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     Tomato (Solanum lycopersicum L.) is one of the most important vegetable/fruit crops in terms of production worldwide, exhibiting significant genetic diversity shaped by domestication and breeding. However, comprehensive analysis of the gene-based super-pangenome has not been fully explored towards a catalog of all genes across sequenced tomatoes genomes. Currently, tomatoPangenome contained 61 tomato genomic sequences, encompassing 13 distant wild relatives, 11 ancestral wild species (SP), 12 early domesticates (SLC), four early cultivars (vintage), 17 modern domesticates, and four modern cultivars (fresh market), with containing 2,092,298 protein-coding genes. The resulting super-pangenome contained 59,066 orthologous groups where 12,843 (21.7%) groups contained genes from all tomato genomes were recognized as the core pan-gene set. Moreover, 3,735 (6.3%), 28,790 (48.7%), and 13,698 (23.2%) groups are classified as softcore (present in >99% of the 61 genomes), dispensable (present in 1-99% of the genomes), and private (present in <1% of the genomes) pan-gene sets, respectively. In the current tomato gene-based super-pangenome, we constructed an LRR-RLKome of 13,068 LRR-RLK pan-genes, representing LRR-RLK genes across the tomato clade. The LRR-RLK genes account for an average of 0.6256% (214.23) of the total genes within each of 61 tomato genomes, but with some variation between different genomes. All the protein sequences in tomatoPangenome were comprehensively annotated including InterPro, Gene Ontology, KEGG, MetaCyc and Reactome, as well as associated homologs in GenBank non-redundant (nr) and UniProt-SwissProt/TrEMBL protein databases.

     The tomatoPangenome provides user-friendly interfaces and search functions, as well as customized third-party tools, such as BLAST and JBrowse, to help users extract interesting information of genomic data in tomato individuals. All data in tomatoPangenome are freely available and will be updated regularly with newly generated shrimp reference genomes.
 

1. The genomic data of nine wild species and two cultivated accessions were re-annotated with public databases and software, and all annotated information of these genomes were added into tomatoPangenome! [May. 2024]

2. The genomic data of 32 new reference-level tomato genomes were included into tomato Pangenome! [Oct. 2022]

3. The genome sequences of two wild tomato relatives, S. habrochaites and S. galapagense were included into tomatoPangenome! [Apr. 2022]

4. tomatoPangenome containing 6 tomato genomes is online now and welcome to access!  [Jan. 2021]

5. tomatoPangenome is conceived to develop and 4 tomato genomic data were collected from public databases!  [Jun. 2020]

01. [Apr. 2023] Ning Li et al., reported chromosome-scale tomato genomes from nine wild species and two cultivated accessions, representative of Solanum section Lycopersicon, the tomato clade.  [PubMed]

02. [Jun. 2022] Yao Zhou et al., reported a graph pangenome of tomato constructed by precisely cataloguing more than 19 million variants from 838 genomes, including 32 new reference-level genome assemblies and captured missing heritability, which empowered tomato breeding.  [Jun. 2022] [PubMed]

03. [Jun. 2022] Lei Gao et al., reported chromosome-scale genome assemblies of wild tomato relatives, S. habrochaites and S. galapagense and revealed structural variants associated with stress tolerance and terpene biosynthesis. [PubMed]

04. [Jan. 2021] Hitomi Takei et al., reported de novo genome assembly of two tomato ancestors, S. pimpinellifolium and S. lycopersicum var. cerasiforme, by long-read sequencing. [PubMed]

05. [Jul. 2020] Michael Alonge et al., used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines and constructed panSV genome, along with 14 new reference assemblies, revealing large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. [PubMed]

06. [Jun. 2019] Lei Gao et al., constructed a tomato pangenome with 'map to pan' strategy and uncovers new genes without in tomato reference genome and a rare allele regulating fruit flavor, TomLoxC. [PubMed]

07. [Oct. 2017] Maximilian H.-W. Schmidt et al., reported de novo assembly of a new S. pennellii (LA716a) accession using nanopore sequencing. [PubMed]

08. [Oct. 2014] Tao Lin et al., reported a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions, and  provided insights into the history of tomato breeding. [PubMed]

09. [Jul. 2014] Anthony Bolger et al., reported the genome of the stress-tolerant wild tomato species Solanum pennellii. [PubMed]

10. [May. 2012] The Tomato Genome Consortium releaseed a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, S. pimpinellifolium, and compared them to each other and to the potato genome (S. tuberosum). [PubMed]