Analysing complex Triticeae genomes - concepts and strategies

Plant Methods

Volumn 9, Issue 1, 2013, Pages

  Spannagl, Manuel ^a   Martis, Mihaela M ^a   Pfeifer, Matthias ^a   Nussbaumer, Thomas ^a   Mayer, Klaus F X ^a  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

Barley genome; Genome analysis; GenomeZipper; Grass genomes; Triticeae genomes; Wheat genome

Indexed keywords

BRACHYPODIUM; BRACHYPODIUM DISTACHYON; HORDEUM; TRITICEAE; TRITICUM AESTIVUM;

EID: 84883527130     PISSN: None     EISSN: 17464811     Source Type: Journal    
DOI: 10.1186/1746-4811-9-35     Document Type: Review

References (37)

1. United States Department of agriculture. World agricultural supply and demand estimates Report No. WASDE-511; 2012, United States.
2. Purugganan MD, Fuller DQ. The nature of selection during plant domestication. Nature 2009, 457:843-848. 10.1038/nature07895, 19212403.
3. Eilam T, Anikster Y, Millet E, Manisterski J, Sagi-Assif O, Feldman M. Genome size and genome evolution in diploid Triticeae species. Genome 2007, 50:1029-1037. 10.1139/G07-083, 18059548.
4. Wicker T, Mayer KF, Gundlach H, Martis M, Steuernagel B, Scholz U, Simkova H, Kubalakova M, Choulet F, Taudien S, et al. Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 2011, 23:1706-1718. 10.1105/tpc.111.086629, 3123954, 21622801.
5. Nesbitt M, Samuel D. Hulled wheats. Proc. 1st Internat. Workshop hulled wheats, international plant genetic resources institute 1996, 41-100. Padulosi S, Hammer K, Heller J.
6. Choulet F, Wicker T, Rustenholz C, Paux E, Salse J, Leroy P, Schlub S, Le Paslier MC, Magdelenat G, Gonthier C, et al. Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 2010, 22:1686-1701. 10.1105/tpc.110.074187, 2910976, 20581307.
7. Flicek P, Birney E. Sense from sequence reads: methods for alignment and assembly. Nat Methods 2009, 6:S6-S12. 10.1038/nmeth.1376, 19844229.
8. Moore G, Devos KM, Wang Z, Gale MD. Cereal genome evolution. Grasses, line up and form a circle. Curr Biol 1995, 5:737-739. 10.1016/S0960-9822(95)00148-5, 7583118.
9. Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, et al. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 2012, 491:705-710. 10.1038/nature11650, 3510651, 23192148.
10. Mayer KF, Waugh R, Brown JW, Schulman A, Langridge P, Platzer M, Fincher GB, Muehlbauer GJ, Sato K, Close TJ, et al. A physical, genetic and functional sequence assembly of the barley genome. Nature 2012, 491:711-716.
11. Mayer KF, Taudien S, Martis M, Simkova H, Suchankova P, Gundlach H, Wicker T, Petzold A, Felder M, Steuernagel B, et al. Gene content and virtual gene order of barley chromosome 1H. Plant Physiol 2009, 151:496-505. 10.1104/pp.109.142612, 2754631, 19692534.
12. Mayer KF, Martis M, Hedley PE, Simkova H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, et al. Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 2011, 23:1249-1263. 10.1105/tpc.110.082537, 3101540, 21467582.
13. Initiative IB. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 2010, 463:763-768. 10.1038/nature08747, 20148030.
14. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, et al. The Sorghum bicolor genome and the diversification of grasses. Nature 2009, 457:551-556. 10.1038/nature07723, 19189423.
15. Project IRGS. The map-based sequence of the rice genome. Nature 2005, 436:793-800. 10.1038/nature03895, 16100779.
16. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13:2178-2189. 10.1101/gr.1224503, 403725, 12952885.
17. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
18. Flavell RB, Bennett MD, Smith JB, Smith DB. Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem Genet 1974, 12:257-269. 10.1007/BF00485947, 4441361.
19. Wicker T, Taudien S, Houben A, Keller B, Graner A, Platzer M, Stein N. A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley. Plant J 2009, 59:712-722. 10.1111/j.1365-313X.2009.03911.x, 19453446.
20. Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics 2010, 95:315-327. 10.1016/j.ygeno.2010.03.001, 2874646, 20211242.
21. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659. 10.1093/bioinformatics/btl158, 16731699.
22. Richter DC, Ott F, Auch AF, Schmid R, Huson DH. MetaSim: a sequencing simulator for genomics and metagenomics. PLoS One 2008, 3:e3373. 10.1371/journal.pone.0003373, 2556396, 18841204.
23. Dolezel J, Vrana J, Safar J, Bartos J, Kubalakova M, Simkova H. Chromosomes in the flow to simplify genome analysis. Funct Integr Genomics 2012, 12:397-416. 10.1007/s10142-012-0293-0, 3431466, 22895700.
24. Luo MC, Gu YQ, You FM, Deal KR, Ma Y, Hu Y, Huo N, Wang Y, Wang J, Chen S, et al. A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proc Natl Acad Sci U S A 2013, 110:7940-7945. 10.1073/pnas.1219082110, 3651469, 23610408.
25. Frank E, Hall M, Trigg L, Holmes G, Witten IH. Data mining in bioinformatics using Weka. Bioinformatics 2004, 20:2479-2481. 10.1093/bioinformatics/bth261, 15073010.
26. Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, Appels R, Pfeifer M, Tao Y, Zhang X, et al. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 2013, 496:91-95. 10.1038/nature12028, 23535592.
27. Ling HQ, Zhao S, Liu D, Wang J, Sun H, Zhang C, Fan H, Li D, Dong L, Tao Y, et al. Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 2013, 496:87-90. 10.1038/nature11997, 23535596.
28. Dvorak J, Terlizzi P, Zhang HB, Resta P. The evolution of polyploid wheats: identification of the A genome donor species. Genome 1993, 36:21-31. 10.1139/g93-004, 18469969.
29. Krasileva KV, Buffalo V, Bailey P, Pearce S, Ayling S, Tabbita F, Soria M, Wang S, Consortium I, Akhunov E, et al. Separating homeologs by phasing in the tetraploid wheat transcriptome. Genome Biol 2013, 14:R66. 10.1186/gb-2013-14-6-r66, 23800085.
30. Chalupska D, Lee HY, Faris JD, Evrard A, Chalhoub B, Haselkorn R, Gornicki P. Acc homoeoloci and the evolution of wheat genomes. Proc Natl Acad Sci U S A 2008, 105:9691-9696. 10.1073/pnas.0803981105, 2474508, 18599450.
31. Soderlund C, Longden I, Mott R. FPC: a system for building contigs from restriction fingerprinted clones. Comput Appl Biosci 1997, 13:523-535.
32. Comadran J, Kilian B, Russell J, Ramsay L, Stein N, Ganal M, Shaw P, Bayer M, Thomas W, Marshall D, et al. Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nat Genet 2012, 44:1388-1392. 10.1038/ng.2447, 23160098.
33. Gale MD, Devos KM. Comparative genetics in the grasses. Proc Natl Acad Sci U S A 1998, 95:1971-1974. 10.1073/pnas.95.5.1971, 33824, 9482816.
34. Hernandez P, Martis M, Dorado G, Pfeifer M, Galvez S, Schaaf S, Jouve N, Simkova H, Valarik M, Dolezel J, Mayer KF. Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J 2012, 69:377-386. 10.1111/j.1365-313X.2011.04808.x, 21974774.
35. Martis MM, Klemme S, Banaei-Moghaddam AM, Blattner FR, Macas J, Schmutzer T, Scholz U, Gundlach H, Wicker T, Simkova H, et al. Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences. Proc Natl Acad Sci USA 2012, 109:13343-13346. 10.1073/pnas.1204237109, 3421217, 22847450.
36. Pfeifer M, Martis M, Asp T, Mayer KF, Lubberstedt T, Byrne S, Frei U, Studer B. The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics. Plant Physiol 2013, 161:571-582. 10.1104/pp.112.207282, 23184232.
37. Lupken T, Stein N, Perovic D, Habekuss A, Kramer I, Hahnel U, Steuernagel B, Scholz U, Zhou R, Ariyadasa R, et al. Genomics-based high-resolution mapping of the BaMMV/BaYMV resistance gene rym11 in barley (Hordeum vulgare L.). Theor Appl Genet 2013, 126:1201-1212. 10.1007/s00122-013-2047-3, 23456135.