Conserved synteny in the genomes of teleost fish aids in the rapid development of genomic tools to query fundamental biological and evolutionary questions
| dc.contributor.author | Rondeau, Eric B. | |
| dc.contributor.supervisor | Koop, Benjamin F. | |
| dc.date.accessioned | 2017-12-21T18:07:42Z | |
| dc.date.copyright | 2017 | en_US |
| dc.date.issued | 2017-12-21 | |
| dc.degree.department | Department of Biology | en_US |
| dc.degree.level | Doctor of Philosophy Ph.D. | en_US |
| dc.description.abstract | As two species diverge, much of their genomes begin to differentiate. In many lineages, however, the genomic structure remains remarkably intact, with orthologous gene content maintained across millions of years and significant changes to their biological characteristics. The maintenance of gene content is defined as conserved synteny while the preservation of gene order is defined as conserved linkage; the conservation of both can be incredibly informative when interrogating and comparing two genomes. In non-model organisms, linkage conservation to a well-developed model allows informed, cost-effective and rapid answers to fundamental biological questions without generation of equivalent resources. With the development of new model organisms, we can begin to discuss more fundamental evolutionary concepts, such as the maintenance of chromosomal gene content across larger evolutionary time-scales, or the reorganization that occurs in chromosomes following major genomic events such as whole-genome duplications. In this work, I utilized the rapid development of primary genomic resources in the non-model teleost sablefish (Anoplopoma fimbria) to demonstrate that conserved linkage to a model genomic reference can identify the gene most likely responsible for genetic sex-control. I then assembled the first genome for a non-duplicated member of the teleost lineage Protacanthopterygii, the northern pike (Esox lucius), and demonstrated the conservation of synteny between three major lineages of teleosts, the Protacanthopterygii, the Acanthopterygii and the Ostariophysi. I further showed that the genome of northern pike retains an ancestral teleost organization and pre-duplicated genome in comparison to the economically important Salmoniformes. Finally, with continued improvements of the genome to the chromosome level, I demonstrated the degree of conserved linkage maintained between Atlantic salmon and northern pike and explained how conserved linkage through both genomes could be used to improve the genome assembly of the other, even with over 125 million years of separation. As genomic technology continues to advance and new genomic resources become available, the continued refinement of genome re-organization post duplication will be revealed, and this pre-duplication outgroup will continue to push our understanding of the effects of genome duplication, as we transition from genome organization to functional modifications of gene duplicates following duplication. | en_US |
| dc.description.embargo | 2018-12-01 | |
| dc.description.scholarlevel | Graduate | en_US |
| dc.identifier.bibliographicCitation | EB Rondeau, AM Messmer, DS Sanderson, SG Jantzen, KR von Schalburg, DR Minkley, JS Leong, GM Macdonald, AE Davidsen, WA Parker, RSA Mazzola, B Campbell, BF Koop (2013). Genomics of Sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene. BMC Genomics 14:452. | en_US |
| dc.identifier.bibliographicCitation | EB Rondeau, DR Minkley, JS Leong, AM Messmer, JR Jantzen, KR von Schalburg, C Lemon, NH Bird, BF Koop (2014). The genome and linkage map of the Northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei. PLOS One 9:e102089. | en_US |
| dc.identifier.bibliographicCitation | EB Rondeau, CV Laurie, SC Johnson, BF Koop (2016). A PCR assay detects a male-specific duplicated copy of Anti-Müllerian hormone (amh) in the lingcod (Ophiodon elongatus). BMC Research Notes 9:230. | en_US |
| dc.identifier.bibliographicCitation | S Lien, BF Koop, SR Sandve, JR Miller, MP Kent, T Nome, TR Hvidsten, JS Leong, DR Minkley, A Zimin, F Grammes, H Grove, A Gjuvsland, B Walenz, RA Hermansen, KR von Schalburg, EB Rondeau, A Di Genova, JKA Samy, JO Vik, MD Vigeland, L Caler, U Grimholt, S Jentoft, DI Vage, P de Jong, T Moen, M Baranski, Y Palti, D Smith, JA Yorke, AJ Nederbragt, A Tooming-Klunderud, KS Jakobsen, X Jiang, D Fan, Y Hu, DA Liberles, R Vidal, P Iturra, SJM Jones, I Jonassen, A Maass, SW Omholt, WS Davidson (2016). The Atlantic salmon genome provides insights into rediploidization. Nature: 17164. | en_US |
| dc.identifier.uri | http://hdl.handle.net/1828/8902 | |
| dc.language | English | eng |
| dc.language.iso | en | en_US |
| dc.rights | Available to the World Wide Web | en_US |
| dc.subject | Synteny | en_US |
| dc.subject | Linkage | en_US |
| dc.subject | Northern pike | en_US |
| dc.subject | Sablefish | en_US |
| dc.subject | Comparative Mapping | en_US |
| dc.subject | Genomics | en_US |
| dc.title | Conserved synteny in the genomes of teleost fish aids in the rapid development of genomic tools to query fundamental biological and evolutionary questions | en_US |
| dc.type | Thesis | en_US |