MaizeGDB Genome Center

Home > Genome Center > Zm-EP1-REFERENCE-TUM-1.0

Zm-EP1-REFERENCE-TUM-1.0 genome assembly

Project Details

Metadata

Browser

European flint genome assemblies

Project description
Resources at MaizeGDB
Downloads
Publications

Project description

Breeding programs in cooler regions of Central Europe exploit heterotic effects between dent and flint lines. To better understand the extent and quality of genomic differences between the flint and dent germplasm pools de novo high-quality sequence assemblies were generated for four flint inbred lines which represent important ancestors of maize hybrid breeding in Central Europe. These include Lacaune (F7, Southern France), Lizargarate (EP1, Northern Spain) and Gelber Badischer Landmais (DK105, Southern Germany), and PE0075, a doubled-haploid line derived from the Petkuser Ferdinand Rot population, a landrace from Northern Germany.

Learn more about this project here: http://www.europeanmaize.net.

Resources at MaizeGDB

Genome Browsers

EP1
F7

Assembly pages

DK105
EP1
F7
PE0075

Gene models

Records for the EP1 and F7 gene models can be viewed individually at the gene data center.

Downloads

MaizeGDB downloads

DK105
EP1
F7
PE0075

GenBank downloads

DK105
EP1
F7
PE0075

Publications

Haberer et al. 2020. European maize genomes highlight intraspecies variation in repeat and gene content.
Unterseer et al., 2017. (Preprint) European Flint reference sequences complement the maize pan-genome.

Project Details

Metadata

Browser

Information about assembly Zm-EP1-REFERENCE-TUM-1.0 (also known as EP1)

Assembly identifier: Zm00010a

Click here to learn about maize genome and gene model nomenclature rules.

Genome Sequencing Project Information

	Project name	EP1 Genome Assembly - Technical University of Munich
	GenBank BioProject	PRJNA360920
	Project PI	Chris-Carolin Schön
	Project start date	2016-10-01
	Release date	1st of February 2017 (pre-release)
	Contributors	Klaus Mayer, Helmholtz Zentrum München
	Funding	Bavarian State Ministry of the Environment; Consumer Protection (Project BayKlimaFit, http://www.bayklimafit.de/)
	Publication status	published
	Project reference	European maize genomes highlight intraspecies variation in repeat and gene content. Georg Haberer, Nadia Kamal, Eva Bauer, Heidrun Gundlach, Iris Fischer, Michael A. Seidel, Manuel Spannagl, Caroline Marcon, Alevtina Ruban, Claude Urbany, Adnane Nemri, Frank Hochholdinger, Milena Ouzunova, Andreas Houben, Chris-Carolin Schön & Klaus F. X. Mayer At MaizeGDB DOI

Stock and Biosample Information

Stock information
	Stock name	EP1_TUM_2015
	Stock record	25146
	Stock details	EP1_TUM_2015
	Stock provided by	Technical University of Munich, Plant Breeding

Biosample information
	Species	Zea mays ssp. mays
	Sample name	EP1
	Sample description	Pedigree: Spanish population 'Lizargarate'; Important line in early European hybrid breeding programs; released in 1950's
	GenBank BioSample	SAMN06216638
	Collection date	missing
	Collected by	Eva Bauer
	Location	Spain
	Plant structure	leaf

Sequencing and Assembly Information

Assembly name

Zm-EP1-REFERENCE-TUM-1.0

Assembly date

December 2016

Assembly accession

GCA_001984235.2

WGS accession

MTTA00000000

Assembly provider

NRGene

Sequencing description

Sequencing technologies: Illumina technologies
Sequencing method: Illumina technologies
Genome coverage: 320X

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_001984235.2_Zm-EP1-REFERENCE-TUM-1.0
https://download.maizegdb.org/Zm-EP1-REFERENCE-TUM-1.0/

Release date

1st of February 2017 (pre-release)

Finishing strategy

Complete genome, 320X 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.

Assembly statistics

	Scaff num	71,196
	Longest scaff	29,676,304 bp
	N50 scaff length	6,134,295 bp
	N50 scaff count	121
	N90 scaff length	1,226,173 bp
	N90 scaff count	439
	Longest contig	766,959 bp
	N50 contig length	82,295 bp
	N50 contig count	8,811
	N90 contig length	17,687 bp
	N90 contig count	31,904

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	Zm00010a.1
	Annotation Date	March 2018
	Is current	yes
	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.
	Data download	https://download.maizegdb.org/Zm-EP1-REFERENCE-TUM-1.0

Welcome to MaizeGDB!

Project

Outreach

Helpful Links

Maize genetics community

Maize Genetics Cooperation - MGC

Articles

Data

Resources

Maize Genetics Meeting

Archive

Featured tools at MaizeGDB

Other tools at MaizeGDB

A-I

L-Z

European flint genome assemblies

Project description

Resources at MaizeGDB

Downloads

Publications

Information about assembly Zm-EP1-REFERENCE-TUM-1.0 (also known as EP1)

Genome Sequencing Project Information

Stock and Biosample Information

Sequencing and Assembly Information

Annotation