Maize genome sequence download

Pdf improved maize reference genome with singlemolecule. The maize genetics and genomics database maizegdb is a central repository for maize sequence, stock, phenotype, genotypic and karyotypic variation, and chromosomal mapping data. Having the genome sequence is like having part of the instruction manual, says study. Insights into the maize pangenome and pantranscriptomew open. Highresolution genetic mapping of maize pangenome sequence. Nov 19, 2009 teams of scientists in the us and mexico have independently sequenced the most complex plant genome to date.

Longrange cisregulatory elements play important roles in regulating agronomic traits, but they are largely uncharacterized in crops. Genomewide identification and analysis of the cngc gene. Highresolution genetic mapping of maize pan genome sequence anchors fei lu1, maria c. We would like to show you a description here but the site wont allow us. Comparison of the new assembly to the previous bacbased maize reference genome assembly revealed more than 99. They provide an indepth genomic characterization of maize at an early point during its evolution as a domesticate, suggesting that human selection occurred as a gradual process.

Maizegdb, the community database for maize genetics and. Reference genome genome has been completely sequenced and assembled into pseudomolecules. Genome sequence of a 5,310yearold maize cob provides. Jun 12, 2017 a new, much more detailed reference genome for maize, or corn, as it is called in the u.

A new, much more detailed reference genome for maize, or corn, as it is called in the u. Hybrids bred from hzsimproved lines hils are planted in more than 60% of maize fields in china. The sequence assemblies will be enhanced by adding information about the nature of the genes and how the genomes differ from each other. In addition to singlenucleotide polymorphisms, structural variation is abundant in many plant genomes. Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphism. Of genes and genomes and the origin of maize sciencedirect. The completion of the maize genome sequence has enabled comparative genomics studies, and also the identification of new maize myb genes zmmybs20 21 22. Maize zea mays is the most produced as measured by tonnes staple crop worldwide and has been the focus of intense breeding efforts to improve agronomic traits for centuries. They attempted to distinguish among three possible modes of polyploidy, each of. Maizegdb is a communityoriented, longterm, federally funded informatics service to researchers focused on the crop plant and model organism zea mays. Our immediate aim is to identify and map genome wide changes in chromatin structure using nuclease sensitivity profiling in five diverse tissues of maize. Jan 01, 2007 as an ancient segmental tetraploid, the maize zea mays l. Efficient targeted genome modification in maize using crisprcas9 system. In july 2005, we released a sequencing ready maize physical map.

On september 20, 2002, the national science foundation nsf announced the launch of the maize genome sequencing project. In its accounting of the sequence of dna letters in the plants 10. Download the complete genome for an organism ncbi nih. This project was funded as part of the maize genome sequencing project.

Maize genome sequencing by methylation filtration science. By genetically mapping 26 m gbs tags in 14,129 maize inbred lines. The 62nd annual maize genetics meeting will be held on march 1215, 2020, at the sheraton kona, kailuakona, hawai. This page contains links to sequence and annotation data downloads for the genome assemblies featured in the ucsc genome browser. In november, 2005, the maize sequencing consortium was formed and awarded to sequence the maize genome. The ten chromosomes of the maize genome are shown here, with concentric circles reflecting various characteristics of the genome. The maize genome sequencing project provided a maize reference genome sequence with finished high quality sequence in low copy regions. Aug 15, 2019 the maize genomics resource contains a set of search and query tools including a blast server, genome browsers for agpv4, and gene report pages for all annotated genes. The maize genome is replete with chromosomal duplications and repetitive dna. The draft genome of the maize inbred line b73 is the template for analyzing genome fluidity and epigenetic regulation on a global scale. Author links open overlay panel shawn white 1 john doebley 2. Dec 19, 2003 we compared the rice genome sequence to the maize mfr, est, and rm data sets in order to estimate the ability of these approaches to capture genes.

Gene enrichment strategies offer an alternative to sequencing large and repetitive genomes such as that of maize. Rice and maize diverged about 55 million years ago and have a high degree of conservation between orthologous genes but relatively low conservation of repetitive elements. A sequenceindexed mutator insertional library for maize. Gene model crossreferences across maize genome assemblies please note that there is not a 1to1 correspondence between all gene models in all annotations. Download the complete genome for an organism starting at the genomes ftp site. Although a food staple in many regions of the world, most is used for animal feed and ethanol fuel.

To facilitate the influx of sequenced maize genomes, a number of. Retrotransposons collectively comprise 76% of the maize genome. Over the years, maizegdb has been cited thousands of times on a wide range of maize related publications. The maize genome represents a significant new challenge for sequencing. The purpose of this resource is to provide a convenient sequencecentered genome view for zea mays. Genome diversity in maize hindawi publishing corporation. Scientific american is the essential guide to the most awe. Download assembly sequence download gene model fasta.

Thin ribbons connect duplicate regions in the maize genome, thereby revealing large related segments and reflecting the maize genome s complicated structure. Representative genome the genome which has been designated as being representative for a species. In this preliminary analysis of the draft genome sequence by josh stein mgsc, cold spring harbor laboratory, cold spring harbor, usa it is clear that just the gypsy family huck element plus the copia relative ji make up nearly onequarter of the genome about 600 mb. Comparison with the rice genome reveals that methylation filtration results in a more comprehensive representation of maize genes than those. Sequence composition and genome organization of maize.

Tools sequence analysis tools accessed from the genome context view menu use the current genomic region as input. Sequence indexed insertional libraries are important resources for functional gene study in model plants. Sequence analyses of the gene space of the maize inbred line b73 genome, coupled with wet lab validation, have revealed. Here, we generated a new sequence indexed maize mutator insertional library named chinamu through highthroughput sequencing of enriched mu tagged sequences. This study provides genetic, epigenomic and functional. Longread sequencing reveals genomic structural variations. Maize cooperation newsletter video tutorials youtube channel ncga podcasts maizegdb twitter page. In many cases, the sequence data is segregated into directories for each chromosome. Pdf highresolution genetic mapping of maize pangenome. Using a bacbased approach with sanger sequencing, this assembly missed about 10 percent of the genome, according to ware.

Zea mays maize has historically been used as a model species for genetics, development, physiology and more recently, genome structure. Maizegdb is a founding member of agbiodata, a consortuim of agriculturerelated online resources which is committed to making agriculturerelated research data fair. Genome sequence of a 5,310yearold maize cob provides insights into the early stages of maize domestication. Nov 19, 2009 scientific american is the essential guide to the most awe. The maize genome sequencing project plant physiology. The genome sequence of a typical female line, b73, was previously released.

Maize is a globally important crop that was a classic model plant for genetic studies. Maize is an important crop with a high level of genome diversity and heterosis. The maize genome sequence will be a key resource for continued use of maize as an experimental system for advancing fundamental biology as well as for the development of new and improved maize varieties in the public and private sector. Zea mays maize has the highest worldwide production of all grain crops, yielding 875 million tonnes in 2012. Search or download any sequence from zmgdb using search download links at left. Nucleotide sequence of a region of maize chloroplast dna containing the 3 end of clpp, exon 1 of rps12 and rpl20 and their cotranscription. However, the genetic basis of numerous phenotypes is still unknown and genomic tools provide a valuable resource to accelerate breeding efforts. Dec 05, 2016 researchers characterized genome of a 5,310yearold maize cob the ancient maize genome is a basal lineage equally related to modern landraces there is genetic evidence of naked kernels 5,310 years ago in tehuacan, mexico human selection on maize domestication traits occurred as a gradual process. A reference genome is a haploid representation of a genome as dna sequence with a defined coordinate system, and accession and version identification. We report an improved draft nucleotide sequence of the 2. Nucleotide sequence and transcription of maize plastid genome bam hi fragment 14 containing orf170. More recently, a study of the maize pangenome was conducted by resequencing six elite maize inbred lines important. Improved maize reference genome with singlemolecule. Illumina pairend sequencing 50x technology was used to sequence the b104 maize line followed by its genome assembly using a referenceguided approach with b73 as the reference genome.

Understanding of the relationship between chromatin structure and genome behavior is a long term goal of this project nsf 1444532. However, the maize zea mays uniformmu library covers only 36% of the annotated maize genes. The maize b73 reference genome has been revised four times since its initial release as a. Widespread longrange cisregulatory elements in the maize. Efficient targeted genome modification in maize using. See the readme file in that directory for general information about the organization of the ftp files. Table downloads are also available via the genome browser ftp server. Maize was domesticated from wild teosinte in central america and its cultivation spread throughout the americas by precolumbian civilisations. This book discusses advances in our understanding of the structure and function of the maize genome since publication of the original b73 reference genome in 2009, and the progress in translating this knowledge into basic biology and trait improvement. This project will assemble the genomes of 26 additional maize lines, chosen to represent a broad cross section of the maize lines used in modern breeding. For quick access to the most recent assembly of each genome, see the current genomes directory. To evaluate the quality of the assembled k0326y genome, a highdensity maize pan genome genetic map containing 4.

In addition, maizegdb provides contact information for over 2400 maize. Jun 12, 2017 comparison of the new assembly to the previous bacbased maize reference genome assembly revealed more than 99. Pdf sequence composition and genome organization of maize. At 2,500 million bp, the maize genome is about 20 times larger than that of arabidopsis. Maize is distinguished from other grasses in that its genome arose from an ancient tetraploidy event unique to its lineage. Complete genome sequence of maize mosaic nucleorhabdovirus. However, genome wide identification and analysis of the cngc gene family in maize has not yet been undertaken.

The genome of mmv is 12,170 bases, and this project completed the 5. Comparison of two varieties offers insight into the early domestication of corn. Analyze the maize genome and more specifically the maize gene space for an increased understanding of how the maize genome functions. As one of the nonselective cation channel gene families, the cyclic nucleotidegated channel cngc gene family plays a vital role in plant physiological processes that are related to signal pathways, plant development, and environmental stresses. Lend guidance to the maizegdb team on their project to make a genome browser available at maizegdb with linkages to other maize genome browsers.

The first reference assembly for maize was released in 2009. Teams of scientists in the us and mexico have independently sequenced the most complex plant genome to date. We report the generation and analysis of nearly 100,000 undermethylated or methylation filtration maize sequences. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. The huangzaosi maize genome provides insights into genomic. The structural variation across a species can be represented by a pan genome, which is essential to fully understand the genetic control.

The duplications resulted from an ancient polyploid event that occurred over 11 million years ago. The complete genome sequence of maize mosaic virus mmv was obtained using nextgeneration sequencing from infected peregrinus maidis and rapid amplification of cdna ends from infected zea mays. Rick wilson washington university school of medicine, st louis, usa, leader of the maize genome sequencing consortium mgsc, reported that maize could be the last genome sequenced using a complete bacterial artificial chromosome bac. Detailed new genome for maize shows the plant has deep.

Some gene models are unique to specific genome assemblies, some have been split or. Genome sequence of the endophytic strain enterobacter sp. N early i dentical p aralogs nips are defined as paralogous genes that exhibit. Based on dna sequence data, the polyploid event occurred after the divergence between sorghum and maize, and hence the polyploid event explains some of the difference in dna content between these two species. Maize corn genome completed cshl dna learning center. Maize genome complexity is primarily driven by polyploidization and explosive. Maize as a model for the evolution of plant nuclear. The maize genome is complex with striking intraspecific variation in gene order, repetitive dna content, and allelic content exceeding the levels observed between primate species. The number of phenotype records has not changed significantly from 1,016 in 2003 to 1,6 in august of 2018. Corn, or maize as it is known by scientists or much of the world, is the most important crop in the americas, and accounts for 47 billion dollars in revenue in the us alone. See the righthand side bar for more terms and explanations. Within that directory a readme file will describe the various files available. This week, scientists in the united states and mexico announced the complete genetic sequence, or genome, of the corn plant. Extensive intraspecific gene order and gene structural.