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Information about assembly Zm-F7-REFERENCE-TUM-1.0
(also known as F7)
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Click
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to learn about maize genome and gene model nomenclature rules.
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Genome Sequencing Project Information |
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The enormous diversity of maize is reflected by a large number of SNPs and substantial structural variation. To remedy the scarcity of sequence resources for the Flint pool, a reference sequence was generated de novo from inbred line F7. The F7 reference sequence complements the maize pan-genome with European Flint diversity.
The Plant Breeding Group (Technical University of Munich) and the Plant Genome and Systems Biology Group (Helmholtz Center Munich) in collaboration with NCBI and MaizeGDB have released a beta-version of the F7 maize genome prior to scientific publication in accordance with guidelines set forth by the Toronto Agreement for prepublication data sharing (Nature. 2009 461:168). The above groups reserve the first right to publish on the available F7 data, including but not limited to whole-genome comparisons, genes, structural annotations, functional annotations, and genome-wide association studies, and to improve the sequence and its annotations. Under the Toronto agreement, researchers can use the sequence to study individual or small sets of genes and localized regions of the genome. Any redistribution of these data should include the full text of the data use policy. This work was funded by the German Federal Ministry of Education and Research (BMBF; Project MAZE; http://www.europeanmaize.net/). |
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This sequence has been released under the
Toronto Agreement. No whole-genome research
may be submitted for publication until the official publication for this genome
assembly has been published.
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GenBank BioProject |
PRJNA360923 |
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Project PI |
Chris-Carolin Schön |
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Project start date |
2016-10-01 |
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Release date |
Feb, 2017 |
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Browse Genome |
Genome browser at MaizeGDB |
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Data download |
ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Zea_mays/latest_assembly_versions/GCA_001990705.1_Zm-F7-REFERENCE-TUM-1.0 |
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Publication status |
pre-print |
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Project reference |
European Flint reference sequences complement the maize pan-genome.
Unterseer, Sandra*; Seidel, Michael A.*; Bauer, Eva; Haberer, Georg; Hochholdinger, Frank; Opitz, Nina, Marcon, Caroline; Baruch, Kobi; Manuel Spannagl; Mayer, Klaus F.X.; Schön, Chris-Carolin * These authors contributed equally.
At MaizeGDB
DOI
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Stock and Biosample Information |
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| Stock information |
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Stock name |
F7_TUM_2015 |
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Stock record |
25145 |
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Stock details |
F7_TUM_2015 |
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Stock provided by |
Technical University of Munich, Plant Breeding |
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| Biosample information |
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GenBank BioSample |
SAMN06216672 |
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Sample description |
Pedigree: French population 'Lacaune'; important line in early European hybrid breeding programs; released in 1950's |
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Collection date |
missing |
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Collected by |
Eva Bauer |
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Plant structure |
leaf |
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Sequencing and Assembly Information |
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Assembly name |
Zm-F7-REFERENCE-TUM-1.0 |
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Sequencing description |
Sequencing technologies: Illumina technologies
Sequencing method: Illumina technologies |
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Assembly description |
Assembly methods: NRGene de novo assembly. The assembly was done using DeNovoMAGIC 2.0 after which NRGene’s internal maize ancestral genome was used to build pseudo chromosomes from the de novo assembled scaffolds.
Construction of pseudomolecules: Yes |
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Browse Genome |
Genome browser at MaizeGDB |
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Data download |
ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Zea_mays/latest_assembly_versions/GCA_001990705.1_Zm-F7-REFERENCE-TUM-1.0 |
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Release date |
Feb, 2017 |
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Sequencing method |
Illumina technologies |
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Finishing strategy |
Complete genome, 225X coverage |
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Comment |
Scaffolds
Ns are applied between contigs using paired-end and mate-pair information and their sizes are determined by the estimated insert sizes.
Negative gaps
Mate-pair and paired-end information is used to estimate the unfilled gap sizes in the scaffolds. In cases where the linking information indicated a "negative" gap size (a gap of undetermined size), an artificial gap size of 10 N’s is used.
Pseudomolecules
Scaffolds in all the rest of of the chromosomes are separated by 100 Ns. The unfilled gaps within scaffolds by a variable number of N’s according to the estimation of gap size between their contigs. |
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Genome coverage |
225X |
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| Assembly statistics |
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Scaff num |
77,899 |
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Longest scaff |
43,780,027 bp |
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N50 scaff length |
9,483,450 bp |
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N50 scaff count |
70 |
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N90 scaff length |
1,716,395 bp |
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N90 scaff count |
284 |
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Longest contig |
704,566 bp |
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N50 contig length |
96,432 bp |
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N50 contig count |
7,368 |
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N90 contig length |
19,659 bp |
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N90 contig count |
26,852 |
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Total number of scaffolds in assembly.
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Longest scaffold in assembly.
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The length of scaffold which takes the sum length (summing from longest to shortest scaffold) past 50% of the total assembly size.
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How many scaffolds are counted in reaching the N50 threshold.
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The length of scaffold which takes the sum length (summing from longest to shortest scaffold) past 90% of the total assembly size.
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How many scaffolds are counted in reaching the N90 threshold.
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The longest contig.
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The length of contig which takes the sum length (summing from longest to shortest contig) past 50% of the total assembly size.
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How many contig are counted in reaching the N50 threshold.
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The length of contig which takes the sum length (summing from longest to shortest contig) past 90% of the total assembly size.
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How many contig are counted in reaching the N90 threshold.
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A contig is a contiguous consensus sequence that is
derived from a collection of overlapping reads.
A scaffold is set of a ordered and orientated contigs
that are linked to one another by mate pairs of sequencing reads.
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Annotation |
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Annotation Identifier |
Zm00011a.1 |
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