BnIR, Brassica napus multi-omics database (information resource)

BnIR Brassica napus multi-omics information resource ————A multi-omics database with various tools for Brassica napus research and breeding

e.g. FLC or AT1G02970

Genome data

Data source

Search:

Genome ID	Species	Genome type	Sequencing technology	Assembly method	Date performed	Publication
Chiifu.v1.5	Brassica rapa ssp.pekinensis	AA	Illumina GA II	SOAPdenovo v1.04	2011/7/14	The Brassica rapa Genome Sequencing Project, C. et al. The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 43, 1035 (2011).
Chiifu.v2.5	Brassica rapa ssp.pekinensis	AA	PacBio; Illumina Hiseq 2500	Pbjelly v. 15.2.20; SOAPDenovo2	2016/11/29	Cai, C. et al. Brassica rapa Genome 2.0: A Reference Upgrade through Sequence Re-assembly and Gene Re-annotation. Mol Plant 10, 649-651 (2017).
Chiifu.v3	Brassica rapa ssp.pekinensis	AA	PacBio; Illumina Hiseq 2500; Hi-C	Canu v. 1.5	2018/8/23	Zhang, L. et al. Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies. Hortic. Res. 5, 50 (2018).
Chiifu.v4	Brassica rapa ssp.pekinensis	AA	Oxford Nanopore Promethion; Illumina Hiseq 2500; Hi-C	NextDenovo v. 2.5; Racon v.1.4.3; Canu v.1.5	2023/1/24	Zhang, L., Liang, J., Chen, H., Zhang, Z., Wu, J., and Wang, X. . A near-complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres. Plant Biotechnol J (2023).
Z1.v2	Brassica rapa ssp.rilocularis	AA	Oxford Nanopore MinION; Illumina HiSeq 2500	Ra assembler	2018/11/6	Belser, C. et al. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nat. Plants 4, 879-887 (2018).
ECD04.v0	Brassica rapa ssp.repifera	AA	PacBio Sequel; Illumina HiSeq; Hi-C	Canu v. 1.5	2022/4/22	Yang Z, et al. R gene triplication confers European fodder turnip with improved clubroot resistance. Plant Biotechnol J. 2022.
CN115125 v1	Brassica nigra	BB	Oxford Nanopore MinION; Illumina HiSeq 2500	Canu v. 1.6	2020/8/1	Perumal, S. et al. A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome. Nature Plants 6, 929-941 (2020).
Ni100 LR v2.0	Brassica nigra	BB	Oxford Nanopore MinION; Illumina HiSeq 2500	Canu v. 1.6	2020/8/1	Perumal, S. et al. A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome. Nature Plants 6, 929-941 (2020).
Ni100 SR	Brassica nigra	BB	Illumina and Roche/454	SOAPdenovo v.1.05	2020/8/1	Perumal, S. et al. A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome. Nature Plants 6, 929-941 (2020).
BnSDH v1.1	Brassica nigra var.sangam	BB	Oxford Nanopore; Illumina HiSeq 1000	MaSuRcA	2020/10/20	Paritosh, K. et al. A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes. Plant Biotechnol J 19, 602-614 (2021).

Showing 1 to 10 of 31 entries

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Data summary

Search:

Genome ID	Species	Genome type	Chromosomes + Scaffolds (FASTA Files)	Predicted genes (GFF3 Files)	Predicted coding sequences (FASTA Files)	Predicted protein sequences (FASTA Files)

Genome ID	Species	Genome type	Chromosomes + Scaffolds (FASTA Files)	Predicted genes (GFF3 Files)	Predicted coding sequences (FASTA Files)	Predicted protein sequences (FASTA Files)
ZS11.v0	Brassica napus ssp.oleifera	AACC	19+3313	100,919	107,233	107,233
Chiifu.v1.5	Brassica rapa ssp.pekinensis	AA	10+40357	41,020	41,020	41,020
Chiifu.v2.5	Brassica rapa ssp.pekinensis	AA	10+86842	48,826	48,826	48,826
Chiifu.v3	Brassica rapa ssp.pekinensis	AA	10+1093	46,250	46,250	46,250
Chiifu.v4	Brassica rapa ssp.pekinensis	AA	10	47,531	83,682	83,682
ECD04.v0	Brassica rapa ssp.repifera	AA	10+63	48,094	48,094	48,094
Z1.v2	Brassica rapa ssp.rilocularis	AA	10+200	46,721	46,721	46,721
CN115125 v1	Brassica nigra	BB	8+955	67,021	67,021	67,021
Ni100 LR v2.0	Brassica nigra	BB	8+50	59,852	59,852	59,852
Ni100 SR	Brassica nigra	BB	8+19195	56,331	56,331	56,331

Showing 1 to 10 of 30 entries

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