An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps

Hosmani, Prashant S.; Flores-Gonzalez, Mirella; Geest, Henri van de; Maumus, Florian; Bakker, Linda V.; Schijlen, Elio; Haarst, Jan C. van; Cordewener, J.H.G.; Sánchez-Pérez, Gabino F.; Peters, Sander; Fei, Zhangjun; Giovannoni, James J.; Mueller, Lukas A.; Saha, Surya

doi:10.1101/767764

Cited by 167 publications

(175 citation statements)

References 55 publications

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“…Alignment of the genome sequences of LA2093 and Heinz 1706 (version 4.0) (Hosmani et al, 2019) showed good collinearity between the two reference genomes (Supplementary Fig. 4).…”

Section: Genomic Svs Between La2093 and Heinz 1706mentioning

confidence: 90%

“…A total of 166 million Hi-C read pairs was generated for constructing chromatin interaction maps. These Hi-C contact maps, together with the synteny with the Heinz 1706 genome (version 4.0) (Hosmani et al, 2019) and the genetic map constructed using the NC EBR-1 × LA2093 RIL population , were used to scaffold the assembled contigs. Finally, 385 contigs with a total length of ~800 Mb, accounting for 99.0% of the assembly, were clustered into 12 pseudomolecules (Fig.…”

Section: Sequencing and Assembly Of The S Pimpinellifolium Genomementioning

confidence: 99%

“…Based on the alignments, the contigs were clustered into pseudomolecules using SALSA (Ghurye et al, 2019) with parameters '-e GATC -i 3'. Furthermore, contigs of LA2093 were compared with the Heinz1706 reference genome (Hosmani et al, 2019) (version 4.0) using RaGOO . Hi-C data and synteny with the Heinz1706 genome were integrated to construct the pseudomolecules.…”

Section: De Novo Assembly Of the La2093 Genomementioning

confidence: 99%

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Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

Wang

Gao

Jiao

et al. 2020

Preprint

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Solanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern breeding of tomato. Here we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 high-confidence structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions unravels alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous novel SVs underlying genes known to regulate important breeding traits such as fruit weight and lycopene content.Expression quantitative trait locus (eQTL) analysis detects hotspots harboring master regulators controlling important fruit quality traits, including cuticular wax accumulation and flavonoid biosynthesis, and novel SVs contributing to these complex regulatory networks. The LA2093 genome sequence and the identified SVs provide rich resources for future research and biodiversity-based breeding.

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“…Alignment of the genome sequences of LA2093 and Heinz 1706 (version 4.0) (Hosmani et al, 2019) showed good collinearity between the two reference genomes (Supplementary Fig. 4).…”

Section: Genomic Svs Between La2093 and Heinz 1706mentioning

confidence: 90%

Section: Sequencing and Assembly Of The S Pimpinellifolium Genomementioning

confidence: 99%

Section: De Novo Assembly Of the La2093 Genomementioning

confidence: 99%

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Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

Wang

Gao

Jiao

et al. 2020

Preprint

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“…Excluding gaps from the assembly, RepeatMasker masked 70% of the genome as repetitive elements, which is in the range of other Solanum accessions, eg. 59.5% for S. pimpinellifolium [17], 64% for S. lycopersicum v4 [55], and 82% for S. pennellii [13].…”

Section: Gene Prediction From the Genome Assemblymentioning

confidence: 97%

De novo genome assembly and transcriptome analysis for the drought and salt resistant Solanum sitiens

Molitor

Kurowski

Almeida

et al. 2020

Preprint

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Solanum sitiens is a self-incompatible wild relative of tomato, characterised by salt and drought resistance traits, with the potential to contribute to crop improvement in cultivated tomato. This species has a distinct morphology, classification and ecotype compared to other stress resistant wild tomato relatives such as S. pennellii and S. chilense. Therefore, the availability of a high-quality reference genome for S. sitiens will facilitate the genetic and molecular understanding of salt and drought resistance.Here, we present a de novo genome and transcriptome assembly for S. sitiens (Accession LA1974). A hybrid assembly strategy was followed using Illumina short reads (~159X coverage) and PacBio long reads (~44X coverage), generating a total of ~262 Gbp of DNA sequence; in addition, ~2,670 Gbp of BioNano data was obtained.A reference genome of 1,245 Mbp, arranged in 1,481 scaffolds with a N50 of 1,826Mbp was generated. Genome completeness was estimated at 95% using the Benchmarking Universal Single-Copy Orthologs (BUSCO) and the K-mer Analysis Tool (KAT); this is within the range of current high-quality reference genomes for other tomato wild relatives. Additionally, we identified three large inversions compared to S. lycopersicum, containing several drought resistance related genes, such as betaamylase 1 and YUCCA7.In addition, ~63 Gbp of RNA-Seq were generated to support the prediction of 31,164 genes from the assembly, and perform a de novo transcriptome. Some of the protein clusters unique to S. sitiens were associated with genes involved in drought and salt resistance, including GLO1 and FQR1.This first reference genome for S. sitiens will provide a valuable resource to progress QTL studies to the gene level, and will assist molecular breeding to improve crop production in water-limited environments.

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“…Solanum lycopersicon (L.) (Solanaceae), commercial variety Heinz 1607)(Hosmani et al 2019) was used as 'carrier DNA'. DNA extraction of S. lycopersicon followed the protocol of Hosmani et al(Hosmani et al 2019).…”

mentioning

confidence: 99%

Braconidae revisited:Bracon brevicornisgenome showcases the potential of linked-read sequencing in identifying a putativecomplementary sex determinergene

Ferguson

Pannebakker

Centurión

et al. 2020

Preprint

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Bracon brevicornis is an ectoparasitoid of a wide range of larval-stage Lepidopterans, including several pests of important crops, such as the corn borer, Ostrinia nubilalis. It is also one of the earliest documented cases of complementary sex determination in Hymenoptera. Here, we present the linked-read genome of B. brevicornis, complete with an ab initio-derived annotation and protein comparisons with fellow braconids, Fopius arisanus and Diachasma alloem. We demonstrate the potential of linked-read assemblies in exploring regions of heterozygosity and search for structural and homology-derived evidence of the complementary sex determiner gene (csd).

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An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps

Cited by 167 publications

References 55 publications

Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

De novo genome assembly and transcriptome analysis for the drought and salt resistant Solanum sitiens

Braconidae revisited:Bracon brevicornisgenome showcases the potential of linked-read sequencing in identifying a putativecomplementary sex determinergene

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