Genome Assembly and Validation of Brassica oleracea

We took a series of checking and filtering measures on reads following the
Illumina-Pipeline, and low-quality reads, adaptor sequences and duplicates were
removed (Supplementary Methods).
The reads after the above filtering and correction steps were used to perform
assembly including contig construction, scaffold construction and gap filling
using SOAPdenovo1.04 ( http://soap.genomics.org.cn/) (Supplementary Methods). Finally, we used
20-kb-span paired-end data generated from the 454 platform and 105-kb-span
BAC-end data downloaded from NCBI ( http://www.ncbi.nlm.nih.gov/nucgss?term=BOT01) to extend scaffold
length (Supplementary Methods). The
B. oleracea genome size was estimated using the distribution curve of
17-mer frequency (Supplementary
Methods).
To anchor the assembled scaffolds onto pseudo-chromosomes, we developed a genetic
map using a double haploid population with 165 lines derived from a F1 cross
between two homozygous lines 02–12 (sequenced) and 0188
(re-sequenced). The genetic map contains 1,227 simple sequence repeat markers
and single nucleotide polymorphism markers in nine linkage groups, which span a
total of 1,180.2 cM with an average of 0.96 cM between the
adjacent loci16 (link). To position these markers to the scaffolds,
marker primers were compared with the scaffold sequences using e-PCR (parameters
-n2 -g1 –d 400–800), with the best-scoring match chosen in
case of multiple matches.
We validated the B. oleracea genome assembly by comparing it with the
published physical map constructed using 73,728 BAC clones ( http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/WebFPC/)17 (link) and a genetic map from B. napus18 (link) (Supplementary Methods). Eleven
Sanger-sequenced B. oleracea BAC sequences were used to assess the
assembled genome using MUMmer-3.22 ( http://mummer.sourceforge.net/) (Supplementary Methods).

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Liu S., Liu Y., Yang X., Tong C., Edwards D., Parkin I.A., Zhao M., Ma J., Yu J., Huang S., Wang X., Wang J., Lu K., Fang Z., Bancroft I., Yang T.J., Hu Q., Wang X., Yue Z., Li H., Yang L., Wu J., Zhou Q., Wang W., King G.J., Pires J.C., Lu C., Wu Z., Sampath P., Wang Z., Guo H., Pan S., Yang L., Min J., Zhang D., Jin D., Li W., Belcram H., Tu J., Guan M., Qi C., Du D., Li J., Jiang L., Batley J., Sharpe A.G., Park B.S., Ruperao P., Cheng F., Waminal N.E., Huang Y., Dong C., Wang L., Li J., Hu Z., Zhuang M., Huang Y., Huang J., Shi J., Mei D., Liu J., Lee T.H., Wang J., Jin H., Li Z., Li X., Zhang J., Xiao L., Zhou Y., Liu Z., Liu X., Qin R., Tang X., Liu W., Wang Y., Zhang Y., Lee J., Kim H.H., Denoeud F., Xu X., Liang X., Hua W., Wang X., Wang J., Chalhoub B, & Paterson A.H. (2014). The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nature Communications, 5, 3930.

Publication 2014

Brassica Chromosomes Clones Genetic map Genome Homozygous Physical Primers Simple sequence repeat Single nucleotide polymorphism

Corresponding Organization :

Other organizations : Chinese Academy of Agricultural Sciences, BGI Group (China), University of Queensland, Agriculture and Agri-Food Canada, North China University of Science and Technology, University of Georgia, University of York, Seoul National University, Sichuan Academy of Agricultural Sciences, Southern Cross University, University of Missouri, Jiangsu Academy of Agricultural Sciences, Australian Research Council, National Research Council Canada, Australian Centre for Plant Functional Genomics, Agriculture and Food, Sahmyook University, Huazhong Agricultural University, South Central University for Nationalities, Institut de Génomique Fonctionnelle, Génomique Métabolique du Genoscope, University of Hong Kong, King Abdulaziz University, Flagstaff Medical Center

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Variable analysis

independent variables

Illumina-Pipeline filtering and correction steps
SOAPdenovo1.04 assembly including contig construction, scaffold construction and gap filling
Use of 20-kb-span paired-end data from 454 platform and 105-kb-span BAC-end data from NCBI to extend scaffold length
Development of a genetic map using a double haploid population with 165 lines derived from a F1 cross between two homozygous lines 02-12 and 0188

dependent variables

Quality of assembled genome
Accuracy of scaffold positioning on pseudo-chromosomes

control variables

Sanger-sequenced B. oleracea BAC sequences used to assess the assembled genome
Comparison of the assembled genome with the published physical map and a genetic map from B. napus

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