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

<strong>=== Genome sequences ===</strong> These are the different genome references (fasta formats) available for: <em>Solanum lycopersicum</em> (assemblies 3.0 and 4.0): S_lycopersicum_chromosomes.3.00.fa.tar.gz S_lycopersicum_chromosomes.4.00.fa.tar.gz <em>Solanum pennellii </em>(one version only from Bolger et al., 2014) : Spenn.fasta.tar.gz <em>Solanum habrochaites</em> LA1777 (technology hotel project 2018): LA1777.final.fasta <em>Solanum habrochaites</em> PI127826 (technology hotel project 2018): PI127826.final.fasta <em>Solanum</em> <em>habrochaites</em> LYC4 (from the paper of Aflitos et al. 2014. 3rd assembly version): S_habrochaites_LYC4... <em>Solanum arcanum</em> LA2172 (from the paper of Aflitos et al. 2014. 3rd assembly version): LA2172.fasta.tar.gz <em>Solanum chilense</em> LA3111 (from the paper of Stam et al. 2019, NCBI assembly ASM601370v1): LA3111.fasta.tar.gz <em>Solanum lycopersicoides</em> 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. <strong>=== Transcriptomes and proteomes ===</strong> <em>Solanum lycopersicum (assembly</em> 4.0): Transcriptome: ITAG4.0_cDNA.fasta Proteome: ITAG4.0_proteins.fasta <em>Solanum pennellii </em>(one version only from Bolger et al., 2014): Transcriptome: Spenn-v2-cds-annot.fa <em>Solanum lycopersicoides</em> (version 1.0) Transcriptome: S_lycopersicoides_LA2951_v1.0_cds.fasta Proteome: S_lycopersicoides_LA2951_v1.0_proteins.fasta <strong>=== Genome annotations files ===</strong> <em>Solanum lycopersicum</em> 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. <em>Solanum lycopersicoides:</em> Gene File Format: S_lycopersicoides_LA2951_v1.0_gene_models_all.gff3 <em>Solanum habrochaites</em> PI127826: a GFF file was produced using RepeatMasker and funannotate (see below). The file is named Solanum_habrochaites_PI127826. <pre><code class="language-bash">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 </code></pre> LA1777 <strong>Reference:</strong> 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 (<em>Solanum</em> section <em>Lycopersicon</em>) clade by whole‐genome sequencing. https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.12616 Stam et al. 2019. The <em>de Novo</em> Reference Genome and Transcriptome Assemblies of the Wild Tomato Species <em>Solanum chilense</em> 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