Information about assembly Zm-B104-DRAFT-ISU_USDA-0.1
(also known as B104)
to learn about maize genome and gene model nomenclature rules.
Genome Sequencing Project Information
The B73 inbred line is the source of our community reference genome. However, B73 cannot be transformed, making it difficult to make use genomic data for genetics studies that involve transformation. Our motivation was to identify an inbred line similar to B73 for plant transformation. Both B73 and B104 are derived from the Iowa Stiff Stalk Synthetic lines. Unlike B73, B104 is readily transformed. The ISU Plant Transformation Facility now offers transformation services for the B104 inbred line. They share about 93% similarity as calculated using TIPSimSelector at MaizeGDB, a tool that assess genetics similarity based on methods described in Romay et al., 2013
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.
B104 seed was ordered from CAD (http://www.cad.iastate.edu/) at Iowa State Univeristy. Available at http://www.cad.iastate.edu/corn/inbreds
Sequencing and Assembly Information
Sequence service provider: Dow AgroSciences Sequencing technologies: Illumina paired end sequencing Sequencing method: Illumina pair-end sequencing (50x) technology was used to sequence the B104 maize line followed by its genome assembly using a reference-guided approach with B73 as the reference genome. De novo assembly was used for assembling the unmapped Illumina reads. Draft beta pseudomolecule assembly was done using reference-guided assembly via ALLMAPS with B73 and W22 synteny markers generated with SynMap using the Ensembl B73 version 4.32 genome or the W22 genome vs the unassembled B104 scaffolds. Many scaffolds with annotations are still unplaced. Additionally, in the upcoming full-release, 20x PacBio reads are being generated to create pseudomolecules. Sequencing hardware: HiSeq2000
Assembly methods: Reference based assembly plus de novo assembly for unmapped reads Construction of pseudomolecules: Yes
Reference Based scaffold assembly based on B73 genome v2 version. Pseudomolecule assembly using B73 v4 and W22.
Seq service provider
Perc seq scaffold
Perc seq unscaffold
Total scaff length
N50 scaff length
N50 scaff count
N90 scaff length
N90 scaff count
Total contig length
N50 contig length
N50 contig count
N90 contig length
N90 contig count
Total number of scaffolds in assembly.
% assembly in scaffolded contigs.
% assembly in UNscaffolded contigs.
Total sequence length represented by scaffolds.
Longest scaffold in assembly.
Shortest 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.
Total sequence length represented by contigs.
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.