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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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4DS GenomeZipper vs. Ae. tauschii genetic map and 4D deletion map. Comparison of 4DS scaffolds anchored and ordered according to the Ae. tauschii genetic map from Jia et al. [16] and the syntenic ordering of contigs obtained by GenomeZipper (this work). Ring 1, annotated repetitive regions from scaffolds. Ring 2, annotated genesfrom scaffolds. Ring 3, 4DS scaffolds (orange) and Genome Zipper contigs (blue) ordered in scale, where 0 represents the telomeres. Ring 4, (blue) ESTs mapped on C-4DS1-0.53 deletion bin. Ring 5 (green) ESTs mapped on 4DS1-0.53–0.67. Ring 6, (red) ESTs on 4DS3-0.67–0.82. Ring 7, (blue) ESTs on 4DS2-0.82–1.00. Ring 8, (green lines) matches between contigs ordered by GenomeZipper and scaffolds anchored to the Ae. tauschii genetic map. EST mapping data from deletion bins was obtained from Miftahudin et al. [26].
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fig0075: 4DS GenomeZipper vs. Ae. tauschii genetic map and 4D deletion map. Comparison of 4DS scaffolds anchored and ordered according to the Ae. tauschii genetic map from Jia et al. [16] and the syntenic ordering of contigs obtained by GenomeZipper (this work). Ring 1, annotated repetitive regions from scaffolds. Ring 2, annotated genesfrom scaffolds. Ring 3, 4DS scaffolds (orange) and Genome Zipper contigs (blue) ordered in scale, where 0 represents the telomeres. Ring 4, (blue) ESTs mapped on C-4DS1-0.53 deletion bin. Ring 5 (green) ESTs mapped on 4DS1-0.53–0.67. Ring 6, (red) ESTs on 4DS3-0.67–0.82. Ring 7, (blue) ESTs on 4DS2-0.82–1.00. Ring 8, (green lines) matches between contigs ordered by GenomeZipper and scaffolds anchored to the Ae. tauschii genetic map. EST mapping data from deletion bins was obtained from Miftahudin et al. [26].

Mentions: For 4DS, well-preserved collinearity was observed in both telomeric and pericentromeric regions. However, some inconsistencies in the gene order were observed in distal parts of the pericentromeric region (Fig. 4, ring 8). It should be noted that most of the wheat scaffolds ordered according to the Ae. tauschii map and anchored in the centromeric region showed no matches with contigs carrying syntenic genes from the 4DS GenomeZipper map, suggesting a very limited number of syntenic genes within this chromosomal region (Fig. 4, ring 8).


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)

4DS GenomeZipper vs. Ae. tauschii genetic map and 4D deletion map. Comparison of 4DS scaffolds anchored and ordered according to the Ae. tauschii genetic map from Jia et al. [16] and the syntenic ordering of contigs obtained by GenomeZipper (this work). Ring 1, annotated repetitive regions from scaffolds. Ring 2, annotated genesfrom scaffolds. Ring 3, 4DS scaffolds (orange) and Genome Zipper contigs (blue) ordered in scale, where 0 represents the telomeres. Ring 4, (blue) ESTs mapped on C-4DS1-0.53 deletion bin. Ring 5 (green) ESTs mapped on 4DS1-0.53–0.67. Ring 6, (red) ESTs on 4DS3-0.67–0.82. Ring 7, (blue) ESTs on 4DS2-0.82–1.00. Ring 8, (green lines) matches between contigs ordered by GenomeZipper and scaffolds anchored to the Ae. tauschii genetic map. EST mapping data from deletion bins was obtained from Miftahudin et al. [26].
© Copyright Policy - CC BY
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4352925&req=5

fig0075: 4DS GenomeZipper vs. Ae. tauschii genetic map and 4D deletion map. Comparison of 4DS scaffolds anchored and ordered according to the Ae. tauschii genetic map from Jia et al. [16] and the syntenic ordering of contigs obtained by GenomeZipper (this work). Ring 1, annotated repetitive regions from scaffolds. Ring 2, annotated genesfrom scaffolds. Ring 3, 4DS scaffolds (orange) and Genome Zipper contigs (blue) ordered in scale, where 0 represents the telomeres. Ring 4, (blue) ESTs mapped on C-4DS1-0.53 deletion bin. Ring 5 (green) ESTs mapped on 4DS1-0.53–0.67. Ring 6, (red) ESTs on 4DS3-0.67–0.82. Ring 7, (blue) ESTs on 4DS2-0.82–1.00. Ring 8, (green lines) matches between contigs ordered by GenomeZipper and scaffolds anchored to the Ae. tauschii genetic map. EST mapping data from deletion bins was obtained from Miftahudin et al. [26].
Mentions: For 4DS, well-preserved collinearity was observed in both telomeric and pericentromeric regions. However, some inconsistencies in the gene order were observed in distal parts of the pericentromeric region (Fig. 4, ring 8). It should be noted that most of the wheat scaffolds ordered according to the Ae. tauschii map and anchored in the centromeric region showed no matches with contigs carrying syntenic genes from the 4DS GenomeZipper map, suggesting a very limited number of syntenic genes within this chromosomal region (Fig. 4, ring 8).

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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