Sequencing of BAC pools by different next generation sequencing platforms and strategies

被引：10

作者：

Taudien S. ^{[1
]}

Steuernagel B. ^{[2
]}

Ariyadasa R. ^{[2
]}

Schulte D. ^{[2
]}

Schmutzer T. ^{[2
]}

Groth M. ^{[1
]}

Felder M. ^{[1
]}

Petzold A. ^{[1
]}

Scholz U. ^{[2
]}

Mayer K.F. ^{[3
]}

Stein N. ^{[2
]}

Platzer M. ^{[1
]}

机构：

[1] Leibniz Institute for Age Research, Fritz Lipmann Institute (FLI), D-07745 Jena

[2] Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben

[3] MIPS/IBIS, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), D-85764 Neuherberg

来源：

BMC Research Notes | / 4卷 / 1期

关键词：

454; BAC pools; barcoding; barley; Illumina; mate pairs; next generation sequencing; scaffolding;

D O I：

10.1186/1756-0500-4-411

中图分类号：

学科分类号：

摘要：

Background: Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs) improve the assemblies by scaffolding and whether barcoding of BACs is dispensable. Results: Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library. Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%. Conclusion: Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs. © 2011 Taudien et al; licensee BioMed Central Ltd.

引用

共 19 条

[1]

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, 59, 5, pp. 712-722, (2009)

[2]

Eversole K., Graner A., Stein N., Wheat and barley genome sequencing, Genetics and Genomics of the Triticeae, pp. 713-742, (2009)

[3]

Varshney R.K., Nayak S.N., May G.D., Jackson S.A., Next-generation sequencing technologies and their implications for crop genetics and breeding, Trends Biotechnol, 27, 9, pp. 522-530, (2009)

[4]

Kaul S., Koo H.L., Jenkins J., Rizzo M., Rooney T., Tallon L.J., Feldblyum T., Nierman W., Benito M.-I., Lin X., Town C.D., Venter J.C., Fraser C.M., Tabata S., Nakamura Y., Kaneko T., Sato S., Asamizu E., Kato T., Kotani H., Sasamoto S., Ecker J.R., Theologis A., Federspiel N.A., Palm C.J., Osborne B.I., Shinn P., Conway A.B., Vysotskaia V.S., Dewar K., Conn L., Lenz C.A., Kim C.J., Hansen N.F., Liu S.X., Buehler E., Altafi H., Sakano H., Dunn P., Lam B., Pham P.K., Chao Q., Nguyen M., Yu G.,

[5]

Sasaki T., The map-based sequence of the rice genome, Nature, 436, 7052, pp. 793-800, (2005)

[6]

Schulte D., Close T.J., Graner A., Langridge P., Matsumoto T., Muehlbauer G., Sato K., Schulman A.H., Waugh R., Wise R.P., Stein N., The international barley sequencing consortium - At the threshold of efficient access to the barley genome, Plant Physiol, 149, 1, pp. 142-147, (2009)

[7]

Wicker T., Zimmermann W., Perovic D., Paterson A.H., Ganal M., Graner A., Stein N., A detailed look at 7 million years of genome evolution in a 439 kb contiguous sequence at the barley Hv-elF4E locus: Recombination, rearrangements and repeats, Plant Journal, 41, 2, pp. 184-194, (2005)

[8]

Wicker T., Schlagenhauf E., Graner A., Close T.J., Keller B., Stein N., 454 sequencing put to the test using the complex genome of barley, BMC Genomics, 7, (2006)

[9]

Rounsley S., Marri P.R., Yu Y., He R., Sisneros N., Goicoechea J.L., Lee S.J., Angelova A., Kudrna D., Luo M., Affourtit J., Desany B., Knight J., Niazi F., Egholm M., Wing R.A., De Novo Next Generation Sequencing of Plant Genomes, Rice, 2, pp. 35-45, (2009)

[10]

Steuernagel B., Taudien S., Gundlach H., Seidel M., Ariyadasa R., Schulte D., Petzold A., Felder M., Graner A., Scholz U., Mayer K.F., Platzer M., Stein N., De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley, BMC Genomics, 10, (2009)

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