| Index of Genome/Melon_genome_v3.5_Garcia-Mas_et_al_2012/ |
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CM_protein_v3.5.fasta
Predicted protein of melon genome in fasta format. Last version was built on 04-05-2011. Reference: Garcia-Mas et al. The genome of melon (Cucumis melo L.). |
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CM_anchoring_scaffold_list.txt
A text file with the anchoring and the orientation of melon scaffolds in the genetic map. Reference: Garcia-Mas et al. The genome of melon (Cucumis melo L.). |
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melon_genome_pseudomolecules_V3.5.fasta
Melon genome assembly v3.5 with scaffold and conting merged in pseudomolecules according to our SNP genetic map with a Ns spacer of 1Kb. Last version was built on 21-06-2012. Reference: Garcia-Mas et al. The genome of melon (Cucumis melo L.). |
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non_coding_RNA_annotation_v3.5.gff3
Annotation of predicted non coding RNAs. Last version was built on 04-05-2011. Reference: Garcia-Mas et al. The genome of melon (Cucumis melo L.). |
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miRNA_predicted_gene_list.txt
Name list of the melon predicted miRNA submitted to the miRBase |
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CM_v3.5_assembly_scaffold_and_unscaffold_contigs.fasta
Melon genome assembly v3.5. Last version was built on 04-05-2011. Reference: Garcia-Mas et al. The genome of melon (Cucumis melo L.). |
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ENA_scaffolds_Acc_No.txt
Scaffolding information and submitted scaffold to the European Nucleotide Archive. |
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CM_annotation_v3.5.gff3
Complete annotation of the melon genome. Last version was built on 04-05-2011. Reference: Garcia-Mas et al. The genome of melon (Cucumis melo L.). |
Melogen unigenes.melo c.fasta
This file contains non-redundant sequences or unigenes and unclustered sequences (also called singletons). This sequences were generated by clustering 29,604 good quality expressed sequence tags (ESTs) with an average length of 674 bp obtained after processing a total of 33, 292 raw sequences.
Raw sequences were produced from eight normalized cDNA libraries were prepared from 4 genotypes. The name of each library and the number of raw sequences/good quality EST is indicated:
-Cucumis melo subsp melo var. inodorus line T-111 (Piel de sapo breeding line) (Semillas Fitó).Mesocarp tissues from fruits collected 15 (15d, 3,936/3,582) and 46 (46d, 3,840/3,493) days after pollination.
-Cucumis melo subsp melo var. inodorus cultivar "Piñonet torpedo" (Semillas Batlle). Root samples collected 14 days after transplanting to sterile soil (PS, 3,840, 3,377) or soil inoculated with Monosporascus cannonballus (PSI, 3,840, 3,555) (genotype fully susceptible to the fungus infection).
-Cucumis melo subsp melo var. cantalupensis accession C-35 (EELM-CSIC). Cotyledons collected 4 days after inoculation with Cucumber Mosaic Virus (CI, 6,605/5,664) and healthy leaves (HS, 3,648/3012).
-Cucumis melo subsp agrestis var.conomon accession Pat81 (COMAV-UPV). Root samples collected 14 days after transplanting to sterile soil (A, 3,936/3,666) or soil inoculated with Monosporascus cannonballus (AI, 3,647/3,255) (genotype partially resistant to the fungus infection).
Reference: MELOGEN: an EST database for melon functional.
Melon transcriptome.comav.v1.fasta
This transcriptome is fully described in José Miguel Blanca, Joaquín Cañizares, Pello Ziarsolo, Cristina Esteras, Gisela Mir, Fernando Nuez, Jordi Garcia-Mas, and María Belén Picó* Melon Transcriptome Characterization: Simple Sequence Repeats and Single Nucleotide Polymorphisms discovery for High Throughput Genotyping across the SpeciesThe Plant Genome 4:118–131. Published 21 June 2011. doi: 10.3835/plantgenome2011.01.0003
These sequences were generated by clustering 589,054 new C. melo high-quality ESTs generated after processing 763,352 raw eads from two 454 sequencing runs, one Genome Sequencer (GS) FLX and one GS FLX Titanium, using four libraries.
These ESTs were combined for assembly with 125,908 ESTs previously produced using Sanger (available at http://www.icugi.org/ and fully described at Clepet et al. (2011) Analysis of expressed sequence tags generated from full-lenght enriched cDNA libraries of melon. BMC Genomics 12:252).
454 Sequences were produced from two nonnormalized and two normalized cDNA libraries prepared from 4 genotypes belonging to the two subspecies of C.melo. The reads/processed reads number and the average lenth of reads/processed reads is indecated:
- Cucumis melo subsp melo var. inodorus line T-111 (Piel de sapo breeding line) (Semillas Fitó). Leaf material (117,352/107,756;225/233).
- Cucumis melo subsp melo var. inodorus cultivar "Piñt torpedo" (Semillas Batlle). Leaf, root, male and female flowers at different stages, seedlings, and dark-grown and ethylene treated seedlings (249,902/206,650;397/403).
© Melonomics is a Spanish project aim at the sequencing and the study of the melon genome.