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Information about assembly Zm-F7-REFERENCE-TUM-1.0    (also known as F7)
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Genome Sequencing Project Information
   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.

This project is part of the European Maize project (http://www.europeanmaize.net/). This work was funded by the Bavarian State Ministry of the Environment and Consumer Protection (Project BayKlimaFit; http://www.bayklimafit.de/)
   GenBank BioProject   PRJNA360923  
   Project PI   Chris-Carolin Schön
   Project start date   2016-10-01
   Release date   1st of February 2017 (pre-release)
   Browse Genome   Genome browser at MaizeGDB
   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
   Publication status   pre-print
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  

Stock and Biosample Information
Stock information
   Stock name   F7_TUM_2015
   Stock record   25145
   Stock details   F7_TUM_2015
   Stock provided by   Technical University of Munich, Plant Breeding
Biosample information
   GenBank BioSample   SAMN06216672  
   Sample description   Pedigree: French population 'Lacaune'; important line in early European hybrid breeding programs; released in 1950's
   Collection date   missing
   Collected by   Eva Bauer
   Plant structure   leaf

Sequencing and Assembly Information
   Assembly name   Zm-F7-REFERENCE-TUM-1.0
   WGS accession   MTTB00000000
   Sequencing description   Sequencing technologies: Illumina technologies
Sequencing method: Illumina technologies
   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
   Browse Genome   Genome browser at MaizeGDB
   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
   Release date   1st of February 2017 (pre-release)
   Sequencing method   Illumina technologies
   Finishing strategy   Complete genome, 225X coverage
   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.
   Genome coverage   225X
Assembly statistics
   Scaff num   77,899
   Longest scaff   43,780,027 bp
   N50 scaff length   9,483,450 bp
   N50 scaff count   70
   N90 scaff length   1,716,395 bp
   N90 scaff count   284
   Longest contig   704,566 bp
   N50 contig length   96,432 bp
   N50 contig count   7,368
   N90 contig length   19,659 bp
   N90 contig count   26,852
Total number of scaffolds in assembly.
Longest scaffold in assembly.
The length of scaffold which takes the sum length (summing from longest to shortest scaffold) past 50% of the total assembly size.
How many scaffolds are counted in reaching the N50 threshold.
The length of scaffold which takes the sum length (summing from longest to shortest scaffold) past 90% of the total assembly size.
How many scaffolds are counted in reaching the N90 threshold.
The longest contig.
The length of contig which takes the sum length (summing from longest to shortest contig) past 50% of the total assembly size.
How many contig are counted in reaching the N50 threshold.
The length of contig which takes the sum length (summing from longest to shortest contig) past 90% of the total assembly size.
How many contig are counted in reaching the N90 threshold.
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.

Annotation
   Annotation Identifier   Zm00011a.1
   Annotation Date   March 2018
   Annotation Description   Annotation version 1.0 was a two-step process using an in-house annotation pipeline at PGSB (Plant Genome and Systems Biology, Helmholtz Zentrum München). In step 1, transcriptome assemblies were made from a pooled RNAseq library of 27 different tissues/conditions using Bridger and Trinity. These assemblies were unified with the Evigene5 pipeline to retrieve a transcript set for each line. The transcriptome assemblies were then used together with public transcriptome assemblies and proteome data from Sb, Bd, Os B73_v4 and PH207 to identify optimal spliced alignments to the reference sequence using GenomeThreader. From this, consensus models were derived and used for AHRD annotation and subsequent filtering for transposons. In step 2, we made pairwise whole-genome alignments (WGA) between EP1, F7, B73_v4 and PH207 to identify syntenic WGA blocks. Coding sequences of each line were mapped to all other lines. If a coding sequence of another line mapped with high confidence in a syntenic block where initially no gene was annotated, we kept the gene as novel gene model if a stringent bit-score threshold was surpassed and coverage was >0.97. These novel gene models were added to those of step 1 to provide annotation v1.0.