Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Scientific Data

Volumn 4, Issue , 2017, Pages

  Beier, Sebastian ^a   Himmelbach, Axel ^a   Colmsee, Christian ^a   Zhang, Xiao Qi ^b   Barrero, Roberto A ^b   Zhang, Qisen ^c   Li, Lin ^d   Bayer, Micha ^e   Bolser, Daniel ^f   Taudien, Stefan ^g   Groth, Marco ^g   Felder, Marius ^g   Hastie, Alex ^h   Šimková, Hana ⁱ   Staňková, Helena ⁱ   Vrána, Jan ⁱ   Chan, Saki ^h   Muñoz Amatriaín, María ^j   Ounit, Rachid ^k   Wanamaker, Steve ^j   Schmutzer, Thomas ^a   Aliyeva Schnorr, Lala ^a   Grasso, Stefano ^l   Tanskanen, Jaakko ^m   Sampath, Dharanya ⁿ   Heavens, Darren ⁿ   Cao, Sujie ^o   Chapman, Brett ^b   Dai, Fei ^p   Han, Yong ^p   Li, Hua ^o   Li, Xuan ^o   Lin, Chongyun ^o   McCooke, John K ^b   Tan, Cong ^b   Wang, Songbo ^o   Yin, Shuya ^p   Zhou, Gaofeng ^b   Poland, Jesse A ^q   Bellgard, Matthew I ^b   Houben, Andreas ^a   Doležel, Jaroslav ⁱ   Ayling, Sarah ⁿ   Lonardi, Stefano ^k   Langridge, Peter ^r   Muehlbauer, Gary J ^d   Kersey, Paul ^f   Clark, Matthew D ^n,s   Caccamo, Mario ^n,t   Schulman, Alan H ^m   Platzer, Matthias ^g   Close, Timothy J ^j   Hansson, Mats ^u   Zhang, Guoping ^p   Braumann, Ilka ^v   Li, Chengdao ^b,w,x   Waugh, Robbie ^e,y   Scholz, Uwe ^a   Stein, Nils ^a,z   Mascher, Martin ^a,aa   more..

^a Department of Breeding Research Leibniz Institute of Plant Genetics Crop Plant Research (IPK) Gatersleben   (Germany)

^b MURDOCH UNIVERSITY   (Australia)

^c Australian Export Grains Innovation Centre (AEGIC)   (Australia)

^d UNIVERSITY OF MINNESOTA   (United States)

^e SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

^f EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^g FRITZ LIPMANN INSTITUTE   (Germany)

^h USA   (United States)

ⁱ PALACKÝ UNIVERSITY   (Czech Republic)

^j UNIVERSITY OF CALIFORNIA   (United States)

^k University of California Riverside   (United States)

^l UNIVERSITY OF UDINE   (Italy)

^m UNIVERSITY OF HELSINKI   (Finland)

ⁿ EARLHAM INSTITUTE   (United Kingdom)

^o BGI SHENZHEN   (China)

^p ZHEJIANG UNIVERSITY   (China)

^q KANSAS STATE UNIVERSITY   (United States)

^r UNIVERSITY OF ADELAIDE   (Australia)

^s UNIVERSITY OF EAST ANGLIA   (United Kingdom)

^t NATIONAL INSTITUTE OF AGRICULTURAL BOTANY   (United Kingdom)

^u LUND UNIVERSITY   (Sweden)

^v CARLSBERG LABORATORY   (Denmark)

^w DEPARTMENT OF HEALTH   (Australia)

^x YANGTZE UNIVERSITY   (China)

^y UNIVERSITY OF DUNDEE   (United Kingdom)

^z UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^aa GERMAN CENTRE FOR INTEGRATIVE BIODIVERSITY RESEARCH IDIV HALLE JENA LEIPZIG   (Germany)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOMAL MAPPING; GENETICS; HORDEUM; PLANT GENOME; SEQUENCE ANALYSIS;

CHROMOSOME MAPPING; GENOME, PLANT; HORDEUM; SEQUENCE ANALYSIS;

EID: 85018297524     PISSN: None     EISSN: 20524463     Source Type: Journal    
DOI: 10.1038/sdata.2017.44     Document Type: Article

References (61)

1. Schulte, D. et al. The international barley sequencing consortium-at the threshold of efficient access to the barley genome. Plant physiology 149, 142-147 (2009).
2. Schulte, D. et al. BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L). BMC genomics 12, 247 (2011).
3. Ariyadasa, R. et al. A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms. Plant physiology 164, 412-423 (2014).
4. International Barley Genome Sequencing Consortium. A physical, genetic and functional sequence assembly of the barley genome. Nature 491, 711-716 (2012).
5. Mascher, M. et al. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). The Plant Journal 76, 718-727 (2013).
6. Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
7. Schnable, P. S. et al. The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112-1115 (2009).
8. Lam, E. T. et al. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nature biotechnology 30, 771-776 (2012).
9. Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293 (2009).
10. Burton, J. N. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nature biotechnology 31, 1119-1125 (2013).
11. Poland, J. A., Brown, P. J., Sorrells, M. E. & Jannink, J.-L. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7, e32253 (2012).
12. Colmsee, C. et al. BARLEX-the Barley Draft Genome Explorer. Mol Plant 8, 964-966 (2015).
13. Munoz-Amatriain, M. et al. Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant Journal 84, 216-227 (2015).
14. Pasquariello, M. et al. The barley Frost resistance-H2 locus. Functional & integrative genomics 14, 85-100 (2014).
15. Meyer, M., Stenzel, U. & Hofreiter, M. Parallel tagged sequencing on the 454 platform. Nature protocols 3, 267-278 (2008).
16. Steuernagel, B. et al. De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley. BMC genomics 10, 547 (2009).
17. Beier, S. et al. Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes. Plant biotechnology journal 14, 1511-1522 (2016).
18. Sambrook, J. & Russell, D. W. Molecular cloning: a laboratory manual. 3rd edition (Coldspring-Harbour Laboratory Press, 2001).
19. Aird, D. et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome biology 12, R18 (2011).
20. Quail, M. A. et al. A large genome center's improvements to the Illumina sequencing system. Nature methods 5, 1005-1010 (2008).
21. Asan et al. Paired-end sequencing of long-range DNA fragments for de novo assembly of large, complex Mammalian genomes by direct intra-molecule ligation. PLoS ONE 7, e46211 (2012).
22. Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc 2010, pdb prot5448 (2010).
23. Adey, A. et al. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome biology 11, R119 (2010).
24. Lonardi, S. et al. Combinatorial pooling enables selective sequencing of the barley gene space. PLoS computational biology 9, e1003010 (2013).
25. Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome research 18, 821-829 (2008).
26. Ounit, R., Wanamaker, S., Close, T. J. & Lonardi, S. CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC genomics 16, 236 (2015).
27. Zhang, Z., Schwartz, S., Wagner, L. & Miller, W. A greedy algorithm for aligning DNA sequences. Journal of computational biology: A Journal of Computational Molecular Cell Biology 7, 203-214 (2000).
28. Chevreux, B., Wetter, T. & Suhai, S. in German conference on bioinformatics (1999); 45-56.
29. Taudien, S. et al. Sequencing of BAC pools by different next generation sequencing platforms and strategies. BMC research notes 4, 411 (2011).
30. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
31. Boetzer, M., Henkel, C. V., Jansen, H. J., Butler, D. & Pirovano, W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27, 578-579 (2011).
32. Brenchley, R. et al. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491, 705-710 (2012).
33. Andrews, S. FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics. babraham.ac.uk/projects/fastqc (2010).
34. Leggett, R. M., Ramirez-Gonzalez, R. H., Clavijo, B. J., Waite, D. & Davey, R. P. Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics. Frontiers in genetics 4, 288 (2013).
35. Simpson, J. T. et al. ABySS: a parallel assembler for short read sequence data. Genome research 19, 1117-1123 (2009).
36. Magoc, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957-2963 (2011).
37. Leggett, R. M., Clavijo, B. J., Clissold, L., Clark, M. D. & Caccamo, M. NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries. Bioinformatics 30, 566-568 (2014).
38. Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1, 18 (2012).
39. Slater, G. S. & Birney, E. Automated generation of heuristics for biological sequence comparison. BMC bioinformatics 6, 31 (2005).
40. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
41. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2015).
42. Mascher, M. et al. A chromosome conformation capture ordered sequence of the barley genome. Nature doi:10.1038/nature22043 (2017).
43. Cao, H. et al. Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology. GigaScience 3, 1 (2014).
44. Chapman, J. A. et al. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome biology 16, 26 (2015).
45. Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/pdf/ 1303.3997v2.pdf (2013).
46. Mascher, M., Wu, S., Amand, P. S., Stein, N. & Poland, J. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS ONE 8, e76925 (2013).
47. Wu, Y., Bhat, P. R., Close, T. J. & Lonardi, S. Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS genetics 4, e1000212 (2008).
48. Csardi, G. & Nepusz, T. The igraph software package for complex network research, InterJournal, Complex Systems 1695 (2006).
49. Prim, R. C. Shortest connection networks and some generalizations. Bell system technical journal 36, 1389-1401 (1957).
50. Wendler, N. et al. Unlocking the secondary gene-pool of barley with next-generation sequencing. Plant biotechnology journal 12, 1122-1131 (2014).
51. Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal 17, 10-12 (2011).
52. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
53. Garrison, E. & Marth, G. Haplotype-based variant detection from short-read sequencing. Preprint at https://arxiv.org/pdf/ 1207.3907v2.pdf (2012).
54. Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F. & Chen, L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nature biotechnology 30, 90-98 (2012).
55. Matsumoto, T. et al. Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant physiology 156, 20-28 (2011).
56. Wu, T. D. & Watanabe, C. K. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21, 1859-1875 (2005).
57. DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature genetics 43, 491-498 (2011).
58. Arend, D. et al. PGP repository: a plant phenomics and genomics data publication infrastructure. Database 2016, baw033 (2016).
59. Arend, D. et al. e!DAL--a framework to store, share and publish research data. BMC bioinformatics 15, 214 (2014).
60. Künzel, G., Korzun, L. & Meister, A. Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154, 397-412 (2000).
61. Aliyeva-Schnorr, L. et al. Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination-poor region comprises more than half of barley chromosome 3H. The Plant Journal 84, 385-394 (2015).