A Physical, Genetic and Functional Sequence Assembly of the Barley Genome

Overview

Journal Nature

Specialty Science

Date 2012 Oct 19

PMID 23075845

Citations 699

Authors

Klaus F X Mayer

Robbie Waugh

John W S Brown

Alan Schulman

Peter Langridge

Matthias Platzer

Geoffrey B Fincher

Gary J Muehlbauer

Kazuhiro Sato

Timothy J Close

Roger P Wise

Nils Stein

Affiliations

Soon will be listed here.

Abstract

Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.

Citing Articles

Genetic mapping of stripe rust resistance in a geographically diverse barley collection and selected biparental populations.

Singh D, Ziems L, Chettri M, Dracatos P, Forrest K, Bhavani S Front Plant Sci. 2024; 15:1352402.

PMID: 39104841 PMC: 11299494. DOI: 10.3389/fpls.2024.1352402.

Growth Properties and Metabolomic Analysis Provide Insight into Drought Tolerance in Barley ( L.).

Wang J, Yao L, Hao J, Li C, Li B, Meng Y Int J Mol Sci. 2024; 25(13).

PMID: 39000330 PMC: 11241679. DOI: 10.3390/ijms25137224.

Analysis of genetic diversity and population structure of some Ethiopian barley (Hordeum vulgare L.) accessions using SSR markers.

Zewodu A, Mohammed W, Shiferaw E PLoS One. 2024; 19(6):e0305945.

PMID: 38917122 PMC: 11198791. DOI: 10.1371/journal.pone.0305945.

Transcriptional changes during crown-root development and emergence in barley (Hordeum vulgare L.).

Nguyen D, Zavadil Kokas F, Gonin M, Lavarenne J, Colin M, Gantet P BMC Plant Biol. 2024; 24(1):438.

PMID: 38778283 PMC: 11110440. DOI: 10.1186/s12870-024-05160-y.

The transcriptome landscape of developing barley seeds.

Kovacik M, Nowicka A, Zwyrtkova J, Strejckova B, Vardanega I, Esteban E Plant Cell. 2024; 36(7):2512-2530.

PMID: 38635902 PMC: 11218782. DOI: 10.1093/plcell/koae095.

References

Trapnell C, Williams B, Pertea G, Mortazavi A, Kwan G, van Baren M . Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010; 28(5):511-5. PMC: 3146043. DOI: 10.1038/nbt.1621. View

Schnable P, Ware D, Fulton R, Stein J, Wei F, Pasternak S . The B73 maize genome: complexity, diversity, and dynamics. Science. 2009; 326(5956):1112-5. DOI: 10.1126/science.1178534. View

Paterson A, Bowers J, Bruggmann R, Dubchak I, Grimwood J, Gundlach H . The Sorghum bicolor genome and the diversification of grasses. Nature. 2009; 457(7229):551-6. DOI: 10.1038/nature07723. View

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley D . Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012; 7(3):562-78. PMC: 3334321. DOI: 10.1038/nprot.2012.016. View

Jiao Y, Tausta S, Gandotra N, Sun N, Liu T, Clay N . A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet. 2009; 41(2):258-63. DOI: 10.1038/ng.282. View

Lu T, Lu G, Fan D, Zhu C, Li W, Zhao Q . Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res. 2010; 20(9):1238-49. PMC: 2928502. DOI: 10.1101/gr.106120.110. View

Kalyna M, Simpson C, Syed N, Lewandowska D, Marquez Y, Kusenda B . Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res. 2011; 40(6):2454-69. PMC: 3315328. DOI: 10.1093/nar/gkr932. View

Wicker T, Mayer K, Gundlach H, Martis M, Steuernagel B, Scholz U . Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell. 2011; 23(5):1706-18. PMC: 3123954. DOI: 10.1105/tpc.111.086629. View

Kronmiller B, Wise R . TEnest: automated chronological annotation and visualization of nested plant transposable elements. Plant Physiol. 2007; 146(1):45-59. PMC: 2230558. DOI: 10.1104/pp.107.110353. View

10.

. The map-based sequence of the rice genome. Nature. 2005; 436(7052):793-800. DOI: 10.1038/nature03895. View

11.

Thiel T, Graner A, Waugh R, Grosse I, Close T, Stein N . Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice. BMC Evol Biol. 2009; 9:209. PMC: 2746218. DOI: 10.1186/1471-2148-9-209. View

12.

Chinen M, Tani T . Diverse functions of nuclear non-coding RNAs in eukaryotic gene expression. Front Biosci (Landmark Ed). 2011; 17(4):1402-17. DOI: 10.2741/3994. View

13.

Comadran J, Ramsay L, Mackenzie K, Hayes P, Close T, Muehlbauer G . Patterns of polymorphism and linkage disequilibrium in cultivated barley. Theor Appl Genet. 2010; 122(3):523-31. PMC: 3026706. DOI: 10.1007/s00122-010-1466-7. View

14.

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

15.

Stein N, Prasad M, Scholz U, Thiel T, Zhang H, Wolf M . A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor Appl Genet. 2007; 114(5):823-39. DOI: 10.1007/s00122-006-0480-2. View

16.

Nevo E, Fu Y, Pavlicek T, Khalifa S, Tavasi M, Beiles A . Evolution of wild cereals during 28 years of global warming in Israel. Proc Natl Acad Sci U S A. 2012; 109(9):3412-5. PMC: 3295258. DOI: 10.1073/pnas.1121411109. View

17.

Close T, Bhat P, Lonardi S, Wu Y, Rostoks N, Ramsay L . Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics. 2009; 10:582. PMC: 2797026. DOI: 10.1186/1471-2164-10-582. View

18.

Halterman D, Wise R . A single-amino acid substitution in the sixth leucine-rich repeat of barley MLA6 and MLA13 alleviates dependence on RAR1 for disease resistance signaling. Plant J. 2004; 38(2):215-26. DOI: 10.1111/j.1365-313X.2004.02032.x. View

19.

Taudien S, Steuernagel B, Ariyadasa R, Schulte D, Schmutzer T, Groth M . Sequencing of BAC pools by different next generation sequencing platforms and strategies. BMC Res Notes. 2011; 4:411. PMC: 3213688. DOI: 10.1186/1756-0500-4-411. View

20.

Steuernagel B, Taudien S, Gundlach H, Seidel M, Ariyadasa R, Schulte D . De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley. BMC Genomics. 2009; 10:547. PMC: 2784808. DOI: 10.1186/1471-2164-10-547. View