An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps
By P. Hosmani, Mirella Flores-Gonzalez, H. van de Geest, F. Maumus, Linda V. Bakker, E. Schijlen, Jan C. van Haarst, J. Cordewener, Gabino Sanchez-Perez, S. Peters and 4 more. bioRxiv, 2019
250 citations recorded by the source corpus.
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. 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 assembly was validated using Bionano optical maps and 10X linked-read sequences. 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. We have found more repeats compared to the previous versions and one of the largest repeat classes identified are the LTR retrotransposons. We also describe updates to the reference genome and annotation since the last publication. The corresponding ITAG4.0 annotation has 4,794 novel genes along with 29,281 genes preserved from ITAG2.4. Most of the updated genes have extensions in the 5’ and 3’ UTRs resulting in doubling of annotated UTRs per gene. The genome and annotation can be accessed using SGN through BLAST database, Pathway database (SolCyc), Apollo, JBrowse genome browser and FTP available at https://solgenomics.net.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/f4b6d36c6320c3f5d9c851dc926cf68a78f4f0e4
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In Molecular Biology
- Fritz J. Sedlazeck
- W. Richard McCombie
- Melanie Kirsche
- Xingang Wang
- T. Ranallo-Benavidez
- Sara Goodwin
- Michael Alonge
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In Plant Science
Citations in the corpus
- Major impacts of widespread structural variation on gene expression and crop improvement in tomato (2020, methodology): “By default, Sniffles provides supporting reads for each insertion call but reports the insertion sequence from a single noisy read.”
- Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing (2022, unknown): “…hundreds of tomato genomes has uncovered vast genomic diversity [1, 2] but chromosome-scale genomes are only available for a few accessions [3–5] and there is a historical discrepancy between the reference genome (Heinz 1706) and genotypes that are commonly used for genetic and molecular…”