Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly
Argyris, Jason (Centre de Recerca en Agrigenòmica)
Ruiz-Herrera Moreno, Aurora (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia)
Madriz-Masis, Pablo (Centre de Recerca en Agrigenòmica)
Sanseverino, Walter (Centre de Recerca en Agrigenòmica)
Morata, Jordi (Centre de Recerca en Agrigenòmica)
Pujol Abajo, Marta (Centre de Recerca en Agrigenòmica)
Ramos-Onsins, Sebastian (Centre de Recerca en Agrigenòmica)
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica)
Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí"

Data: 2015
Resum: 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.
Ajuts: Ministerio de Ciencia e Innovación CSD2007-00036
Drets: Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original. Creative Commons
Llengua: Anglès
Document: Article ; recerca ; Versió publicada
Matèria: Melon ; SNP ; Genome ; Scaffold ; Pseudomolecules ; FISH ; Karyotype
Publicat a: BMC genomics, Vol. 16 (Jan. 2015) , art. 4, ISSN 1471-2164

PMID: 25612459

14 p, 1.7 MB

El registre apareix a les col·leccions:
Documents de recerca > Documents dels grups de recerca de la UAB > Centres i grups de recerca (producció científica) > Ciències de la salut i biociències > Institut de Biotecnologia i de Biomedicina (IBB)
Documents de recerca > Documents dels grups de recerca de la UAB > Centres i grups de recerca (producció científica) > Ciències > CRAG (Centre de Recerca en Agrigenòmica)
Articles > Articles de recerca
Articles > Articles publicats

 Registre creat el 2017-07-18, darrera modificació el 2024-06-01

   Favorit i Compartir