Dataset Open Access

Assembly and comparison of two closely related Brassica napus genomes

Bayer, Philipp Emanuel; Hurgobin, Bhavna; Golicz, Agnieszka A.; Chan, Chon-Kit Kenneth; Yuan, Yuxuan; Lee, HueyTyng; Renton, Michael; Meng, Jinling; Li, Ruiyuan; Long, Yan; Zou, Jun; Bancroft, Ian; Chalhoub, Boulos; King, Graham J.; Batley, Jacqueline; Edwards, David

Here we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the B. napus cultivar Darmor-bzh. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor-bzh contains a greater number of genes than the genome of Tapidor.

The authors would like to acknowledge funding support from the Australian Research Council (Projects LP110100200, LP130100925, LP140100537 and DP160104497), from the UK Biotechnology and Biological Sciences Research Council (BBSRC) to GK (BB/E017797/1) and IB (BB/E017363/1) and from the National Basic Research and Development Programme of China (2006CB101600). This work was supported by resources provided by the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia, the Australian Genome Research Facility (AGRF), the Queensland Cyber Infrastructure Foundation (QCIF) and the Australian Partnership for Advanced Computing (APAC).
Files (563.6 MB)
Name Size
Darmor_v81_assembly.all.maker.augustus_masked.proteins_filtered.fasta.gz
md5:b1e82c0e73a756d032731104419e428c
18.2 MB Download
Darmor_v81_assembly.all.maker.augustus_masked.transcripts_filtered.fasta.gz
md5:e59043a5e5d1f513ffcba88f47c783ae
28.2 MB Download
Darmor_v81_assembly.augustus_masked_filtered.gff.gz
md5:15204096f1e30d9bb8e82bdaf7593366
11.5 MB Download
Darmor_v81_assembly.fasta.gz
md5:fb05e8a600bc921cf2c2ecdd3ce2237f
225.8 MB Download
Darmor_v81_Tapidor_Ningyou_SNPs.zip
md5:3936ed7e811a328f4382f5d63b416eee
17.8 MB Download
GO_Arabidopsis_Terms.zip
md5:cf391adc16d9ef27a973440d47d1a4b9
986.8 kB Download
MSTMap_Input.zip
md5:d588bfee2b37e922bb854b4f52c9f059
137.2 kB Download
MSTMap_Results.txt.gz
md5:cd984306b8b1c22f8dedb8b230050ac2
50.4 kB Download
Repetitive_Collapsed_Genes.zip
md5:c47e6d1fa1b16163d5c2dfef1f851433
29.4 kB Download
Repetitive_Collapsed_Regions.zip
md5:5b0907ab6b8f6f988397df6c6fab4ed7
816.1 kB Download
SwissProt_Pfam_hits_Repetitive_Collapsed_Genes.zip
md5:9c8051f3dab47b152645a9907d5b9e42
408.4 kB Download
Tapidor_v63_assembly.all.maker.augustus_masked.proteins_filtered.fasta.gz
md5:4086a436ffd876f0de401311706e6180
14.5 MB Download
Tapidor_v63_assembly.all.maker.augustus_masked.proteins_Pfam_results.gff.gz
md5:24f54b23f55a4f267994643057e005a7
6.0 MB Download
Tapidor_v63_assembly.all.maker.augustus_masked.transcripts_filtered.fasta.gz
md5:f056173e753add31f4834d4e9568c55c
22.8 MB Download
Tapidor_v63_assembly.augustus_masked_filtered.gff.gz
md5:92068fa0c05d6be4c1a6ae53a2a36baa
9.9 MB Download
Tapidor_v63_assembly.fasta.gz
md5:152d059ebaa4201fa846cdee25c618e9
190.4 MB Download
Tapidor_v63_Tapidor_Ningyou_SNPs.zip
md5:1352c0cd5f2057dbd5d2f2181fa1a089
16.1 MB Download
16
0
views
downloads
All versions This version
Views 1616
Downloads 00
Data volume 0 Bytes0 Bytes
Unique views 1515
Unique downloads 00

Share

Cite as