MaizeGDB is a community-oriented, long-term, federally funded
informatics service to researchers focused on the crop plant and
model organism Zea mays.
MaizeGDB is a founding member of
AgBioData,
a consortuim of agriculture-related online resources which is
committed to making agriculture-related research data FAIR.
GCV: A web-app that visualizes genomic context data in a single, federated interface by using functional annotations as a unit of search and comparison.
Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution.
Nicolas Blavet, Hua Yang, Handong Su, Pavel Solanský, Ryan N. Douglas, Miroslava Karafiátová, Lucie Šimková, Jing Zhang, Yalin Liu, Jie Hou, Xiaowen Shi, Chen Chen, Mohamed El-Walid, Morgan E. McCaw, Patrice S. Albert, Zhi Gao, Changzeng Zhao, Gil Ben-Zvi, Lior Glick, Guy Kol, Jinghua Shi , Jan Vrána, Hana Šimková, Jonathan C. Lamb, Kathleen Newton, R. Kelly Dawe, Jaroslav Doležel, Tieming Ji, Kobi Baruch, Jianlin Cheng, Fangpu Han, James A. Birchler, and Jan Bartoš
DOI
Stock and Biosample Information
Stock information
Stock name
B73 + B chromosome(s)
Stock provided by
James Birchler
Biosample information
Species
Zea mays ssp. mays (maize)
Sample name
maize_B73+B
Sample description
maize line B73 + B chromosome -> maize flow-sorted B chromosome
Sequencing technologies: ilumina Sequencing method: illumina pair-ends, mate-pairs, Hi-C Genome coverage: raw reads > 250X; assembled scaffolds - 89.5% of estimated chromosome size; pseudomolecule - 75.8% of estimated chromosome size
Assembly description
Assembly methods: NRGene - DeNovoMAGIC v2.0, Bionano optical mapping, HiC-scaffolding Construction of pseudomolecules: pseudomolecule assembly was done manually based on information from deficiency mapping
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.
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
Zm00044a.1
Annotation Provider
Maize B-chromosome Sequencing Consortium
Annotation Date
Jun-1-2020
Is current
yes
Annotation Software
MAKER-P, Augustus, FGENESH
Annotation Description
Gene annotation based on Genbank cDNA, PacBio Iso-seq RNA used for maize B73v4, MAKER-P gene model annotation using : Arabidopsis, rice, sorghum, Setaria, and Brachypodium (Ensembl_plants r43) and maize v3, and Augustus and FGENESH gene model prediction.
Metadata
Browser
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