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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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4DL GenomeZipper vs. Ae. tauschii genetic map and 4D deletion map. Comparison of 4DL scaffolds anchored and ordered according to the genetic map from Jia et al. [16] and the syntenic ordering of contigs obtained by the GenomeZipper approach (this work). Ring 1, annotated repetitive regions from scaffolds. Ring 2, annotated genes from scaffolds. Ring 3, 4DL scaffolds (orange) and GenomeZipper contigs (blue) ordered in scale where 0 represents the centromeres. Ring 4, (blue) ESTs mapped on C-4DL9-0.31 deletion bin. Ring 5, (green) ESTs mapped on 4DL9-0.31–0.56. Ring 6, (red) ESTs in 4DL13-0.56–0.71. Ring 7 (blue) ESTs in 4DL12-0.71–1.00. Ring 8, (green lines) matches between contigs ordered by GenomeZipper and scaffolds anchored to the Ae. tauschii genetic map. Deletion bin-mapping data of ESTs was obtained from Miftahudin et al. [26].
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fig0080: 4DL GenomeZipper vs. Ae. tauschii genetic map and 4D deletion map. Comparison of 4DL scaffolds anchored and ordered according to the genetic map from Jia et al. [16] and the syntenic ordering of contigs obtained by the GenomeZipper approach (this work). Ring 1, annotated repetitive regions from scaffolds. Ring 2, annotated genes from scaffolds. Ring 3, 4DL scaffolds (orange) and GenomeZipper contigs (blue) ordered in scale where 0 represents the centromeres. Ring 4, (blue) ESTs mapped on C-4DL9-0.31 deletion bin. Ring 5, (green) ESTs mapped on 4DL9-0.31–0.56. Ring 6, (red) ESTs in 4DL13-0.56–0.71. Ring 7 (blue) ESTs in 4DL12-0.71–1.00. Ring 8, (green lines) matches between contigs ordered by GenomeZipper and scaffolds anchored to the Ae. tauschii genetic map. Deletion bin-mapping data of ESTs was obtained from Miftahudin et al. [26].

Mentions: A similar analysis was performed with the 4DL GenomeZipper map. Well-preserved collinearity was again observed in the pericentromeric and proximal telomeric regions with a few inconsistencies in the distal telomeric region (Fig. 5 ring 8). Also as in 4DS but to a lesser degree, wheat scaffolds ordered according to the Ae. tauschii map and anchored in the centromeric region showed a low number of matches with contigs carrying syntenic genes from the 4DL GenomeZipper map.


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)

4DL GenomeZipper vs. Ae. tauschii genetic map and 4D deletion map. Comparison of 4DL scaffolds anchored and ordered according to the genetic map from Jia et al. [16] and the syntenic ordering of contigs obtained by the GenomeZipper approach (this work). Ring 1, annotated repetitive regions from scaffolds. Ring 2, annotated genes from scaffolds. Ring 3, 4DL scaffolds (orange) and GenomeZipper contigs (blue) ordered in scale where 0 represents the centromeres. Ring 4, (blue) ESTs mapped on C-4DL9-0.31 deletion bin. Ring 5, (green) ESTs mapped on 4DL9-0.31–0.56. Ring 6, (red) ESTs in 4DL13-0.56–0.71. Ring 7 (blue) ESTs in 4DL12-0.71–1.00. Ring 8, (green lines) matches between contigs ordered by GenomeZipper and scaffolds anchored to the Ae. tauschii genetic map. Deletion bin-mapping data of ESTs was obtained from Miftahudin et al. [26].
© Copyright Policy - CC BY
Related In: Results  -  Collection

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

fig0080: 4DL GenomeZipper vs. Ae. tauschii genetic map and 4D deletion map. Comparison of 4DL scaffolds anchored and ordered according to the genetic map from Jia et al. [16] and the syntenic ordering of contigs obtained by the GenomeZipper approach (this work). Ring 1, annotated repetitive regions from scaffolds. Ring 2, annotated genes from scaffolds. Ring 3, 4DL scaffolds (orange) and GenomeZipper contigs (blue) ordered in scale where 0 represents the centromeres. Ring 4, (blue) ESTs mapped on C-4DL9-0.31 deletion bin. Ring 5, (green) ESTs mapped on 4DL9-0.31–0.56. Ring 6, (red) ESTs in 4DL13-0.56–0.71. Ring 7 (blue) ESTs in 4DL12-0.71–1.00. Ring 8, (green lines) matches between contigs ordered by GenomeZipper and scaffolds anchored to the Ae. tauschii genetic map. Deletion bin-mapping data of ESTs was obtained from Miftahudin et al. [26].
Mentions: A similar analysis was performed with the 4DL GenomeZipper map. Well-preserved collinearity was again observed in the pericentromeric and proximal telomeric regions with a few inconsistencies in the distal telomeric region (Fig. 5 ring 8). Also as in 4DS but to a lesser degree, wheat scaffolds ordered according to the Ae. tauschii map and anchored in the centromeric region showed a low number of matches with contigs carrying syntenic genes from the 4DL GenomeZipper map.

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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