An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts
The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here,...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
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Public Library of Science
2014
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| Online Access: | http://hdl.handle.net/1721.1/86301 |
| _version_ | 1811096101794611200 |
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| author | Hoeppner, Marc P. Lundquist, Andrew Pirun, Mono Meadows, Jennifer R. S. Zamani, Neda Johnson, Jeremy Sundstrom, Gorel Cook, April FitzGerald, Michael G. Swofford, Ross Mauceli, Evan Moghadam, Behrooz Torabi Greka, Anna Alfoldi, Jessica Abouelleil, Amr Aftuck, Lynne Bessette, Daniel Berlin, Aaron M. Brown, Adam Gearin, Gary Lui, Annie Macdonald, J. Pendexter Priest, Margaret Shea, Terrance Turner-Maier, Jason Zimmer, Andrew di Palma, Federica Lindblad-Toh, Kerstin Grabherr, Manfred G. Lander, Eric Steven |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Hoeppner, Marc P. Lundquist, Andrew Pirun, Mono Meadows, Jennifer R. S. Zamani, Neda Johnson, Jeremy Sundstrom, Gorel Cook, April FitzGerald, Michael G. Swofford, Ross Mauceli, Evan Moghadam, Behrooz Torabi Greka, Anna Alfoldi, Jessica Abouelleil, Amr Aftuck, Lynne Bessette, Daniel Berlin, Aaron M. Brown, Adam Gearin, Gary Lui, Annie Macdonald, J. Pendexter Priest, Margaret Shea, Terrance Turner-Maier, Jason Zimmer, Andrew di Palma, Federica Lindblad-Toh, Kerstin Grabherr, Manfred G. Lander, Eric Steven |
| author_sort | Hoeppner, Marc P. |
| collection | MIT |
| description | The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here, we present an improved genome build, canFam3.1, which includes 85 MB of novel sequence and now covers 99.8% of the euchromatic portion of the genome. We also present multiple RNA-Sequencing data sets from 10 different canine tissues to catalog ~175,000 expressed loci. While about 90% of the coding genes previously annotated by EnsEMBL have measurable expression in at least one sample, the number of transcript isoforms detected by our data expands the EnsEMBL annotations by a factor of four. Syntenic comparison with the human genome revealed an additional ~3,000 loci that are characterized as protein coding in human and were also expressed in the dog, suggesting that those were previously not annotated in the EnsEMBL canine gene set. In addition to ~20,700 high-confidence protein coding loci, we found ~4,600 antisense transcripts overlapping exons of protein coding genes, ~7,200 intergenic multi-exon transcripts without coding potential, likely candidates for long intergenic non-coding RNAs (lincRNAs) and ~11,000 transcripts were reported by two different library construction methods but did not fit any of the above categories. Of the lincRNAs, about 6,000 have no annotated orthologs in human or mouse. Functional analysis of two novel transcripts with shRNA in a mouse kidney cell line altered cell morphology and motility. All in all, we provide a much-improved annotation of the canine genome and suggest regulatory functions for several of the novel non-coding transcripts. |
| first_indexed | 2024-09-23T16:38:16Z |
| format | Article |
| id | mit-1721.1/86301 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T16:38:16Z |
| publishDate | 2014 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | mit-1721.1/863012022-09-29T20:28:43Z An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts Hoeppner, Marc P. Lundquist, Andrew Pirun, Mono Meadows, Jennifer R. S. Zamani, Neda Johnson, Jeremy Sundstrom, Gorel Cook, April FitzGerald, Michael G. Swofford, Ross Mauceli, Evan Moghadam, Behrooz Torabi Greka, Anna Alfoldi, Jessica Abouelleil, Amr Aftuck, Lynne Bessette, Daniel Berlin, Aaron M. Brown, Adam Gearin, Gary Lui, Annie Macdonald, J. Pendexter Priest, Margaret Shea, Terrance Turner-Maier, Jason Zimmer, Andrew di Palma, Federica Lindblad-Toh, Kerstin Grabherr, Manfred G. Lander, Eric Steven Massachusetts Institute of Technology. Department of Biology Lander, Eric S. The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here, we present an improved genome build, canFam3.1, which includes 85 MB of novel sequence and now covers 99.8% of the euchromatic portion of the genome. We also present multiple RNA-Sequencing data sets from 10 different canine tissues to catalog ~175,000 expressed loci. While about 90% of the coding genes previously annotated by EnsEMBL have measurable expression in at least one sample, the number of transcript isoforms detected by our data expands the EnsEMBL annotations by a factor of four. Syntenic comparison with the human genome revealed an additional ~3,000 loci that are characterized as protein coding in human and were also expressed in the dog, suggesting that those were previously not annotated in the EnsEMBL canine gene set. In addition to ~20,700 high-confidence protein coding loci, we found ~4,600 antisense transcripts overlapping exons of protein coding genes, ~7,200 intergenic multi-exon transcripts without coding potential, likely candidates for long intergenic non-coding RNAs (lincRNAs) and ~11,000 transcripts were reported by two different library construction methods but did not fit any of the above categories. Of the lincRNAs, about 6,000 have no annotated orthologs in human or mouse. Functional analysis of two novel transcripts with shRNA in a mouse kidney cell line altered cell morphology and motility. All in all, we provide a much-improved annotation of the canine genome and suggest regulatory functions for several of the novel non-coding transcripts. European Science Foundation (EURYI award) National Human Genome Research Institute (U.S.) (NHGRI (U54 HG003067)) Uppsala University Swedish Medical Research Council Swedish Research Council FORMAS European Commission (FP7-LUPA, GA-201370) Science for Life Laboratory (Stockholm, Sweden) (Start-up grant) 2014-04-30T19:29:53Z 2014-04-30T19:29:53Z 2014-03 2013-11 Article http://purl.org/eprint/type/JournalArticle 1932-6203 http://hdl.handle.net/1721.1/86301 Hoeppner, Marc P., Andrew Lundquist, Mono Pirun, Jennifer R. S. Meadows, Neda Zamani, Jeremy Johnson, Görel Sundström, et al. “An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts.” Edited by Brian P. Chadwick. PLoS ONE 9, no. 3 (March 13, 2014): e91172. en_US http://dx.doi.org/10.1371/journal.pone.0091172 PLoS ONE Creative Commons Attribution http://creativecommons.org/licenses/by/4.0/ application/pdf Public Library of Science PLoS |
| spellingShingle | Hoeppner, Marc P. Lundquist, Andrew Pirun, Mono Meadows, Jennifer R. S. Zamani, Neda Johnson, Jeremy Sundstrom, Gorel Cook, April FitzGerald, Michael G. Swofford, Ross Mauceli, Evan Moghadam, Behrooz Torabi Greka, Anna Alfoldi, Jessica Abouelleil, Amr Aftuck, Lynne Bessette, Daniel Berlin, Aaron M. Brown, Adam Gearin, Gary Lui, Annie Macdonald, J. Pendexter Priest, Margaret Shea, Terrance Turner-Maier, Jason Zimmer, Andrew di Palma, Federica Lindblad-Toh, Kerstin Grabherr, Manfred G. Lander, Eric Steven An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts |
| title | An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts |
| title_full | An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts |
| title_fullStr | An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts |
| title_full_unstemmed | An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts |
| title_short | An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts |
| title_sort | improved canine genome and a comprehensive catalogue of coding genes and non coding transcripts |
| url | http://hdl.handle.net/1721.1/86301 |
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