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Information about assembly ZeaMays_PT_EDMX2233_1.0    (also known as Palomero)
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Genome Sequencing Project Information

   Sequencing of the EDMX-2233 genotype of the Palomero Toluqueño (Palomero) landrace, a highland popcorn from San Lorenzo Teotuitlán, Mexico.
   GenBank BioProject   PRJNA51041  
   Project PI   Alfredo Herrera-Estrella
   Project start date   2011-08-01
   Release date   2011
   Data download   ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Zea_mays/all_assembly_versions/GCA_000223545.1_ZeaMays_PT_EDMX2233_1.0
   Publication status   Published
Project reference The Palomero genome suggests metal effects on domestication.. Vielle-Calzada JP1, Martínez de la Vega O, Hernández-Guzmán G, Ibarra-Laclette E, Alvarez-Mejía C, Vega-Arreguín JC, Jiménez-Moraila B, Fernández-Cortés A, Corona-Armenta G, Herrera-Estrella L, Herrera-Estrella A.
At MaizeGDB  
DOI  

Stock and Biosample Information

Stock information
   Stock name   cultivar: Palomero Toluqueno EDMX-2231
   Stock details   cultivar: Palomero Toluqueno EDMX-2231
   Stock provided by   Germplasm Bank of the Instituto Nacional de Investigaciones Forestales y Agropecuarias (INIFAP) in Chapingo
Biosample information
   GenBank BioSample   SAMN02981271  
   Sample description   Obtained from the Germplasm Bank of the Instituto Nacional de Investigaciones Forestales y Agropecuarias (INIFAP) in Chapingo
   Plant structure   aerial tissue

Sequencing and Assembly Information

   Assembly name   ZeaMays_PT_EDMX2233_1.0
   WGS accession  
   Sequencing description   Sequencing method: 454 GS20; 454 Titanium; Sanger
   Assembly description   Assembly methods: MUEGANO v. 1.0: Multiple Unrelated Element Genome Assembler in a Non-random Order (MUEGANO) protocol deveoloped by Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO) CINVESTAV Irapuato
Construction of pseudomolecules: none; scaffolds only
   Data download   ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Zea_mays/all_assembly_versions/GCA_000223545.1_ZeaMays_PT_EDMX2233_1.0
   Release date   2011
   Finishing strategy   partial
   Genome coverage   4.2X
Assembly statistics
   Scaff num   196
   N50 scaff length   44,576 bp
   N50 scaff count   1
   N50 contig length   44,576 bp
   N50 contig count   1
Total number of scaffolds in assembly.
The length of scaffold which takes the sum length (summing from longest to shortest scaffold) past 50% of the total assembly size.
How many scaffolds are counted in reaching the N50 threshold.
The length of contig which takes the sum length (summing from longest to shortest contig) past 50% of the total assembly size.
How many contig are counted in reaching the N50 threshold.
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   n/a