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, 16 (1), 4

Use of Targeted SNP Selection for an Improved Anchoring of the Melon (Cucumis Melo L.) Scaffold Genome Assembly

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Use of Targeted SNP Selection for an Improved Anchoring of the Melon (Cucumis Melo L.) Scaffold Genome Assembly

Jason M Argyris et al. BMC Genomics.

Abstract

Background: The genome of the melon (Cucumis melo L.) double-haploid line DHL92 was recently sequenced, with 87.5 and 80.8% of the scaffold assembly anchored and oriented to the 12 linkage groups, respectively. However, insufficient marker coverage and a lack of recombination left several large, gene rich scaffolds unanchored, and some anchored scaffolds unoriented. To improve the anchoring and orientation of the melon genome assembly, we used resequencing data between the parental lines of DHL92 to develop a new set of SNP markers from unanchored scaffolds.

Results: A high-resolution genetic map composed of 580 SNPs was used to anchor 354.8 Mb of sequence, contained in 141 scaffolds (average size 2.5 Mb) and corresponding to 98.2% of the scaffold assembly, to the 12 melon chromosomes. Over 325.4 Mb (90%) of the assembly was oriented. The genetic map revealed regions of segregation distortion favoring SC alleles as well as recombination suppression regions coinciding with putative centromere, 45S, and 5S rDNA sites. New chromosome-scale pseudomolecules were created by incorporating to the previous v3.5 version an additional 38.3 Mb of anchored sequence representing 1,837 predicted genes contained in 55 scaffolds. Using fluorescent in situ hybridization (FISH) with BACs that produced chromosome-specific signals, melon chromosomes that correspond to the twelve linkage groups were identified, and a standardized karyotype of melon inbred line T111 was developed.

Conclusions: By utilizing resequencing data and targeted SNP selection combined with a large F2 mapping population, we significantly improved the quantity of anchored and oriented melon scaffold genome assembly. Using genome information combined with FISH mapping provided the first cytogenetic map of an inodorus melon type. With these results it was possible to make inferences on melon chromosome structure by relating zones of recombination suppression to centromeres and 45S and 5S heterochromatic regions. This study represents the first steps towards the integration of the high-resolution genetic and cytogenetic maps with the genomic sequence in melon that will provide more information on genome organization and allow for the improvement of the melon genome draft sequence.

Figures

Figure 1
Figure 1
Anchoring of the melon scaffold genome assembly to the PS x SC F2 genetic map. Red bars represent the 12 melon linkage groups; SNPs are located according to genetic distance (cM). Melon genome scaffolds were positioned in each linkage group with corresponding genetic markers. Blue, scaffolds in positive orientation; green, scaffolds with negative orientation (reverse and complemented); yellow, scaffolds that were anchored but not oriented. Red dots represent locations of centromere-specific repeats inferred by in silico analysis.* Not all SNP names are represented in the genetic map.
Figure 2
Figure 2
The ratio between genetic and physical distances and recombination frequency of the 12 melon pseudomolecules. For each SNP marker (filled red circle) in the PS x SC F2 genetic map, the genetic distance in centimorgans (cM) is plotted according to its physical position in megabases (Mb) on the pseudomolecule (PM). Recombination (solid line) rate was plotted in 1 Mb sliding intervals (see methods).
Figure 3
Figure 3
Standarized karyotype of the 12 PS melon chromosomes. Karyotype of PS (A) and 2 color FISH with BAC probes and ideograms for location of centromere specific, 45S, and 5S repeats identified by BLAST for CME2 (B), CME4 (C) and CME6 (D).

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