RT Journal Article
SR Electronic
T1 An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 767764
DO 10.1101/767764
A1 Prashant S. Hosmani
A1 Mirella Flores-Gonzalez
A1 Henri van de Geest
A1 Florian Maumus
A1 Linda V. Bakker
A1 Elio Schijlen
A1 Jan van Haarst
A1 Jan Cordewener
A1 Gabino Sanchez-Perez
A1 Sander Peters
A1 Zhangjun Fei
A1 James J. Giovannoni
A1 Lukas A. Mueller
A1 Surya Saha
YR 2019
UL http://biorxiv.org/content/early/2019/09/14/767764.abstract
AB 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.