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Items: 31

1.

The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication.

Varadharajan S, Sandve SR, Gillard GB, Tørresen OK, Mulugeta TD, Hvidsten TR, Lien S, Asbjørn Vøllestad L, Jentoft S, Nederbragt AJ, Jakobsen KS.

Genome Biol Evol. 2018 Oct 1;10(10):2785-2800. doi: 10.1093/gbe/evy201.

2.

Shifting the limits in wheat research and breeding using a fully annotated reference genome.

International Wheat Genome Sequencing Consortium (IWGSC); IWGSC RefSeq principal investigators:, Appels R, Eversole K, Feuillet C, Keller B, Rogers J, Stein N; IWGSC whole-genome assembly principal investigators:, Pozniak CJ, Stein N, Choulet F, Distelfeld A, Eversole K, Poland J, Rogers J, Ronen G, Sharpe AG; Whole-genome sequencing and assembly:, Pozniak C, Ronen G, Stein N, Barad O, Baruch K, Choulet F, Keeble-Gagnère G, Mascher M, Sharpe AG, Ben-Zvi G, Josselin AA; Hi-C data-based scaffolding:, Stein N, Mascher M, Himmelbach A; Whole-genome assembly quality control and analyses:, Choulet F, Keeble-Gagnère G, Mascher M, Rogers J, Balfourier F, Gutierrez-Gonzalez J, Hayden M, Josselin AA, Koh C, Muehlbauer G, Pasam RK, Paux E, Pozniak CJ, Rigault P, Sharpe AG, Tibbits J, Tiwari V; Pseudomolecule assembly:, Choulet F, Keeble-Gagnère G, Mascher M, Josselin AA, Rogers J; RefSeq genome structure and gene analyses:, Spannagl M, Choulet F, Lang D, Gundlach H, Haberer G, Keeble-Gagnère G, Mayer KFX, Ormanbekova D, Paux E, Prade V, Šimková H, Wicker T; Automated annotation:, Choulet F, Spannagl M, Swarbreck D, Rimbert H, Felder M, Guilhot N, Gundlach H, Haberer G, Kaithakottil G, Keilwagen J, Lang D, Leroy P, Lux T, Mayer KFX, Twardziok S, Venturini L; Manual gene curation:, Appels R, Rimbert H, Choulet F, Juhász A, Keeble-Gagnère G; Subgenome comparative analyses:, Choulet F, Spannagl M, Lang D, Abrouk M, Haberer G, Keeble-Gagnère G, Mayer KFX, Wicker T; Transposable elements:, Choulet F, Wicker T, Gundlach H, Lang D, Spannagl M; Phylogenomic analyses:, Lang D, Spannagl M, Appels R, Fischer I; Transcriptome analyses and RNA-seq data:, Uauy C, Borrill P, Ramirez-Gonzalez RH, Appels R, Arnaud D, Chalabi S, Chalhoub B, Choulet F, Cory A, Datla R, Davey MW, Hayden M, Jacobs J, Lang D, Robinson SJ, Spannagl M, Steuernagel B, Tibbits J, Tiwari V, van Ex F, Wulff BBH; Whole-genome methylome:, Pozniak CJ, Robinson SJ, Sharpe AG, Cory A; Histone mark analyses:, Benhamed M, Paux E, Bendahmane A, Concia L, Latrasse D; BAC chromosome MTP IWGSC–Bayer Whole-Genome Profiling (WGP) tags:, Rogers J, Jacobs J, Alaux M, Appels R, Bartoš J, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, Letellier T, Olsen OA, Šimková H, Singh K, Valárik M, van der Vossen E, Vautrin S, Weining S; Chromosome LTC mapping and physical mapping quality control:, Korol A, Frenkel Z, Fahima T, Glikson V, Raats D, Rogers J; RH mapping:, Tiwari V, Gill B, Paux E, Poland J; Optical mapping:, Doležel J, Číhalíková J, Šimková H, Toegelová H, Vrána J; Recombination analyses:, Sourdille P, Darrier B; Gene family analyses:, Appels R, Spannagl M, Lang D, Fischer I, Ormanbekova D, Prade V; CBF gene family:, Barabaschi D, Cattivelli L; Dehydrin gene family:, Hernandez P, Galvez S, Budak H; NLR gene family:, Steuernagel B, Jones JDG, Witek K, Wulff BBH, Yu G; PPR gene family:, Small I, Melonek J, Zhou R; Prolamin gene family:, Juhász A, Belova T, Appels R, Olsen OA; WAK gene family:, Kanyuka K, King R; Stem solidness (SSt1) QTL team:, Nilsen K, Walkowiak S, Pozniak CJ, Cuthbert R, Datla R, Knox R, Wiebe K, Xiang D; Flowering locus C (FLC) gene team:, Rohde A, Golds T; Genome size analysis:, Doležel J, Čížková J, Tibbits J; MicroRNA and tRNA annotation:, Budak H, Akpinar BA, Biyiklioglu S; Genetic maps and mapping:, Muehlbauer G, Poland J, Gao L, Gutierrez-Gonzalez J, N'Daiye A; BAC libraries and chromosome sorting:, Doležel J, Šimková H, Číhalíková J, Kubaláková M, Šafář J, Vrána J; BAC pooling, BAC library repository, and access:, Berges H, Bellec A, Vautrin S; IWGSC sequence and data repository and access:, Alaux M, Alfama F, Adam-Blondon AF, Flores R, Guerche C, Letellier T, Loaec M, Quesneville H; Physical maps and BAC-based sequences:; 1A BAC sequencing and assembly:, Pozniak CJ, Sharpe AG, Walkowiak S, Budak H, Condie J, Ens J, Koh C, Maclachlan R, Tan Y, Wicker T; 1B BAC sequencing and assembly:, Choulet F, Paux E, Alberti A, Aury JM, Balfourier F, Barbe V, Couloux A, Cruaud C, Labadie K, Mangenot S, Wincker P; 1D, 4D, and 6D physical mapping:, Gill B, Kaur G, Luo M, Sehgal S; 2AL physical mapping:, Singh K, Chhuneja P, Gupta OP, Jindal S, Kaur P, Malik P, Sharma P, Yadav B; 2AS physical mapping:, Singh NK, Khurana J, Chaudhary C, Khurana P, Kumar V, Mahato A, Mathur S, Sevanthi A, Sharma N, Tomar RS; 2B, 2D, 4B, 5BL, and 5DL IWGSC–Bayer Whole-Genome Profiling (WGP) physical maps:, Rogers J, Jacobs J, Alaux M, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, van der Vossen E, Vautrin S; 3AL physical mapping:, Gill B, Kaur G, Luo M, Sehgal S; 3DS physical mapping and BAC sequencing and assembly:, Bartoš J, Holušová K, Plíhal O; 3DL BAC sequencing and assembly:, Clark MD, Heavens D, Kettleborough G, Wright J; 4A physical mapping, BAC sequencing, assembly, and annotation:, Valárik M, Abrouk M, Balcárková B, Holušová K, Hu Y, Luo M; 5BS BAC sequencing and assembly:, Salina E, Ravin N, Skryabin K, Beletsky A, Kadnikov V, Mardanov A, Nesterov M, Rakitin A, Sergeeva E; 6B BAC sequencing and assembly:, Handa H, Kanamori H, Katagiri S, Kobayashi F, Nasuda S, Tanaka T, Wu J; 7A physical mapping and BAC sequencing:, Appels R, Hayden M, Keeble-Gagnère G, Rigault P, Tibbits J; 7B physical mapping, BAC sequencing, and assembly:, Olsen OA, Belova T, Cattonaro F, Jiumeng M, Kugler K, Mayer KFX, Pfeifer M, Sandve S, Xun X, Zhan B; 7DS BAC sequencing and assembly:, Šimková H, Abrouk M, Batley J, Bayer PE, Edwards D, Hayashi S, Toegelová H, Tulpová Z, Visendi P; 7DL physical mapping and BAC sequencing:, Weining S, Cui L, Du X, Feng K, Nie X, Tong W, Wang L; Figures:, Borrill P, Gundlach H, Galvez S, Kaithakottil G, Lang D, Lux T, Mascher M, Ormanbekova D, Prade V, Ramirez-Gonzalez RH, Spannagl M, Stein N, Uauy C, Venturini L; Manuscript writing team:, Stein N, Appels R, Eversole K, Rogers J, Borrill P, Cattivelli L, Choulet F, Hernandez P, Kanyuka K, Lang D, Mascher M, Nilsen K, Paux E, Pozniak CJ, Ramirez-Gonzalez RH, Šimková H, Small I, Spannagl M, Swarbreck D, Uauy C.

Science. 2018 Aug 17;361(6403). pii: eaar7191. doi: 10.1126/science.aar7191. Epub 2018 Aug 16.

PMID:
30115783
3.

A systemic study of lipid metabolism regulation in salmon fingerlings and early juveniles fed plant oil.

Jin Y, Olsen RE, Gillard GB, Østensen MA, Korsvoll SA, Santi N, Vik JO, Sandve SR, Olsen Y.

Br J Nutr. 2018 Sep;120(6):653-664. doi: 10.1017/S0007114518001885. Epub 2018 Aug 1.

PMID:
30064538
4.

Subfunctionalization versus neofunctionalization after whole-genome duplication.

Sandve SR, Rohlfs RV, Hvidsten TR.

Nat Genet. 2018 Jul;50(7):908-909. doi: 10.1038/s41588-018-0162-4. No abstract available.

PMID:
29955176
5.

Erratum.

Kirubakaran TG, Grove H, Kent MP, Sandve SR, Baranski M, Nome T, De Rosa MC, Righino B, Johansen T, Otterå H, Sonesson A, Lien SR, Andersen Ø.

Mol Ecol. 2018 Mar;27(6):1520. doi: 10.1111/mec.14530. No abstract available.

PMID:
29663587
6.

Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry.

Jin Y, Olsen RE, Østensen MA, Gillard GB, Korsvoll SA, Santi N, Gjuvsland AB, Vik JO, Torgersen JS, Sandve SR, Olsen Y.

BMC Genomics. 2018 Apr 16;19(1):253. doi: 10.1186/s12864-018-4651-8.

7.

Life-stage-associated remodelling of lipid metabolism regulation in Atlantic salmon.

Gillard G, Harvey TN, Gjuvsland A, Jin Y, Thomassen M, Lien S, Leaver M, Torgersen JS, Hvidsten TR, Vik JO, Sandve SR.

Mol Ecol. 2018 Mar;27(5):1200-1213. doi: 10.1111/mec.14533. Epub 2018 Mar 12.

PMID:
29431879
8.

Stable Core Gut Microbiota across the Freshwater-to-Saltwater Transition for Farmed Atlantic Salmon.

Rudi K, Angell IL, Pope PB, Vik JO, Sandve SR, Snipen LG.

Appl Environ Microbiol. 2018 Jan 2;84(2). pii: e01974-17. doi: 10.1128/AEM.01974-17. Print 2018 Jan 15.

9.

Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture.

Macqueen DJ, Primmer CR, Houston RD, Nowak BF, Bernatchez L, Bergseth S, Davidson WS, Gallardo-Escárate C, Goldammer T, Guiguen Y, Iturra P, Kijas JW, Koop BF, Lien S, Maass A, Martin SAM, McGinnity P, Montecino M, Naish KA, Nichols KM, Ólafsson K, Omholt SW, Palti Y, Plastow GS, Rexroad CE Rd, Rise ML, Ritchie RJ, Sandve SR, Schulte PM, Tello A, Vidal R, Vik JO, Wargelius A, Yáñez JM; FAASG Consortium.

BMC Genomics. 2017 Jun 27;18(1):484. doi: 10.1186/s12864-017-3862-8.

10.

SalmoBase: an integrated molecular data resource for Salmonid species.

Samy JKA, Mulugeta TD, Nome T, Sandve SR, Grammes F, Kent MP, Lien S, Våge DI.

BMC Genomics. 2017 Jun 26;18(1):482. doi: 10.1186/s12864-017-3877-1.

11.

Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification.

Robertson FM, Gundappa MK, Grammes F, Hvidsten TR, Redmond AK, Lien S, Martin SAM, Holland PWH, Sandve SR, Macqueen DJ.

Genome Biol. 2017 Jun 14;18(1):111. doi: 10.1186/s13059-017-1241-z.

12.

Extracting functional trends from whole genome duplication events using comparative genomics.

Hermansen RA, Hvidsten TR, Sandve SR, Liberles DA.

Biol Proced Online. 2016 May 10;18:11. doi: 10.1186/s12575-016-0041-2. eCollection 2016. Review.

13.

The Atlantic salmon genome provides insights into rediploidization.

Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, Grammes F, Grove H, Gjuvsland A, Walenz B, Hermansen RA, von Schalburg K, Rondeau EB, Di Genova A, Samy JK, Olav Vik J, Vigeland MD, Caler L, Grimholt U, Jentoft S, Våge DI, de Jong P, Moen T, Baranski M, Palti Y, Smith DR, Yorke JA, Nederbragt AJ, Tooming-Klunderud A, Jakobsen KS, Jiang X, Fan D, Hu Y, Liberles DA, Vidal R, Iturra P, Jones SJ, Jonassen I, Maass A, Omholt SW, Davidson WS.

Nature. 2016 May 12;533(7602):200-5. doi: 10.1038/nature17164. Epub 2016 Apr 18.

PMID:
27088604
14.

Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod.

Kirubakaran TG, Grove H, Kent MP, Sandve SR, Baranski M, Nome T, De Rosa MC, Righino B, Johansen T, Otterå H, Sonesson A, Lien S, Andersen Ø.

Mol Ecol. 2016 May;25(10):2130-43. doi: 10.1111/mec.13592. Epub 2016 Apr 20. Erratum in: Mol Ecol. 2018 Mar;27(6):1520.

PMID:
26923504
15.

Population Structure, Genetic Variation, and Linkage Disequilibrium in Perennial Ryegrass Populations Divergently Selected for Freezing Tolerance.

Kovi MR, Fjellheim S, Sandve SR, Larsen A, Rudi H, Asp T, Kent MP, Rognli OA.

Front Plant Sci. 2015 Nov 12;6:929. doi: 10.3389/fpls.2015.00929. eCollection 2015.

16.

Chloroplast phylogeny of Triticum/Aegilops species is not incongruent with an ancient homoploid hybrid origin of the ancestor of the bread wheat D-genome.

Sandve SR, Marcussen T, Mayer K, Jakobsen KS, Heier L, Steuernagel B, Wulff BB, Olsen OA.

New Phytol. 2015 Oct;208(1):9-10. doi: 10.1111/nph.13487. Epub 2015 May 21. No abstract available.

17.

Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome.

Belova T, Grønvold L, Kumar A, Kianian S, He X, Lillemo M, Springer NM, Lien S, Olsen OA, Sandve SR.

Theor Appl Genet. 2014 Sep;127(9):2029-40. doi: 10.1007/s00122-014-2358-z. Epub 2014 Aug 19.

PMID:
25134516
18.

Ancient hybridizations among the ancestral genomes of bread wheat.

Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M; International Wheat Genome Sequencing Consortium,, Jakobsen KS, Wulff BB, Steuernagel B, Mayer KF, Olsen OA.

Science. 2014 Jul 18;345(6194):1250092. doi: 10.1126/science.1250092.

19.

Genome interplay in the grain transcriptome of hexaploid bread wheat.

Pfeifer M, Kugler KG, Sandve SR, Zhan B, Rudi H, Hvidsten TR; International Wheat Genome Sequencing Consortium, Mayer KF, Olsen OA.

Science. 2014 Jul 18;345(6194):1250091. doi: 10.1126/science.1250091.

20.

The evolution and functional divergence of the beta-carotene oxygenase gene family in teleost fish--exemplified by Atlantic salmon.

Helgeland H, Sandve SR, Torgersen JS, Halle MK, Sundvold H, Omholt S, Våge DI.

Gene. 2014 Jun 15;543(2):268-74. doi: 10.1016/j.gene.2014.02.042. Epub 2014 Feb 26.

PMID:
24583166
21.

Adaptation to seasonality and the winter freeze.

Preston JC, Sandve SR.

Front Plant Sci. 2013 Jun 3;4:167. doi: 10.3389/fpls.2013.00167. eCollection 2013.

22.

Evidence for adaptive evolution of low-temperature stress response genes in a Pooideae grass ancestor.

Vigeland MD, Spannagl M, Asp T, Paina C, Rudi H, Rognli OA, Fjellheim S, Sandve SR.

New Phytol. 2013 Sep;199(4):1060-8. doi: 10.1111/nph.12337. Epub 2013 May 23.

23.

Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat.

Belova T, Zhan B, Wright J, Caccamo M, Asp T, Simková H, Kent M, Bendixen C, Panitz F, Lien S, Doležel J, Olsen OA, Sandve SR.

BMC Genomics. 2013 Apr 4;14:222. doi: 10.1186/1471-2164-14-222.

24.

Comparative analyses reveal potential uses of Brachypodium distachyon as a model for cold stress responses in temperate grasses.

Li C, Rudi H, Stockinger EJ, Cheng H, Cao M, Fox SE, Mockler TC, Westereng B, Fjellheim S, Rognli OA, Sandve SR.

BMC Plant Biol. 2012 May 8;12:65. doi: 10.1186/1471-2229-12-65.

25.

Identification of candidate genes important for frost tolerance in Festuca pratensis Huds. by transcriptional profiling.

Rudi H, Sandve SR, Opseth LM, Larsen A, Rognli OA.

Plant Sci. 2011 Jan;180(1):78-85. doi: 10.1016/j.plantsci.2010.07.014. Epub 2010 Jul 24.

PMID:
21421350
26.

Molecular mechanisms underlying frost tolerance in perennial grasses adapted to cold climates.

Sandve SR, Kosmala A, Rudi H, Fjellheim S, Rapacz M, Yamada T, Rognli OA.

Plant Sci. 2011 Jan;180(1):69-77. doi: 10.1016/j.plantsci.2010.07.011. Epub 2010 Jul 27. Review.

PMID:
21421349
27.

Genetic mapping of DArT markers in the Festuca-Lolium complex and their use in freezing tolerance association analysis.

Bartoš J, Sandve SR, Kölliker R, Kopecký D, Christelová P, Stočes S, Ostrem L, Larsen A, Kilian A, Rognli OA, Doležel J.

Theor Appl Genet. 2011 Apr;122(6):1133-47. doi: 10.1007/s00122-010-1518-z. Epub 2011 Jan 7.

PMID:
21212931
28.

Relationship of larval desiccation to Anopheles gambiae Giles and An. arabiensis Patton survival.

Benedict MQ, Sandve SR, Wilkins EE, Roberts JM.

J Vector Ecol. 2010 Jun;35(1):116-23. doi: 10.1111/j.1948-7134.2010.00037.x.

29.

Did gene family expansions during the Eocene-Oligocene boundary climate cooling play a role in Pooideae adaptation to cool climates?

Sandve SR, Fjellheim S.

Mol Ecol. 2010 May;19(10):2075-88. doi: 10.1111/j.1365-294X.2010.04629.x. Epub 2010 Apr 16.

PMID:
20406386
30.

Tracking the evolution of a cold stress associated gene family in cold tolerant grasses.

Sandve SR, Rudi H, Asp T, Rognli OA.

BMC Evol Biol. 2008 Sep 5;8:245. doi: 10.1186/1471-2148-8-245.

31.

Evidence of anopheline mosquito resistance to agrochemicals in northern Thailand.

Overgaard HJ, Sandve SR, Suwonkerd W.

Southeast Asian J Trop Med Public Health. 2005;36 Suppl 4:152-7.

PMID:
16438202

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