publication . Article . Other literature type . 2017

Assembly and comparison of two closely relatedBrassica napusgenomes

Bayer, Philipp E.; Hurgobin, Bhavna; Golicz, Agnieszka A.; Chan, Chon‐Kit Kenneth; Yuan, Yuxuan; Lee, HueyTyng; Renton, Michael; Meng, Jinling; Li, Ruiyuan; Long, Yan; ...
Open Access English
  • Published: 01 Dec 2017
  • Publisher: HAL CCSD
Abstract
Summary As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. Here, we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the Brassica napus cultivar Darmor-bzh. Both cultivars were annotated using the same method t...
Subjects
Medical Subject Headings: food and beverages
free text keywords: genome assembly, whole genome comparison, genotyping by sequencing, genome assembly improvement, Brassica napus, Tapidor, contigPlacer, [SDV]Life Sciences [q-bio], Research Article, Research Articles, genome assembly;whole genome comparison;genotyping by sequencing;genome assembly improvement;Brassica napus;Tapidor;contigPlacer, Biotechnology, Agronomy and Crop Science, Plant Science, Biology, Gene, Genome, Genome comparison, Genetics, Brassica, biology.organism_classification, Sequence assembly, Reference genome, Annotation, Sources of error, Botany
Funded by
RCUK| Sequencing and exploitation of the Brassica A genome
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: BB/E017363/1
  • Funding stream: BBSRC
,
ARC| Linkage Projects - Grant ID: LP140100537
Project
  • Funder: Australian Research Council (ARC) (ARC)
  • Project Code: LP140100537
  • Funding stream: Linkage Projects
,
ARC| Linkage Projects - Grant ID: LP130100925
Project
  • Funder: Australian Research Council (ARC) (ARC)
  • Project Code: LP130100925
  • Funding stream: Linkage Projects
,
ARC| Discovery Projects - Grant ID: DP160104497
Project
  • Funder: Australian Research Council (ARC) (ARC)
  • Project Code: DP160104497
  • Funding stream: Discovery Projects
,
ARC| Future Fellowships - Grant ID: FT130100604
Project
  • Funder: Australian Research Council (ARC) (ARC)
  • Project Code: FT130100604
  • Funding stream: Future Fellowships
58 references, page 1 of 4

Alexa, A. and Rahnenfuhrer, J. (2010) topGO: enrichment analysis for gene ontology. R package version, 2.

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410.

Arumuganathan, K. and Earle, E.D. (1991) Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 211-215. [OpenAIRE]

Bayer, P.E., Ruperao, P., Mason, A.S., Stiller, J., Chan, C.-K.K., Hayashi, S., Long, Y. et al. (2015) High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theor. Appl. Genet. 128, 1039-1047. [OpenAIRE]

Brown, C.T., Howe, A., Zhang, Q., Pyrkosz, A.B. and Brom, T.H. (2012) A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data. http://arxiv.org/abs/1203.4802.

Cai, G., Yang, Q., Yi, B., Fan, C., Edwards, D., Batley, J., Zhou, Y. et al. (2014) A complex recombination pattern in the genome of allotetraploid Brassica napus as revealed by a high-density genetic Map ed. H. Candela. PLoS One, 9, e109910.

Cantarel, B.L., Korf, I., Robb, S.M.C., Parra, G., Ross, E., Moore, B., Holt, C. et al. (2008) MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18, 188-196.

Chalhoub, B., Denoeud, F., Liu, S., Parkin, I.A.P., Tang, H., Wang, X., Chiquet, J. et al. (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 345, 950-953. [OpenAIRE]

Cheng, F., Sun, R., Hou, X., Zheng, H., Zhang, F., Zhang, Y., Liu, B. et al. (2016) Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nat. Genet. 1-10.

Crusoe, M.R., Alameldin, H.F., Awad, S., Boucher, E., Caldwell, A., Cartwright, R., Charbonneau, A. et al. (2015) The khmer software package: enabling efficient nucleotide sequence analysis. F1000Research, 4, 900. [OpenAIRE]

Edwards, D., Batley, J. and Snowdon, R.J. (2013) Accessing complex crop genomes with next-generation sequencing. Theor. Appl. Genet. 126, 1-11.

Foisset, N., Delourme, R., Barret, P. and Renard, M. (1995) Molecular tagging of the dwarf BREIZH (Bzh) gene in Brassica napus. Theor. Appl. Genet. 91, 756-761.

Gladman, S. and Seemann, T. (2012) VelvetOptimiser (Version 2.2.4) [Software]. http://www.bioinformatics.net.au/software.velvetoptimiser. shtml.

Golicz, A.A., Martinez, P.A., Zander, M., Patel, D.A., Van De Wouw, A.P., Visendi, P., Fitzgerald, T.L. et al. (2014) Gene loss in the fungal canola pathogen Leptosphaeria maculans. Funct. Integr. Genomics, 15, 189-196. [OpenAIRE]

Golicz, A.A., Batley, J. and Edwards, D. (2016a) Towards plant pangenomics. Plant Biotechnol. J. 14, 1099-1105. [OpenAIRE]

58 references, page 1 of 4
Abstract
Summary As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. Here, we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the Brassica napus cultivar Darmor-bzh. Both cultivars were annotated using the same method t...
Subjects
Medical Subject Headings: food and beverages
free text keywords: genome assembly, whole genome comparison, genotyping by sequencing, genome assembly improvement, Brassica napus, Tapidor, contigPlacer, [SDV]Life Sciences [q-bio], Research Article, Research Articles, genome assembly;whole genome comparison;genotyping by sequencing;genome assembly improvement;Brassica napus;Tapidor;contigPlacer, Biotechnology, Agronomy and Crop Science, Plant Science, Biology, Gene, Genome, Genome comparison, Genetics, Brassica, biology.organism_classification, Sequence assembly, Reference genome, Annotation, Sources of error, Botany
Funded by
RCUK| Sequencing and exploitation of the Brassica A genome
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: BB/E017363/1
  • Funding stream: BBSRC
,
ARC| Linkage Projects - Grant ID: LP140100537
Project
  • Funder: Australian Research Council (ARC) (ARC)
  • Project Code: LP140100537
  • Funding stream: Linkage Projects
,
ARC| Linkage Projects - Grant ID: LP130100925
Project
  • Funder: Australian Research Council (ARC) (ARC)
  • Project Code: LP130100925
  • Funding stream: Linkage Projects
,
ARC| Discovery Projects - Grant ID: DP160104497
Project
  • Funder: Australian Research Council (ARC) (ARC)
  • Project Code: DP160104497
  • Funding stream: Discovery Projects
,
ARC| Future Fellowships - Grant ID: FT130100604
Project
  • Funder: Australian Research Council (ARC) (ARC)
  • Project Code: FT130100604
  • Funding stream: Future Fellowships
58 references, page 1 of 4

Alexa, A. and Rahnenfuhrer, J. (2010) topGO: enrichment analysis for gene ontology. R package version, 2.

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410.

Arumuganathan, K. and Earle, E.D. (1991) Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 211-215. [OpenAIRE]

Bayer, P.E., Ruperao, P., Mason, A.S., Stiller, J., Chan, C.-K.K., Hayashi, S., Long, Y. et al. (2015) High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theor. Appl. Genet. 128, 1039-1047. [OpenAIRE]

Brown, C.T., Howe, A., Zhang, Q., Pyrkosz, A.B. and Brom, T.H. (2012) A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data. http://arxiv.org/abs/1203.4802.

Cai, G., Yang, Q., Yi, B., Fan, C., Edwards, D., Batley, J., Zhou, Y. et al. (2014) A complex recombination pattern in the genome of allotetraploid Brassica napus as revealed by a high-density genetic Map ed. H. Candela. PLoS One, 9, e109910.

Cantarel, B.L., Korf, I., Robb, S.M.C., Parra, G., Ross, E., Moore, B., Holt, C. et al. (2008) MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18, 188-196.

Chalhoub, B., Denoeud, F., Liu, S., Parkin, I.A.P., Tang, H., Wang, X., Chiquet, J. et al. (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 345, 950-953. [OpenAIRE]

Cheng, F., Sun, R., Hou, X., Zheng, H., Zhang, F., Zhang, Y., Liu, B. et al. (2016) Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nat. Genet. 1-10.

Crusoe, M.R., Alameldin, H.F., Awad, S., Boucher, E., Caldwell, A., Cartwright, R., Charbonneau, A. et al. (2015) The khmer software package: enabling efficient nucleotide sequence analysis. F1000Research, 4, 900. [OpenAIRE]

Edwards, D., Batley, J. and Snowdon, R.J. (2013) Accessing complex crop genomes with next-generation sequencing. Theor. Appl. Genet. 126, 1-11.

Foisset, N., Delourme, R., Barret, P. and Renard, M. (1995) Molecular tagging of the dwarf BREIZH (Bzh) gene in Brassica napus. Theor. Appl. Genet. 91, 756-761.

Gladman, S. and Seemann, T. (2012) VelvetOptimiser (Version 2.2.4) [Software]. http://www.bioinformatics.net.au/software.velvetoptimiser. shtml.

Golicz, A.A., Martinez, P.A., Zander, M., Patel, D.A., Van De Wouw, A.P., Visendi, P., Fitzgerald, T.L. et al. (2014) Gene loss in the fungal canola pathogen Leptosphaeria maculans. Funct. Integr. Genomics, 15, 189-196. [OpenAIRE]

Golicz, A.A., Batley, J. and Edwards, D. (2016a) Towards plant pangenomics. Plant Biotechnol. J. 14, 1099-1105. [OpenAIRE]

58 references, page 1 of 4
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publication . Article . Other literature type . 2017

Assembly and comparison of two closely relatedBrassica napusgenomes

Bayer, Philipp E.; Hurgobin, Bhavna; Golicz, Agnieszka A.; Chan, Chon‐Kit Kenneth; Yuan, Yuxuan; Lee, HueyTyng; Renton, Michael; Meng, Jinling; Li, Ruiyuan; Long, Yan; ...