solgenomics

solgenomics provides access to and analysis of the SL4.0 tomato reference genome and its ITAG4.0 annotation to support genomic, structural, and functional studies in Solanaceae.

Key Features:

• Reference genome (SL4.0): A de novo assembly of the tomato reference genome SL4.0 representing 12 chromosomes.
• Sequencing data: Assembly generated from PacBio long reads to increase contiguity and reduce gaps.
• Scaffolding: Scaffolds anchored and oriented to 12 chromosomes using Hi-C contact maps.
• Validation: Assembly validated with Bionano optical maps and 10X linked-read sequences.
• Repeat annotation: Increased detection of repetitive elements, notably LTR retrotransposons as a major repeat class.
• Gene annotation (ITAG4.0): ITAG4.0 includes 4,794 novel genes and 29,281 genes preserved from ITAG2.4 with extended 5' and 3' UTR annotations, effectively doubling annotated UTRs per gene.
• Computational resources: Associated resources include BLAST, SolCyc, Apollo, JBrowse, and FTP access for sequence search, pathway analysis, curation/editing, visualization, and data download.

Scientific Applications:

• Genome assembly and structural genomics: Use SL4.0 and Hi-C scaffolding information to study chromosomal structure and contiguity.
• Gene discovery and annotation: Leverage ITAG4.0 to analyze novel genes and preserved gene models from ITAG2.4.
• UTR and regulatory studies: Exploit extended 5' and 3' UTR annotations for investigations of gene regulation and transcript structure.
• Repeat and transposable element analysis: Characterize LTR retrotransposons and other repetitive elements revealed in SL4.0.
• Comparative and evolutionary genomics: Compare SL4.0 gene content and structure across Solanaceae using preserved and novel annotations.
• Pathway analysis: Integrate genome annotation with SolCyc for metabolic and pathway studies.
• Sequence search and alignment: Perform sequence alignment and similarity searches using the BLAST database.
• Genome curation and editing: Use Apollo for manual curation and editing of gene models.
• Genome visualization and data access: Visualize features in JBrowse and retrieve data via FTP for downstream analyses.

Methodology:

De novo assembly using PacBio long reads; scaffolding with Hi-C contact maps anchoring scaffolds to the 12 chromosomes; validation with Bionano optical maps and 10X linked-read sequences; annotation updated to ITAG4.0 with novel genes and extended 5' and 3' UTRs.