Zea mays genome annotation software

Oryza longistaminata aa genome type is a wild rice, perennial, tall 2 m or more, erect, and rhizomatous grass. Maizegdb is a communityoriented, longterm, federally funded informatics service to researchers focused on the crop plant and model organism zea mays. Help annotate the zea mays genome using our yrgate gene structure annotation tool see overview, aided by gaeval tables that flag problematic gene. To catalog new maize zea mays transcripts and identify genomic loci that regulate alternative splicing, we analyzed over 90 rnaseq libraries from maize inbred lines b73 and mo17, as well as syn10 doubled haploid lines progenies from b73. Intense artificial selection over the last 100 years has produced elite maize zea mays inbred lines that combine to produce highyielding hybrids. The number and type of evidence retrieved from public. Maizegdb is a founding member of agbiodata, a consortuim of agriculturerelated online resources which is committed to making agriculturerelated research data fair. Dec 08, 2011 recently we have expanded our annotation track offerings with new human variant frequency catalogs such as the genomes phase 1 data. Makerp identified and annotated 4,466 additional, wellsupported proteincoding genes not present in. The refseq genome records for zea mays were annotated by the ncbi.

Org was developed daniel vera, katie kyle, and hank bass using the ucsc browser and is hosted by fsus dept. The ph207 genome assembly was first masked using repeatmasker and a maize custom repeat library smit et al. The agpv4 genome, agpv4 annotation, and the michigan state university msu functional annotation is available to download below. Oct 31, 2011 genome browser has been updated with 81 tracks of data. This report presents statistics on the annotation products, the input data used in the pipeline and.

Maizegdbs overall aim is to provide longterm storage, support, and stability. Azs224 22 kda alphazein 4 precursor zea mays maize. However, quality metrics generated by the makerp gene annotation pipeline identified 17,225 of,330 % proteincoding transcripts in the b73 reference genome v4 gene set with models of low concordance to. The software uses technologies from the html5 standard, such as scalable vector graphics and allows the local upload of huge genomic data files that can be dynamically. The genome annotation and rnaseq coverage can also be viewed in the jbrowse genome browser. Blast basic local alignment search tool blast standalone cn3d. The ucsc genome browser is developed and maintained by the genome bioinformatics group, a cross. Although a food staple in many regions of the world, most is used for animal feed and ethanol fuel. Maize was domesticated from wild teosinte in central america and its cultivation spread throughout the americas by precolumbian civilisations. The maize genome is most likely the next plant genome that will be sequenced after arabidopsis and rice jorgensen, 2004. Although the physiological functions related to husk have been extensively studied, little is known about its morphological variation and genetic basis in natural population. A genome wide association analysis enables one to analyze allelic diversity of complex traits and identify superior alleles. Jun 12, 2017 an improved reference genome for maize, using singlemolecule sequencing and highresolution optical mapping, enables characterization of structural variation and repetitive regions, and.

The maize genetics and genomics database maizegdb is the community database and global web resource for zea mays, used each year by tens of thousands of researchers to access millions of pages, images, tools, documents, and datasets. Maker tutorial for wgs assembly and annotation winter school 2018. Gene annotation was performed in the laboratory of doreen ware cshlusda. Genome annotation information is available from many sources including publications on the sequencing and annotation of genes for whole genomes, individual chromosomes, and whole genome annotation computed by multiple bioinformatics groups. Improved maize reference genome with singlemolecule. The maize b73 reference genome has been revised four times since its initial release as a bacbybac assembly in 2009. Versatile and open software for comparing large genomes. Of course, we also curate data for plant and animal genomes some of which are currently available in our software and some of which will be available in our next release.

In annotation release 101 a total of 47,446 genes were annotated, including 37,380 that code for proteins. Homologues are provided for several other monocots and arabidopsis thaliana. New plantanimal genomes and annotation tracks now available. As of january 2018, 8,955 eukaryotic genome projects were at various stages of completion 4,683 were still being sequenced and 4,272 had at least a.

In response, we have developed makerp, a fast and easytouse genome annotation engine for plants. Details zea mays ensembl genomes 47 ensembl plants. 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. The diploid genome 730 mb has a haploid chromosome number of 10. Loc103632253 gene cdna orf clone, zea mays genscript. To our knowledge, this is the first report of a comparative genome wide analysis of the rna helicase gene family in arabidopsis, oryza sativa, zea mays and glycine max. The msu rice genome annotation project database and resource is a national science foundation project and provides sequence and annotation data for the rice genome. The tabs below show categories for template queries, which provide simple search menus. Genomewide analysis of alternative splicing in zea mays. Zea mays maize has the highest worldwide production of all grain crops, yielding 875 million tonnes in 2012.

Allows to browse several genomes and annotations by fetching data from cellbase rest web services. Key enzyme in glycolysis that catalyzes the first step of the pathway by converting dglyceraldehyde 3phosphate g3p into 3phosphodglyceroyl phosphate. Maize dnsdifferential nuclease sensitivity references. Probe sequence data for microarrays of type mgu74a. Alternative splicing enhances transcriptome diversity in all eukaryotes and plays a role in plant tissue identity and stress adaptation. Analysis of dna sequence with genome annotation software tools allow finding and mapping genes, exonsintrons, regulatory elements, repeats and mutations. Gene coexpression analysis has been performed on 15 different publically available gene expression data sets. Oct 31, 2011 feb 6, 20 a paper describing the unified osnipponbarereferenceirgsp1. Plant lipoxygenase may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. Genome browser has been updated with 81 tracks of data. The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of highquality gene structure annotations challenging.

Genome annotation is a key process for identifying the coding and noncoding regions of a genome, gene locations and functions. Genomewide association analysis of seedling root development. Annotation and expression profile analysis of 2073 full. Our data describe targeted genome modification in zea mays. The purpose of this resource is to provide a convenient sequencecentered genome view for zea mays, with a narrow focus on gene structure annotation. Zea mays b73 agpv2 zea mays b73 agpv3 zea mays b73 agpv4 zea mays w22 v1 zea mays ph207 v1. The sophistication of gene prediction algorithms and the abundance of rnabased evidence for the maize genome may suggest that manual curation of gene models is no longer necessary. Draft assembly of elite inbred line ph207 provides.

Genome maps is a genome browser that implements a model of data transfer and management. In response we have developed makerp, a fast and easytouse genome annotation engine for plants. Pdf a beginners guide to eukaryotic genome annotation. The large size and relative complexity of many plant genomes makes creation, quality control, and dissemination of high quality genestructure annotations challenging. Affymetrix murine genome u74v2 annotation data chip mgu74a mgu74acdf.

This data is now available for download and can be explored in the genome data viewer, with blast, and in the gene database. Contributions of zea mays subspecies mexicana haplotypes. Understanding the sequence, structural, and expression variation that contributes to phenotypic diversity would facilitate more efficient varietal improvement. Plants rely on the root system for anchorage to the ground and the acquisition and absorption of nutrients critical to sustaining productivity. Orthologous group analysis has been updated to include zea mays release 5b filtered gene models. Zxgdb is being developed as a part of our nsffunded project cyberinfrastructure for comparative plant genome research through plantgdb pi. More information about the nuprime project is available at. A blast server is also available for searching your sequences against b73 v2 through v4 genome and annotation. Gene annotations were updated using 11 fulllength transcripts obtained by. Genomewide analysis of cyclins in maize zea mays request pdf. Proteincoding genes were identified using makerp software version 3.

Loc100283323 nacetyltransferase zea mays gene ncbi. Ensembl and the national center for biotechnology information ncbi independently developed computational processes to annotate vertebrate genomes kitts. However, quality metrics generated by the makerp gene annotation pipeline identified 17,225 of,330 % proteincoding transcripts in the b73 reference genome v4 gene set with. Genome databases are essential to retrieve information on gene name, protein product and dna sequence functions. Zmgdb is being developed as a part of our nsffunded project cyberinfrastructure for comparative plant genome research through plantgdb pi. Unfortunately, advances in annotation technology have not kept pace with genome sequencing, and annotation is rapidly becoming a major bottleneck affecting modern genomics research. Loc103645976 gene cdna orf clone, zea mays genscript. It is also used as biofuel crop and potential cellulosic feedstock. The rice genome annotation project web pages may be unavailable or only. Plant model organism databases beangenes beans phaseolus and vigna species the brachypodium distachyon information resource model grass brachypodium distachyon chlamydomonas center green alga chlamydomonas foresttreedb white spruce, loblolly pine, and poplar picea glauca, pinus taeda, and populus species graingenes grasses triticum. Although highly repetitive, the genome is more tractable for sequencing than its close relative, zea mays.

The whole 94 genome sequence of maize was downloaded from ncbi. Essential for the maintenance of cellular atp levels and carbohydrate metabolism by similarity. Rna based sequencing rnaseq is a powerful approach for transcriptional analysis, assessing sequence variation, and identifying novel transcript sequences, particularly in large. Browse the list download sequence and annotation from refseq or genbank. Maize zea mays husk referring to the leafy outer enclosing the ear, plays an important role in grain production by directly contributing photosynthate and protecting ear from pathogen infection. As of 2016, the maize nomenclature committee has adopted naming standards to accommodate multiple zea species, multiple accessions, and multiple versions.

Loc100194160 gene cdna orf clone, zea mays genscript. Make sure you use the gff3 option to match your genes. These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the refseq versions in the current genome build. To catalog new maize zea mays transcripts and identify genomic loci that regulate alternative splicing, we analyzed over 90 rnaseq libraries from maize inbred lines b73 and mo17, as well as syn10 doubled haploid lines progenies from. Genomewide analysis of immunophilin fkbp genes and.

To identify the csl gene family members in maize, 95 the genome sequence of maize was aligned with all rice csl genes using ncbiblast2. 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. Zea mays assembly and gene annotation about zea mays zea mays maize has the highest worldwide production of all grain crops, yielding 875 million tonnes in 2012. Contributions of zea mays subspecies mexicana haplotypes to. Automated update, revision and quality control of the zea. Rna based sequencing rnaseq is a powerful approach for transcriptional analysis, assessing sequence variation, and identifying novel transcript. Precise genome modification in the crop species zea mays. Genomewide analysis of cyclins in maize zea mays article in genetics and molecular research. The presence of 2920 anomalous coding sequences and 928 overlapping genes emerged from. Double triage to identify poorly annotated genes in maize. Ensembl and the national center for biotechnology information ncbi independently developed computational.