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... 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> * ITAG4.0_cDNA.fasta * ITAG4.0_proteins.fasta <strong>Annotations files</strong> * ITAG4.0_gene_models.gff * S_lycopersicum_ITAG4.0_mapping_Mercator_v.3.6.tsv: the MapMan mapping file generated with Mercator 3.6 using the ITAG4.0_proteins.fasta file. link to Mercator results <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<strong>基因组序列</strong> 本数据集包含适用于以下物种的各类基因组参考序列（采用FASTA格式）： <em>Solanum lycopersicum</em>（栽培番茄，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 <em>Solanum pennellii</em>（类番茄茄，仅1个版本，源自Bolger等人2014年的研究）：Spenn.fasta.tar.gz <em>Solanum habrochaites</em>（茸毛番茄）LA1777（2018年Technology Hotel项目）：LA1777.final.fasta <em>Solanum habrochaites</em>（茸毛番茄）PI127826（2018年Technology Hotel项目）：PI127826.final.fasta <em>Solanum habrochaites</em>（茸毛番茄）LYC4（源自Aflitos等人2014年论文的第3版组装序列）：S_habrochaites_LYC4... 其中，茸毛番茄LA1777与PI127826的两套基因组组装结果通过10X Linked-Reads（10X连接读长技术）与BioNano光学图谱（BioNano Optical Mapping）联合测序获得，该测序项目由DTL Technology Hotel 2018资助计划支持。 <strong>转录组与蛋白质组数据</strong> * ITAG4.0_cDNA.fasta * ITAG4.0_proteins.fasta <strong>注释文件</strong> * ITAG4.0_gene_models.gff * S_lycopersicum_ITAG4.0_mapping_Mercator_v.3.6.tsv：该文件为基于ITAG4.0_proteins.fasta文件，通过Mercator 3.6软件生成的MapMan映射文件，附带Mercator结果链接。 <strong>参考文献：</strong> 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. 《自然》（*Nature*），第485卷，第635–641页。 2. Bolger等人. 2014. 耐胁迫野生番茄物种<em>Solanum pennellii</em>的基因组. 原文链接：http://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邻近连接与光学图谱技术优化的番茄参考基因组从头组装与注释. 原文链接：https://www.biorxiv.org/content/10.1101/767764v1 4. Aflitos等人. 2014. 基于全基因组测序解析番茄（<em>Solanum</em>属<em>Lycopersicon</em>组）分支的遗传变异. 原文链接：https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.12616