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New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing.

Helguera M, Rivarola M, Clavijo B, Martis MM, Vanzetti LS, González S, Garbus I, Leroy P, Šimková H, Valárik M, Caccamo M, Doležel J, Mayer KF, Feuillet C, Tranquilli G, Paniego N, Echenique V - Plant Sci. (2014)

Bottom Line: The virtual order showed a higher collinearity with homeologous 4B compared to 4A.Additionally, a virtual map was constructed and ∼5700 genes (∼2200 on 4DS and ∼3500 on 4DL) predicted.The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information.

View Article: PubMed Central - PubMed

Affiliation: Estación Experimental Agropecuaria Marcos Juárez, Instituto Nacional de Tecnología Agropecuaria (INTA), Marcos Juárez, Córdoba, Argentina. Electronic address: helguera.marcelo@inta.gob.ar.

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GenomeZipper analysis of wheat chromosome 4DS. Wheat 4DS contigs mapped onto the genomes of Brachypodium distachyon (A) Oryza sativa (B) and Sorghum bicolor (C) using the GenomeZipper approach. The heat map depicts read density across each of the chromosomes, with a blue-red color scale (blue = 0, red = 80).
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fig0065: GenomeZipper analysis of wheat chromosome 4DS. Wheat 4DS contigs mapped onto the genomes of Brachypodium distachyon (A) Oryza sativa (B) and Sorghum bicolor (C) using the GenomeZipper approach. The heat map depicts read density across each of the chromosomes, with a blue-red color scale (blue = 0, red = 80).

Mentions: Using a series of bioinformatics tools (ChromoWiz, GenomeZipper) that integrated 4D contigs with the reference genomes of rice (Oryza sativa – Os), sorghum (Sorghum bicolor – Sb), and B. distachyon (Bd), 1973 genes from chromosome 4D were ordered as syntenic blocks. Blocks of conserved synteny were observed on Bd chromosomes 1 and 4, Os chromosomes 3, 9 and 11 and Sb chromosomes 1, 2 and 5 for the 4DS chromosomal arm (Fig. 2), and on Bd chromosome 1, Os chromosome 3 and Sb chromosome 1 for the 4DL chromosome arm (Fig. 3).


New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing.

Helguera M, Rivarola M, Clavijo B, Martis MM, Vanzetti LS, González S, Garbus I, Leroy P, Šimková H, Valárik M, Caccamo M, Doležel J, Mayer KF, Feuillet C, Tranquilli G, Paniego N, Echenique V - Plant Sci. (2014)

GenomeZipper analysis of wheat chromosome 4DS. Wheat 4DS contigs mapped onto the genomes of Brachypodium distachyon (A) Oryza sativa (B) and Sorghum bicolor (C) using the GenomeZipper approach. The heat map depicts read density across each of the chromosomes, with a blue-red color scale (blue = 0, red = 80).
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4352925&req=5

fig0065: GenomeZipper analysis of wheat chromosome 4DS. Wheat 4DS contigs mapped onto the genomes of Brachypodium distachyon (A) Oryza sativa (B) and Sorghum bicolor (C) using the GenomeZipper approach. The heat map depicts read density across each of the chromosomes, with a blue-red color scale (blue = 0, red = 80).
Mentions: Using a series of bioinformatics tools (ChromoWiz, GenomeZipper) that integrated 4D contigs with the reference genomes of rice (Oryza sativa – Os), sorghum (Sorghum bicolor – Sb), and B. distachyon (Bd), 1973 genes from chromosome 4D were ordered as syntenic blocks. Blocks of conserved synteny were observed on Bd chromosomes 1 and 4, Os chromosomes 3, 9 and 11 and Sb chromosomes 1, 2 and 5 for the 4DS chromosomal arm (Fig. 2), and on Bd chromosome 1, Os chromosome 3 and Sb chromosome 1 for the 4DL chromosome arm (Fig. 3).

Bottom Line: The virtual order showed a higher collinearity with homeologous 4B compared to 4A.Additionally, a virtual map was constructed and ∼5700 genes (∼2200 on 4DS and ∼3500 on 4DL) predicted.The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information.

View Article: PubMed Central - PubMed

Affiliation: Estación Experimental Agropecuaria Marcos Juárez, Instituto Nacional de Tecnología Agropecuaria (INTA), Marcos Juárez, Córdoba, Argentina. Electronic address: helguera.marcelo@inta.gob.ar.

Show MeSH
Related in: MedlinePlus