Genomic sequences and annotations for Solanum lycopersicum, Solanum pennellii and Solanum habrochaites

=== Genome sequences ===

These are the different genome references (fasta formats) available for:

• Solanum lycopersicum (assemblies 3.0 and 4.0):
  • S_lycopersicum_chromosomes.3.00.fa.tar.gz
  • S_lycopersicum_chromosomes.4.00.fa.tar.gz
• Solanum pennellii (one version only from Bolger et al., 2014) : Spenn.fasta.tar.gz
• Solanum habrochaites LA1777 (technology hotel project 2018): LA1777.final.fasta  
• Solanum habrochaites PI127826 (technology hotel project 2018): PI127826.final.fasta  
• Solanum habrochaites LYC4 (from the paper of Aflitos et al. 2014. 3rd assembly version): S_habrochaites_LYC4...
• Solanum arcanum LA2172 (from the paper of Aflitos et al. 2014. 3rd assembly version): LA2172.fasta.tar.gz
• Solanum chilense LA3111 (from the paper of Stam et al. 2019, NCBI assembly ASM601370v1): LA3111.fasta.tar.gz
• Solanum lycopersicoides LA2951 (from the work of The Boyce Thompson Institute and RWTH Aachen University: link): S_lycopersicoides_LA2951_v1.0_chromosomes.fasta.tar.gz

The two genome assemblies of S. habrochaites LA1777 and PI127826 were obtained through a combination of 10X Linked-Reads and BioNano Optical Mapping. This sequencing has been funded by the DTL Technology Hotel 2018 funding scheme.

=== Transcriptomes and proteomes ===

Solanum lycopersicum (assembly 4.0):

• Transcriptome: ITAG4.0_cDNA.fasta 
• Proteome: ITAG4.0_proteins.fasta

Solanum pennellii (one version only from Bolger et al., 2014):

• Transcriptome: Spenn-v2-cds-annot.fa

Solanum lycopersicoides (version 1.0)

• Transcriptome: S_lycopersicoides_LA2951_v1.0_cds.fasta
• Proteome: S_lycopersicoides_LA2951_v1.0_proteins.fasta

=== Genome annotations files ===

Solanum lycopersicum

• Gene File Format: ITAG4.0_gene_models.gff
• MapMan annotation: S_lycopersicum_ITAG4.0_mapping_Mercator_v.3.6.tsv was obtained with Mercator 3.6 using the ITAG4.0_proteins.fasta file.

Solanum lycopersicoides:

• Gene File Format: S_lycopersicoides_LA2951_v1.0_gene_models_all.gff3

Solanum habrochaites

• PI127826: a GFF file was produced using RepeatMasker and funannotate (see below). The file is named Solanum_habrochaites_PI127826.

  RepeatMasker -qq -e rmblast -small -xsmall -pa 10 -lib mipsREdat_9.3p_Eudicot_TEs.fasta -dir repeat_masking_run/ PI127826.fasta
  
  funannotate sort -i PI127826.fasta -b scaffold -o PI127826.sorted.fasta 
  
  funannotate mask -i PI127826.sorted.fasta \
                   -o PI127826.sorted.masked.fasta \
                   -m tantan \
                   -s tomato \
                   --cpus 12
  
  funannotate train -i PI127826.sorted.masked.fasta -o 01_train_step/ \
                    --left fastq/PI127826_01_R1.fastq.gz fastq/PI127826_06_R1.fastq.gz \
                    --right fastq/PI127826_01_R2.fastq.gz fastq/PI127826_06_R2.fastq.gz \
                    --single fastq/PI127826_02_R1.fastq.gz fastq/PI127826_03_R1.fastq.gz fastq/PI127826_04_R1.fastq.gz fastq/PI127826_05_R1.fastq.gz \
                   --species "Solanum lycopersicum" \
                   --cpus 16
                   --max_intronlen 3000
  
  funannotate predict -i 00_mask_step/PI127826.sorted.masked.fasta \
                      --out 01_train_step/ \
                      -s "Solanum lycopersicum" \
                      --cpus 16 \
                      --organism other \
                      --min_intronlen 10 \
                      --max_intronlen 10000 \
                      --repeats2evm 
  
  funannotate update -i 01_train_step/ \
                       --fasta 00_mask_step/PI127826.sorted.masked.fasta \
                        --cpus 16 \
                        --species "Solanum lycopersicum" \
                        --max_intronlen 10000 
  
  # [09:07 AM]: Previous annotation consists of: 75,886 protein coding gene models and 1,617 non-coding gene models.
  
  
  # After update:
  # 45,235 contigs containing 78,629 protein coding genes and 1,583 tRNA genes
  # ~ 45000 contigs = super-scaffolds + contigs
  
  
  funannotate fix -i 01_train_step/update_results/Solanum_lycopersicum.gbk -t 01_train_step/update_results/Solanum_lycopersicum.tbl
  
  
  # used Docker image https://github.com/blaxterlab/interproscan-docker
  # singularity pull docker://blaxterlab/interproscan-docker
  # singularity run interproscan.simg (create and start a container + enters inside)
  # then typed:
  
  
  # run eggnog to annotate proteins
  ./emapper.py --cpu 20 \
               -i ../01_train_step/update_results/Solanum_lycopersicum.proteins.fa \
               -m diamond \
               -o Solanum_habrochaites_PI127826_eggnog  
  
  # add functional preduction from eggnog
  funannotate annotate -i 01_train_step/ \
  --gff Solanum_habrochaites_PI127826.gff3 \
  --out 03_annotate \
  --species "Solanum habrochaites" \
  --eggnog eggnog-mapper/Solanum_habrochaites_PI127826_eggnog.emapper.annotations \
  --busco_db embryophyta \
  --cpus 10
  
  
  # Annotation consists of: 77,297 gene models
  
  

   

• LA1777

Reference:

Tomato Genome Sequencing Consortium. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature volume 485, pages 635–641.

Bolger et al. 2014. The genome of the stress-tolerant wild tomato species Solanum pennellii http://www.nature.com/ng/journal/v46/n9/full/ng.3046.html 

Hosmani et al. 2019. An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps. https://www.biorxiv.org/content/10.1101/767764v1

Aflitos et al. 2014. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole‐genome sequencing. https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.12616

Stam et al. 2019. The de Novo Reference Genome and Transcriptome Assemblies of the Wild Tomato Species Solanum chilense Highlights Birth and Death of NLR Genes Between Tomato Species. G3: Genes, Genomes, Genetics December 1, 2019 vol. 9 no. 12 3933-3941; https://doi.org/10.1534/g3.119.400529