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Items: 16

1.

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
2.

The transcriptional landscape of polyploid wheat.

Ramírez-González RH, Borrill P, Lang D, Harrington SA, Brinton J, Venturini L, Davey M, Jacobs J, van Ex F, Pasha A, Khedikar Y, Robinson SJ, Cory AT, Florio T, Concia L, Juery C, Schoonbeek H, Steuernagel B, Xiang D, Ridout CJ, Chalhoub B, Mayer KFX, Benhamed M, Latrasse D, Bendahmane A; International Wheat Genome Sequencing Consortium, Wulff BBH, Appels R, Tiwari V, Datla R, Choulet F, Pozniak CJ, Provart NJ, Sharpe AG, Paux E, Spannagl M, Bräutigam A, Uauy C.

Science. 2018 Aug 17;361(6403). pii: eaar6089. doi: 10.1126/science.aar6089.

PMID:
30115782
3.

Impact of transposable elements on genome structure and evolution in bread wheat.

Wicker T, Gundlach H, Spannagl M, Uauy C, Borrill P, Ramírez-González RH, De Oliveira R; International Wheat Genome Sequencing Consortium, Mayer KFX, Paux E, Choulet F.

Genome Biol. 2018 Aug 17;19(1):103. doi: 10.1186/s13059-018-1479-0.

4.

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.

Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu FH, McKenzie N, Raats D, Ramirez-Gonzalez RH, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser DM, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Palma FD, Phillips AL, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD.

Genome Res. 2017 May;27(5):885-896. doi: 10.1101/gr.217117.116.

5.

Uncovering hidden variation in polyploid wheat.

Krasileva KV, Vasquez-Gross HA, Howell T, Bailey P, Paraiso F, Clissold L, Simmonds J, Ramirez-Gonzalez RH, Wang X, Borrill P, Fosker C, Ayling S, Phillips AL, Uauy C, Dubcovsky J.

Proc Natl Acad Sci U S A. 2017 Feb 7;114(6):E913-E921. doi: 10.1073/pnas.1619268114. Epub 2017 Jan 17.

6.

Genome sequence and genetic diversity of European ash trees.

Sollars ES, Harper AL, Kelly LJ, Sambles CM, Ramirez-Gonzalez RH, Swarbreck D, Kaithakottil G, Cooper ED, Uauy C, Havlickova L, Worswick G, Studholme DJ, Zohren J, Salmon DL, Clavijo BJ, Li Y, He Z, Fellgett A, McKinney LV, Nielsen LR, Douglas GC, Kjær ED, Downie JA, Boshier D, Lee S, Clark J, Grant M, Bancroft I, Caccamo M, Buggs RJ.

Nature. 2017 Jan 12;541(7636):212-216. doi: 10.1038/nature20786. Epub 2016 Dec 26.

PMID:
28024298
7.

Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data.

Daly GM, Leggett RM, Rowe W, Stubbs S, Wilkinson M, Ramirez-Gonzalez RH, Caccamo M, Bernal W, Heeney JL.

PLoS One. 2015 Jun 22;10(6):e0129059. doi: 10.1371/journal.pone.0129059. eCollection 2015.

8.

bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby.

Etherington GJ, Ramirez-Gonzalez RH, MacLean D.

Bioinformatics. 2015 Aug 1;31(15):2565-7. doi: 10.1093/bioinformatics/btv178. Epub 2015 Mar 29.

PMID:
25819670
9.

Field pathogenomics reveals the emergence of a diverse wheat yellow rust population.

Hubbard A, Lewis CM, Yoshida K, Ramirez-Gonzalez RH, de Vallavieille-Pope C, Thomas J, Kamoun S, Bayles R, Uauy C, Saunders DG.

Genome Biol. 2015 Feb 25;16:23. doi: 10.1186/s13059-015-0590-8.

10.

PolyMarker: A fast polyploid primer design pipeline.

Ramirez-Gonzalez RH, Uauy C, Caccamo M.

Bioinformatics. 2015 Jun 15;31(12):2038-9. doi: 10.1093/bioinformatics/btv069. Epub 2015 Feb 2.

11.

RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat.

Ramirez-Gonzalez RH, Segovia V, Bird N, Fenwick P, Holdgate S, Berry S, Jack P, Caccamo M, Uauy C.

Plant Biotechnol J. 2015 Jun;13(5):613-24. doi: 10.1111/pbi.12281. Epub 2014 Nov 8.

12.

Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics.

Leggett RM, Ramirez-Gonzalez RH, Clavijo BJ, Waite D, Davey RP.

Front Genet. 2013 Dec 17;4:288. doi: 10.3389/fgene.2013.00288. Review.

13.

Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

Leggett RM, Ramirez-Gonzalez RH, Verweij W, Kawashima CG, Iqbal Z, Jones JD, Caccamo M, Maclean D.

PLoS One. 2013;8(3):e60058. doi: 10.1371/journal.pone.0060058. Epub 2013 Mar 25.

14.

StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics.

Ramirez-Gonzalez RH, Leggett RM, Waite D, Thanki A, Drou N, Caccamo M, Davey R.

Version 2. F1000Res. 2013 Nov 15 [revised 2014 Jan 1];2:248. doi: 10.12688/f1000research.2-248.v2. eCollection 2013.

15.

Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs.

Murcia PR, Hughes J, Battista P, Lloyd L, Baillie GJ, Ramirez-Gonzalez RH, Ormond D, Oliver K, Elton D, Mumford JA, Caccamo M, Kellam P, Grenfell BT, Holmes EC, Wood JL.

PLoS Pathog. 2012;8(5):e1002730. doi: 10.1371/journal.ppat.1002730. Epub 2012 May 31.

16.

Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments.

Ramirez-Gonzalez RH, Bonnal R, Caccamo M, Maclean D.

Source Code Biol Med. 2012 May 28;7(1):6. doi: 10.1186/1751-0473-7-6.

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