Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly
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Author
Ruiz-Herrera, Aurora
Madriz-Masis, Pablo
Sanseverino, Walter
Morata, Jordi
Ramos-Onsins, Sebastián E.
Garcia-Mas, Jordi
Publication date
2015-01-22ISSN
1471-2164
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.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
633 - Field crops and their production
Pages
14
Publisher
BMC
Is part of
BMC Genomics
Citation
Argyris, Jason M, Aurora Ruiz-Herrera, Pablo Madriz-Masis, Walter Sanseverino, Jordi Morata, Marta Pujol, Sebastián E Ramos-Onsins, and Jordi Garcia-Mas. 2015. "Use Of Targeted SNP Selection For An Improved Anchoring Of The Melon (Cucumis Melo L.) Scaffold Genome Assembly". BMC Genomics 16 (1). doi:10.1186/s12864-014-1196-3.
Grant agreement number
MEC/Programa nacional de medios de transporte/CSD2007-00036/ES/Centro de Genómica Básica y de orientación Agroalimentaria/
Program
Genòmica i Biotecnologia
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2503]
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Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/