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: 2018 Hotel Project: PI127826.final.fasta 2021 Dovetails assembly: PI127826_hirise_assembly.fasta.gz <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><strong>Solanum lycopersicum</strong> (assembly</em> 4.0): Transcriptome: ITAG4.0_cDNA.fasta Proteome: ITAG4.0_proteins.fasta <em><strong>Solanum pennellii</strong> </em>(one version only from Bolger et al., 2014): Transcriptome: Spenn-v2-cds-annot.fa Proteome: Spenn-v2-aa-annot.fa <strong><em>Solanum lycopersicoides</em></strong> (version 1.0) Transcriptome: S_lycopersicoides_LA2951_v1.0_cds.fasta Proteome: S_lycopersicoides_LA2951_v1.0_proteins.fasta <strong><em>Solanum habrochaites </em>PI127826 </strong> <strong>Transcriptome: </strong>Solanum_habrochaites_PI12826_mRNAs.fasta (2018 Hotel Project assembly) <strong>Transcriptome (2021 Dovetails): </strong>Solanum_habrochaites_PI127826_CDS_Dovetails_2021.fasta <strong>Proteome (2021 Dovetails): </strong>Solanum_habrochaites_PI127826_protein_Dovetails_2021.fasta<strong> </strong> <strong>=== Genome annotations files ===</strong> <strong><em>Solanum lycopersicum </em>Heinz1706</strong> Gene File Format: ITAG4.0_gene_models.gff General Transfer Format (GTF): ITAG4.0_gene_models.gtf 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. <strong><em>Solanum lycopersicoides </em>LA2951</strong> Gene File Format: S_lycopersicoides_LA2951_v1.0_gene_models_all.gff3 <strong><em>Solanum habrochaites </em>PI127826</strong> (Based on the 2018 Hotel Project assembly): a GFF file was produced using RepeatMasker and funannotate and is named Solanum_habrochaites_PI127826.gff3. The companion script with the performed steps is available in this data record as well and is called S_habrochaites_PI127826_funannotate_steps.sh (Based on the 2021 Dovetails Genomic project): Solanum_habrochaites_PI127826_gene_models.gff <strong>Additional information:</strong> 2021 Dovetails Genomics complete <strong>assembly</strong> project report<strong>: </strong>dovetails_genomics_2021.tar.gz 2021 Dovetails Genomics complete <strong>annotation </strong>project report: dovetails_genomics_annotation_report_2021.tar.gz <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**=== 基因组序列 ===** 本部分提供以下物种的各类基因组参考序列（格式为FASTA）： 1. 栽培番茄（*Solanum lycopersicum*），包含组装版本3.0与4.0： S_lycopersicum_chromosomes.3.00.fa.tar.gz、S_lycopersicum_chromosomes.4.00.fa.tar.gz 2. 潘那利番茄（*Solanum pennellii*），仅包含1个版本（源自Bolger等人2014年的研究）： Spenn.fasta.tar.gz 3. 哈克尼西番茄（*Solanum habrochaites*）LA1777（源自2018年Technology Hotel项目）： LA1777.final.fasta 4. 哈克尼西番茄（*Solanum habrochaites*）PI127826： - 2018 Hotel项目组装版本：PI127826.final.fasta - 2021年Dovetails组装版本：PI127826_hirise_assembly.fasta.gz 5. 哈克尼西番茄（*Solanum habrochaites*）LYC4（源自Aflitos等人2014年论文，为第3版组装序列）： S_habrochaites_LYC4... 6. 隐秘番茄（*Solanum arcanum*）LA2172（源自Aflitos等人2014年论文，为第3版组装序列）： LA2172.fasta.tar.gz 7. 智利番茄（*Solanum chilense*）LA3111（源自Stam等人2019年论文，NCBI组装版本ASM601370v1）： LA3111.fasta.tar.gz 8. 番茄状番茄（*Solanum lycopersicoides*）LA2951（源自博伊斯汤普森研究所与亚琛工业大学的研究工作，链接见原文）： S_lycopersicoides_LA2951_v1.0_chromosomes.fasta.tar.gz 哈克尼西番茄LA1777与PI127826的两套基因组组装序列均通过10X Linked-Reads与BioNano光学图谱联合测序技术获得，该测序项目由DTL Technology Hotel 2018资助计划支持。 **=== 转录组与蛋白质组 ===** **栽培番茄（*Solanum lycopersicum*）（组装版本4.0）**： - 转录组文件：ITAG4.0_cDNA.fasta - 蛋白质组文件：ITAG4.0_proteins.fasta **潘那利番茄（*Solanum pennellii*）**（仅包含1个版本，源自Bolger等人2014年研究）： - 转录组文件：Spenn-v2-cds-annot.fa - 蛋白质组文件：Spenn-v2-aa-annot.fa **番茄状番茄（*Solanum lycopersicoides*）（版本1.0）**： - 转录组文件：S_lycopersicoides_LA2951_v1.0_cds.fasta - 蛋白质组文件：S_lycopersicoides_LA2951_v1.0_proteins.fasta **哈克尼西番茄（*Solanum habrochaites*）PI127826**： - 转录组文件（2018 Hotel项目组装版本）：Solanum_habrochaites_PI12826_mRNAs.fasta - 2021年Dovetails组装版本转录组：Solanum_habrochaites_PI127826_CDS_Dovetails_2021.fasta - 2021年Dovetails组装版本蛋白质组：Solanum_habrochaites_PI127826_protein_Dovetails_2021.fasta **=== 基因组注释文件 ===** **栽培番茄（*Solanum lycopersicum*）Heinz1706**： - 基因模型文件（GFF格式）：ITAG4.0_gene_models.gff - 通用转移格式（GTF）文件：ITAG4.0_gene_models.gtf - MapMan注释文件：S_lycopersicum_ITAG4.0_mapping_Mercator_v.3.6.tsv，该文件通过Mercator 3.6工具，以ITAG4.0_proteins.fasta为参考序列生成。 **番茄状番茄（*Solanum lycopersicoides*）LA2951**： - 基因模型文件（GFF3格式）：S_lycopersicoides_LA2951_v1.0_gene_models_all.gff3 **哈克尼西番茄（*Solanum habrochaites*）PI127826**： - 基于2018 Hotel项目组装版本：通过RepeatMasker与funannotate工具生成GFF格式注释文件，文件名为Solanum_habrochaites_PI127826.gff3；本数据集同时提供该分析流程配套脚本S_habrochaites_PI127826_funannotate_steps.sh - 基于2021年Dovetails基因组项目组装版本：注释文件为Solanum_habrochaites_PI127826_gene_models.gff **附加信息：** 1. 2021年Dovetails基因组学完整组装项目报告：dovetails_genomics_2021.tar.gz 2. 2021年Dovetails基因组学完整注释项目报告：dovetails_genomics_annotation_report_2021.tar.gz **参考文献：** 1. 番茄基因组测序联盟. 2012. 番茄基因组序列为肉质果实演化研究提供新视角. *Nature*（《自然》），第485卷，第635–641页 2. Bolger等人. 2014. 耐胁迫野生番茄物种潘那利番茄（*Solanum pennellii*）的基因组. https://www.nature.com/ng/journal/v46/n9/full/ng.3046.html 3. Hosmani等人. 2019. 基于单分子测序、Hi-C邻接连接与光学图谱技术的番茄参考基因组优化从头组装与注释. https://www.biorxiv.org/content/10.1101/767764v1 4. Aflitos等人. 2014. 通过全基因组测序探究番茄（*Solanum*属*Lycopersicon*组）分支的遗传变异. https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.12616 5. Stam等人. 2019. 野生智利番茄（*Solanum chilense*）的从头参考基因组与转录组组装揭示番茄物种间NLR基因的生死演化. *G3: Genes, Genomes, Genetics*，2019年12月1日，第9卷第12期，第3933–3941页；https://doi.org/10.1534/g3.119.400529