Genome

Zea mays Zea mays Organism overview Lineage: Eukaryota[15557]; Viridiplantae[1758]; Streptophyta[1641]; Embryophyta[1630]; Tracheophyta[1603]; Spermatophyta[1585]; Magnoliopsida[1558]; Liliopsida[245]; Poales[144]; Poaceae[120]; PACMAD clade[50]; Panicoideae[36]; Andropogonodae[21]; Andropogoneae[19]; Tripsacinae[2]; Zea[2]; Zea mays[1]

Maize is an economically important crop, along with rice and wheat. It is the premier cash crop in the United States. In addition to being used as grain and fodder, it is also used extensively in pharmaceutical production as well as a commodity feedstock for other organic chemical products like rubber, ethanol and plastic. Apart from its economic importance, More...it has been a classical plant model for genetic studies for decades.The maize nuclear genome is thought to be amphidiploid - a fusion of two diploid genomes (Helentjaris T, Weber D, Wright S. 1988) - or allopolyploid - (Wilson WA et al. 1999) with knob heterochromatin. The knob heterochromatin has been characterized as a duplication of a 185-bp element (Peacock WJ et al. 1981) and a 350-bp element (Ananiev EV et al. 1998) with the amount of duplication varying up to 3 to 4 orders of magnitude between different races of corn. This leads to a wide range of genome sizes among corn. The minimum size is estimated to be 2400 Mbp with a high proportion of repetitive DNA.Contemporary US corn crops are the consequence of introgressing various traits into a group of corn varieties. Examination of the pedigrees shows that each is a mixture, in differing proportions, of two ancestral maize strains: northern flint and southern dent [(Allard RW. 1999); (Doebley et al. Econ Bot 1988 42:120-131)]. With the application of inexpensive tools to precisely perform genotypic analysis (Matsuoka Y et al. 2002) the initial findings were confirmed and expanded (Liu K et al. 2003). This investigation was expanded to examine the genetic relationships between individual local populations of different corn land races (Vigouroux Y et al. 2005). The conclusion is that there are five maize land races which arose from independent efforts across the Americas following a single domestication of maize (Matsuoka Y et al. 2002).The first draft of the nucleotide sequence of the Zea mays subspecies mays (maize) genome was announced on February 28, 2007 at the 50th Maize Genetics Conference. Less...

Summary Sequence data:  genome assemblies: 74; sequence reads: 112  (See  Genome Assembly and Annotation report) Statistics:  median total length (Mb): 2192.76  median protein count: 57578  median GC%: 46.7893 NCBI Annotation Release:  103 Publications (limited to 20 most recent records) Pattern and variation in simple sequence repeat (SSR) at different genomic regions and its implications to maize evolution and breeding. Zhao M, et al. BMC Genomics 2023 Mar 21 Genome assembly of the Chinese maize elite inbred line RP125 and its EMS mutant collection provide new resources for maize genetics research and crop improvement. Nie S, et al. Plant J 2021 Oct Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Sun S, et al. Nat Genet 2018 Sep Improved maize reference genome with single-molecule technologies. Jiao Y, et al. Nature 2017 Jun 22 Contributions of Zea mays subspecies mexicana haplotypes to modern maize. Yang N, et al. Nat Commun 2017 Nov 30 Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. Hirsch CN, et al. Plant Cell 2016 Nov High-resolution genetic mapping of maize pan-genome sequence anchors. Lu F, et al. Nat Commun 2015 Apr 16 Insights into corn genes derived from large-scale cDNA sequencing. Alexandrov NN, et al. Plant Mol Biol 2009 Jan Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs. Soderlund C, et al. PLoS Genet 2009 Nov The Palomero genome suggests metal effects on domestication. Vielle-Calzada JP, et al. Science 2009 Nov 20 The B73 maize genome: complexity, diversity, and dynamics. Schnable PS, et al. Science 2009 Nov 20 Sequence and comparative analysis of the maize NB mitochondrial genome. Clifton SW, et al. Plant Physiol 2004 Nov Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. Maier RM, et al. J Mol Biol 1995 Sep 1 Nucleotide sequence of maize chloroplast rpl32: completing the apparent set of plastid ribosomal protein genes and their tentative operon organization. Weglöhner W, et al. Plant Mol Biol 1993 Feb Identification of editing positions in the ndhB transcript from maize chloroplasts reveals sequence similarities between editing sites of chloroplasts and plant mitochondria. Maier RM, et al. Nucleic Acids Res 1992 Dec 11 Nucleotide sequence of a maize chloroplast DNA fragment containing an inversion breakpoint, trnG (GCC), trnG (UCC), trnfM, and a trnG pseudogene. Rodermel SR Nucleic Acids Res 1992 Nov 11 Nucleotide sequence of a region of maize chloroplast DNA containing the 3' end of clpP, exon 1 of rps12 and rpl20 and their cotranscription. Weglöhner W, et al. Plant Mol Biol 1992 Jan Nucleotide sequence and transcription of maize plastid genome Bam HI fragment 14 containing ORF170. Kangasjärvi J, et al. Plant Mol Biol 1991 Sep Nucleotide sequence and map positions of the duplicated gene for maize (Zea mays) chloroplast ribosomal protein L2. Kavousi M, et al. Nucleic Acids Res 1990 Jul 25 Nucleotide sequence of the maize chloroplast rpo B/C1/C2 operon: comparison between the derived protein primary structures from various organisms with respect to functional domains. Igloi GL, et al. Mol Gen Genet 1990 May More...  Representative (genome information for reference and representative genomes) Reference genome:   Zea mays Zm-B73-REFERENCE-NAM-5.0 Loc Type Name RefSeq INSDC Size (Mb) GC% Protein rRNA tRNA Other RNA Gene Pseudogene Chr 1 NC_050096.1 LR618874.1 308.45 46.9 8,556 2 129 2,443 6,907 718 Chr 2 NC_050097.1 LR618875.1 243.68 46.9 6,753 209 153 2,038 5,866 616 Chr 3 NC_050098.1 LR618876.1 238.02 46.9 6,099 - 85 1,710 4,813 502 Chr 4 NC_050099.1 LR618877.1 250.33 46.5 5,986 - 118 1,778 4,981 543 Chr 5 NC_050100.1 LR618878.1 226.35 46.8 6,519 - 109 1,936 5,207 547 Chr 6 NC_050101.1 LR618879.1 181.36 47.0 4,907 671 80 1,512 4,614 455 Chr 7 NC_050102.1 LR618880.1 185.81 46.7 4,835 - 54 1,401 3,702 410 Chr 8 NC_050103.1 LR618881.1 182.41 46.9 4,881 - 78 1,705 4,120 412 Chr 9 NC_050104.1 LR618882.1 163.01 46.9 4,363 - 61 1,407 3,624 409 Chr 10 NC_050105.1 LR618883.1 152.44 46.9 4,007 3 47 1,185 3,195 394 MT NC_007982.1 - 0.57 43.9 163 4 29 - 214 26 Pltd NC_001666.2 - 0.14 38.5 111 8 38 - 158 1 Un - . - 50.23 44.7 398 1,543 393 132 2,496 161 Chromosomes Click on chromosome name to open Genome Data Viewer External Resources AGI Donald Danforth Plant Science Center Gramene MGSP - MIPS Maize Full Length cDNA Project Maize GDB Maize Genetics Cooperation PGIR Panzea PlantGDB