MaizeGDB Genome Center

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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.

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The 66th Annual Maize Genetics Meeting was held from February 29th - March 3rd, 2024 at the Raleigh Convention Center in Raleigh, North Carolina, USA.

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Featured tools at MaizeGDB

A resource to BLAST your sequence against maize genomes and annotations.

A data warehouse to access genomic, proteomic, and literature data for maize.

A platform to compare gene and protein expression data across multiple genomes.

A set of comprehensive metabolic pathway resources for maize.

Other tools at MaizeGDB

SNPversity

SNPversity: A tool to access large-scale maize diversity data.

TYPSimSelector

TYPSimSelector: A tool that sorts identity-by-state values derived from SNP datasets for accessions in the Ames Diversity Panel.

PanEffect

PanEffect: A tool to explore the variant effects across the maize pan-genome.

Bin viewer

Bin Viewer: A tool to explore data in regions defined by genetic bins.

GenomeQC

GenomeQC: A tool to assess the quality of genome assemblies and annotations.

Maize Feature Store

MFS: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications.

Pedigree Viewer

Pedigree Viewer: A tool to visualize maize pedigree data and networks.

PAST

PAST: A tool that assigns your SNPs to genes and your genes to metabolic pathways.

Genome Context Viewer

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.

Home > Genome Center > Zv-Ames21814-REFERENCE-CEMPS-1.0

Zv-Ames21814-REFERENCE-CEMPS-1.0 genome assembly

Project Details

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Information about assembly Zv-Ames21814-REFERENCE-CEMPS-1.0

Assembly identifier: Zv00003a

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

Genome Sequencing Project Information

	This sequence has been released under the Toronto Agreement. No whole-genome or whole-annotation research may be submitted for publication until the official publication for this genome assembly and/or annotation has been published.
	Project name	Sequencing of Ames 21814
	GenBank BioProject	PRJCA011706(NGDC)
	Project PI	Yongrui Wu
	Project start date	2021
	Contributors	Wenqin Wang
	Publication status	published
	Project reference	THP9 enhances seed protein content and nitrogen-use efficiency in maize. Yongcai Huang, Haihai Wang, Yidong Zhu, Xing Huang, Shuai Li, Xingguo Wu, Yao Zhao, Zhigui Bao, Li Qin, Yongbo Jin, Yahui Cui, Guangjin Ma, Qiao Xiao, Qiong Wang, Jiechen Wang, Xuerong Yang, Hongjun Liu, Xiaoduo Lu, Brian A Larkins, Wenqin Wang, Yongrui W DOI

Stock and Biosample Information

Stock information
	Stock name	Ames 21814
	Stock details	Ames 21814
	Stock provided by	Yongcai Huang

Biosample information
	Species	Zea mays ssp. mays (maize)
	Sample name	Ames 21814
	Sample description	Leaf tissue collected from Zea mays ssp. Parviglumis Ames21814 plant
	GenBank BioSample	SAMN27190938
	Collection date	1-Feb-20
	Collected by	Yongcai Huang
	Location	Americas Mexico Balsas River basin
	Plant structure	Leaf tissue collected from Zea mays ssp. Parviglumis Ames21814 plant

Sequencing and Assembly Information

Assembly name

Zv-Ames21814-REFERENCE-CEMPS-1.0

Assembly date

Aug-22

Assembly accession

GCA_025175245.1

WGS accession

JAOALF000000000.1

Assembly provider

Xingguo Wu

Sequencing description

Sequencing technologies: Pacbio Hi-Fi
Sequencing method: PacBio HiFi long reads + HiC
Genome coverage: 40X

Assembly description

Assembly methods: Trio
Construction of pseudomolecules: 10

Data download

https://download.cncb.ac.cn/gwh/Plants/Zea_mays_Teo.hap.fasta_GWHBKHM00000000/GWHBKHM00000000.genome.fasta.gz

Finishing strategy

HiC

Assembly statistics

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	Zv00003aa.1
	Annotation Date	Oct-23
	Is current	yes
	Annotation Software	MAKER and Braker
	Annotation Description	Pipeline using MAKER and Braker. Released under Toronto agreement.

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