![]() ![]() Rapid technical advancements in single-molecule sequencing and chromosome conformation capture technologies have enabled the assembly of high-quality genome assemblies for plants ( Zhang et al. There are also 3136 contigs in S元.0 assembly that were not placed in chromosomal locations based on the available evidence at the time. However, a large number of inter and intra-scaffold gaps (81.71Mb) remain that can limit the resolution of genetic and genomic analysis besides confounding genome annotation. Furthermore, the tomato S元.0 reference genome has accurate scaffold order and orientation that has been manually validated using FISH data ( Shearer et al. However, later, other chromosomes were also covered and these BACs were integrated into the assembly, which resulted in a more complete assembly S元.0. The project initially focused on chromosomes 1 and 10, which had been assigned to the US partners in the BAC by BAC approach. Altogether these resulted in the assembly SL2.40 as well as the ITAG2.30 annotation that was published in 2012 ( The Tomato Genome Consortium 2012).Īfter the publication, the US partners of the genome project continued targeted full BAC sequencing for filling intra-scaffold gaps. ![]() 2007), resulting in re-ordering and re-orientation of a limited number of scaffolds, providing a major improvement in scaffold order. In addition, FISH data was generated to size the inter-scaffold gaps ( Chang et al. Illumina short reads ( Voelkerding, Dames, and Durtschi 2009) were used to correct the homopolymer errors in 454 sequences. With the remarkable progress in sequencing technology around that time, a whole genome shotgun approach became feasible around 2010, using the 454 sequencing technology ( Margulies et al. Many resources were established during that phase, including BAC libraries, BAC-end sequences, and fosmid libraries. At the outset, it followed a BAC-by-BAC sequencing approach, mirroring the strategy that was used for Arabidopsis. In 2003, three years after the completion of the first plant genome ( Initiative and The Arabidopsis Genome Initiative 2000), the tomato genome sequencing project was launched as an international collaboration. 1992), as well as an improved map with higher marker densities in 2000 called the F2-2000 map, based on conserved ortholog set (COS) markers ( Fulton et al. published the first genetic map in 1992 ( Tanksley et al. The previous tomato genome sequence was published by an international consortium in 2012 ( The Tomato Genome Consortium 2012), culminating years of effort to characterize the genome. 1992 Klee and Giovannoni 2011), plant defense ( Rosli and Martin 2015), and secondary metabolism ( Schilmiller et al. Tomato ( Solanum lycopersicum) is one of the most valuable vegetable crops as well as an important model for processes such as fruit ripening ( Tanksley et al. The genome and annotation can be accessed using SGN through BLAST database, Pathway database (SolCyc), Apollo, JBrowse genome browser and FTP available at. ![]() Most of the updated genes have extensions in the 5’ and 3’ UTRs resulting in doubling of annotated UTRs per gene. The corresponding ITAG4.0 annotation has 4,794 novel genes along with 29,281 genes preserved from ITAG2.4. We also describe updates to the reference genome and annotation since the last publication. ![]() We have found more repeats compared to the previous versions and one of the largest repeat classes identified are the LTR retrotransposons. This assembly is highly contiguous with fewer gaps compared to previous genome builds and almost all scaffolds have been anchored and oriented to the 12 tomato chromosomes. The assembly was validated using Bionano optical maps and 10X linked-read sequences. We present here the latest tomato reference genome (SL4.0) assembled de novo from PacBio long reads and scaffolded using Hi-C contact maps. The original Heinz 1706 reference genome was produced by a large team of scientists from across the globe from a variety of input sources that included 454 sequences in addition to full-length BACs, BAC and fosmid ends sequenced with Sanger technology. ![]()
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