-model species, comprising a physical map and a linkage map. RESULTS We combined all available tammar wallaby mapping data to create a tammar wallaby integrated map, using the Location DataBase (LDB) strategy. This first-generation integrated map combines all available information from the second-generation tammar wallaby linkage map with 148 loci, and extensive FISH mapping data for 492 loci, especially for genes likely to be located at the ends of wallaby chromosomes or at evolutionary breakpoints inferred from comparative information. For loci whose positions are only approximately known, their location in the integrated map was refined on the basis of comparative information from opossum (Monodelphis domestica) and human. Interpolation of segments from the opossum and human assemblies into the integrated map enabled the subsequent construction of a tammar wallaby first-generation virtual genome map, which comprises 14336 markers, including 13783 genes recruited from opossum and human assemblies. Both maps are freely available at http://compldb.angis.org.au. CONCLUSIONS The first-generation integrated map and the first-generation virtual genome map provide a backbone for the chromosome assembly of the tammar wallaby genome sequence. For example, 78% of the 10257 gene-scaffolds in the Ensembl annotation of the tammar wallaby genome sequence (including 10522 protein-coding genes) can now be given a chromosome location in the tammar wallaby virtual genome map.
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Affiliation(s)
- Chenwei Wang
- Australian Research Council (ARC) Centre of Excellence for Kangaroo Genomics
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
| | - Janine E Deakin
- Australian Research Council (ARC) Centre of Excellence for Kangaroo Genomics
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Willem Rens
- Department of Veterinary Medicine, University of Cambridge, UK
| | - Kyall R Zenger
- Australian Research Council (ARC) Centre of Excellence for Kangaroo Genomics
- School of Marine & Tropical Biology, James Cook University, Townsville, QLD 4811, Australia
| | - Katherine Belov
- Australian Research Council (ARC) Centre of Excellence for Kangaroo Genomics
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
| | - Jennifer A Marshall Graves
- Australian Research Council (ARC) Centre of Excellence for Kangaroo Genomics
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Frank W Nicholas
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
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Thomas R, Seiser EL, Motsinger-Reif A, Borst L, Valli VE, Kelley K, Suter SE, Argyle D, Burgess K, Bell J, Lindblad-Toh K, Modiano JF, Breen M. Refining tumor-associated aneuploidy through 'genomic recoding' of recurrent DNA copy number aberrations in 150 canine non-Hodgkin lymphomas. Leuk Lymphoma 2011; 52:1321-35. [PMID: 21375435 PMCID: PMC4304668 DOI: 10.3109/10428194.2011.559802] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Identification of the genomic regions most intimately associated with non-Hodgkin lymphoma (NHL) pathogenesis is confounded by the genetic heterogeneity of human populations. We hypothesize that the restricted genetic variation of purebred dogs, combined with the contrasting architecture of the human and canine karyotypes, will increase the penetrance of fundamental NHL-associated chromosomal aberrations in both species. We surveyed non-random aneuploidy in 150 canine NHL cases, revealing limited genomic instability compared to their human counterparts and no evidence for CDKN2A/B deletion in canine B-cell NHL. 'Genomic recoding' of canine NHL data into a 'virtual human' chromosome format showed remarkably few regions of copy number aberration (CNA) shared between both species, restricted to regions of dog chromosomes 13 and 31, and human chromosomes 8 and 21. Our data suggest that gene discovery in NHL may be enhanced through comparative studies exploiting the less complex association between CNAs and tumor pathogenesis in canine patients.
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Affiliation(s)
- Rachael Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27606, USA
| | - Eric L. Seiser
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA
| | - Alison Motsinger-Reif
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27606, USA
- Department of Statistics, College of Agriculture and Life Sciences, North Carolina State University, Patterson Hall, 2501 Founders Drive, Raleigh, NC 27695, USA
- Cancer Genetics Program, UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
| | - Luke Borst
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27606, USA
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Victor E. Valli
- VDx Veterinary Diagnostics, 2019 Anderson Rd Suite C, Davis CA 95616, USA
| | - Kathryn Kelley
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA
| | - Steven E. Suter
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27606, USA
- Cancer Genetics Program, UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA
| | - David Argyle
- Royal (Dick) School of Veterinary Studies and Roslin Institute, The University of Edinburgh, Roslin, Midlothian, Scotland, UK
| | - Kristine Burgess
- Department of Clinical Sciences, Tufts Cummings School of Veterinary Medicine, Grafton, MA 01536, USA
| | - Jerold Bell
- Department of Clinical Sciences, Tufts Cummings School of Veterinary Medicine, Grafton, MA 01536, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Jaime F. Modiano
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27606, USA
- Cancer Genetics Program, UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
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