As an ancient segmental tetraploid, the maize zea mays l. Maize is thought to have originated 5570 million years ago in what is now central or south america and has since diversified into nearly 10 000 nondomestic relatives. A new maize zea mays genome annotation has been produced by the refseq eukaryotic genome annotation pipeline. Plants rely on the root system for anchorage to the ground and the acquisition and absorption of nutrients critical to sustaining productivity.
Thatcher,a wengang zhou,b april leonard,a bingbing wang,b,c mary beatty,b gina zastrowhayes,b xiangyu zhao,a,d andy baumgarten,b and bailin lia,1 a dupont pioneer, wilmington, delaware 19880 b dupont pioneer, johnston, iowa 501. To further our understanding of how genome and transcriptome variation contribute to the production of highyielding hybrids, we generated a draft genome assembly of the inbred line ph207 to complement and compare with the existing b73. The maize genome provides a complex landscape of interspersed genes and transposons. Hzs, comparative genomic analysis, tandem duplication. Corn insects and crop genetics research unit and department of genetics, development, and cell biology.
Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary bac. A comprehensive genome scale metabolic reconstruction of maize metabolism article pdf available in plos one 67. Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. Pdf insilico structural annotation of methylthioadenosine.
Pdf maize has a long history of genetic and genomic tool development and is. Zmgdb is being developed as a part of our nsffunded project cyberinfrastructure for comparative plant genome research through plantgdb pi. This report presents statistics on the annotation products, the input data used in the. Sep 01, 2019 genotypes for the goodman diversity panel flintgarcia et al. Characterization of introgression from the teosinte zea. Genomewide analysis of immunophilin fkbp genes and. From the first step of nbsfilter, a total of 217 nbsencoding genes were identified in the genomic sequence of maize inbred line b73 and collected. This data is now available for download and can be explored in the genome data viewer, with blast, and in the gene database. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary bac bibac libraries for the maize inbred b73 and the sorghum landrace nengsi1. Eukaryotic chromosomes consist of dnaprotein complexes referred to as chromatin.
The aim of this study was insilico structural annotation of an amino. The grasses originated 5570 million years ago mya and subsequently diversified to include all the major cereal crop species in addition to nearly. Zheng58, chang72, and mo17 and maize wild relatives zea mays ssp. The number of fulllength cdnas from maize zea mays l. N2 previous studies have indicated a positive correlation between genome size and altitude among plant species. Our immediate aim is to identify and map genome wide changes in chromatin structure using nuclease sensitivity profiling in five diverse tissues of maize. Contributions of zea mays subspecies mexicana haplotypes to. Homologues are provided for several other monocots and arabidopsis thaliana.
Maizegdb is a founding member of agbiodata, a consortuim of agriculturerelated online resources which is committed to making agriculturerelated research data fair. Gene annotations were updated using 11 fulllength transcripts. Draft assembly of elite inbred line ph207 provides insights. The leafy stalk of the plant produces pollen inflorescences and separate ovuliferous inflorescences called ears that yield kernels or seeds, which are fruits. Draft assembly of elite inbred line ph207 provides. Fulllength cdnas are very important for genome annotation and functional analysis of genes. Genome wide analysis of alternative splicing in zea mays. Pdf genetic and genomic toolbox of zea mays researchgate. Praise and stargaze yingjie xiao 1,4, haijun liu, liuji wu2, marilyn warburton3 and jianbing yan1, 1national key laboratory of crop genetic improvement, huazhong agricultural university, wuhan 430070, china 2synergetic innovation center of henan grain crops, henan agricultural university, zhengzhou 450002, china.
Our data describe targeted genome modification in zea mays. The genome annotation and rnaseq coverage can also be viewed in the jbrowse genome browser. In response, we have developed makerp, a fast and easytouse genome annotation engine for plants. Letters precise genome modification in the crop species zea mays using zincfinger nucleases vipula k. Previous studies have indicated a positive correlation between genome size and altitude among plant species. Contributions of zea mays subspecies mexicana haplotypes. Availability of the complete zea mays genome sequence maize inbred line b73 has made it possible for the first time to identify all the lrrcontaining receptorlike genes in this plant species. Additional two letter codes can be used for other species in the genus zea as follows. Zeamap, a comprehensive database adapted to the maize. Zxgdb is being developed as a part of our nsffunded project cyberinfrastructure for comparative plant genome research through plantgdb pi. Variants segregating above 5% minor allele frequency maf in the union of all lines were considered for mapping. The dna binding domain, also named the dof domain, has. Dof proteins have two functional domains, a dnabinding domain at the nterminus and a transcriptional regulatory domain at the cterminus 14.
The refseq genome records for zea mays were annotated by the ncbi eukaryotic genome annotation pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. Genomewide analysis of alternative splicing in zea mays. It has been hypothesized that increasing genome size occurs due to increasing cbanded heterochromatin. Praise and stargaze yingjie xiao 1,4, haijun liu, liuji wu2, marilyn warburton3 and jianbing yan1, 1national key laboratory of crop genetic improvement, huazhong agricultural university, wuhan 430070, china. The huangzaosi maize genome provides insights into. Insights into the maize pangenome and pantranscriptome. A reference genome is a haploid representation of a genome as dna sequence with a defined coordinate system, and accession and version identification. To further our understanding of how genome and transcriptome variation contribute to the production of highyielding hybrids, we generated a draft genome assembly of the inbred line ph207 to complement and compare with the existing b73 reference. Annotation and expression profile analysis of 2073 full. Shared protocolpreparingarabidopsisdnafor20kbsmrtbelllibraries. Browse the list download sequence and annotation from refseq or genbank. The agpv4 genome, agpv4 annotation, and the michigan state university msu functional annotation is available to download below. The mass genome annotation mga repository is a resource designed to store published next generation sequencing data and other genome annotation data such as gene start sites, snps, etc.
Genomewide association analysis of seedling root development. There will be disappointment when the research communities realize that they dont have the gold standard of sequence as present in arabidopsis and rice. A comprehensive genome scale metabolic reconstruction of maize metabolism rajib saha, patrick f. Nevertheless, attempts to engineer plant metabolism for desired overproductions have been met with only limited success 12. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement. Maizegdb is a communityoriented, longterm, federally funded informatics service to researchers focused on the crop plant and model organism zea mays. Zea mays maize has the highest worldwide production of all grain crops, yielding 875 million tonnes in 2012. The chromatin interaction and histone modification data were. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary bac bibac libraries for the maize inbred b73 and the. Precise genome modification in the crop species zea mays. Automated update, revision and quality control of the zea mays. Zea mays data mapped to agpv4 reference for structural variant. The tabs below show categories for template queries, which provide simple search menus.
A genome wide characterization of microrna genes in maize. Maize was domesticated from wild teosinte in central america and its cultivation spread throughout the americas by precolumbian civilisations. Background the spread of maize cultivation to the highlands of central mexico was accompanied by substantial introgression from the endemic wild teosinte zea mays ssp. Gene annotations were updated using 111,000 fulllength transcripts. The maize oligonucleotide array maizearray is one of the few microarray platforms designed for genome wide gene expression analysis in zea mays l. Dna methylation and dimethylation of lysine 9 of histone h3 h3k9me2 are two chromatin modifications that can be associated with gene expression or recombination rate. We report an improved draft nucleotide sequence of the 2. Pdf genome assembly of a tropical maize inbred line. Over 10% of the maize genome shows evidence of introgression from the mexicana genome, suggesting that mexicana contributed to maize adaptation and improvement. Methods we used whole genome sequence data to map regions of zea mays ssp. Herein, we introduce a genome scale model for a plant with direct applications to food and bioenergy production i. Genomic distribution of h3k9me2 and dna methylation in a. In corn, increasing altitude has been correlated with decreasing knob cbanded heterochromatin, suggesting that dna content may decrease with increasing altitude. In addition to its agronomic importance, maize has been a keystone model organism for basic research for nearly a century.
A genome wide association analysis enables one to analyze allelic diversity of complex traits and identify superior alleles. New lncrna annotation reveals extensive functional divergence. Identification of immune related lrrcontaining genes in. Zea mays subspecies mays zm zea mays subspecies parviglumis zv zea mays subspecies mexicana zx zea mays subspecies huehuetenangensis zh. Rnasequencing of different b73 tissues were from 9, and rnaseq data of developing maize kernels from 368 amp inbred lines were from 10.
Ncbi is actively annotating genes in the version 3 maize genome with comprehensive details of gene structure, neighboring loci, expression. Transcriptomewide association supplements genomewide. The microarray technology has become an established approach for largescale gene expression analysis with mature protocols for sample, microarray, and data processing. Characterizing the pan genome of maize with pacbio smrt sequencing michelle vierra, greg concepcion, aaron wenger, david rank, paul peluso pacbio, 5 obrien drive, menlo park, ca 94025 improved genome annotation the era of the pangenome7 acknowledgements the authors would like to thank everyone associated with the. Characterizing the pangenome of maize with pacbio smrt. Thiolspecific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively by similarity. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results. A genome wide analysis of the cellulose synthaselike csl gene family in maize zea mays yongkai li 2 1, xiaojie cheng 1, yaqin fu 1, qinqin wu 1, yuli guo 1, jiayu peng, wei zhang corresp. Intense artificial selection over the last 100 years has produced elite maize zea mays inbred lines that combine to produce highyielding hybrids. The counts and characteristics of the annotated features. In response we have developed makerp, a fast and easytouse genome annotation engine for plants.
Improved maize reference genome with singlemolecule. In annotation release 101 a total of 47,446 genes were annotated, including 37,380 that code for proteins. Maize is an important model organism for fundamental research into the inheritance and functions of genes, the physical linkage of genes to chromosomes, the mechanistic relation between cytological crossovers. N early i dentical p aralogs nips are defined as paralogous genes that exhibit.
The scope and breadth of genome scale metabolic reconstructions have continued to expand over the last decade. Our data offer a rich resource for constructing the pan genome of zea mays and genetic improvement of modern maize varieties. Zea mays, more commonly referred to as maize, is a member of the grass family poaceae, or true grasses. The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of highquality gene structure annotations challenging. Maranas department of chemical engineering, the pennsylvania state university, university park, pennsylvania, united states of america. Sequence analyses of the gene space of the maize inbred line b73 genome, coupled with wet lab validation, have revealed. 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. Caveats of genome annotationgreatly impacted by the quality of the sequence. Automated update, revision and quality control of the zea. Zea mays maize has historically been used as a model species for genetics, development, physiology and more recently, genome structure.
Further information about the species will be included in the title and metadata of the assembly. Makerp identified and annotated 4,466 additional, wellsupported proteincoding genes not present in. Genomic resources for gene discovery, functional genome. The genome assembly and annotations of zea mays ssp.
A blast server is also available for searching your sequences against b73 v2 through v4 genome and annotation. Apr 29, 2009 our data describe targeted genome modification in zea mays. Although a food staple in many regions of the world, most is used for animal feed and ethanol fuel. The purpose of this resource is to provide a convenient sequencecentered genome view for zea mays, with a narrow focus on gene structure annotation. The genome wide distribution of dna methylation and h3k9me2 were investigated in seedling tissue for the maize inbred b73 and compared to. Understanding of the relationship between chromatin structure and genome behavior is a long term goal of this project nsf 1444532. Using transcriptome sequencing of seedling rna from 503 maize zea mays inbred lines to characterize the maize pan genome, we identified 8681 representative transcript assemblies rtas1 with 16. Here we report the construction of a fulllength enriched cdna library from osmotically stressed maize seedlings by using the modi. Many genome projects have annotations that embody years of manual curation and revision. Seems to contribute to the inhibition of germination during stress by similarity. A near complete snapshot of the zea mays seedling transcriptome revealed from ultradeep sequencing. Jan 01, 2007 as an ancient segmental tetraploid, the maize zea mays l. Automated update, revision, and quality control of the.