DOI: 10.5061/dryad.nk98sf7td
title: Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning

description: Cloning agronomically important genes from large, complex crop genomes
 remains challenging. Here, we generate a 14.7-gigabase chromosome-scale
 assembly of the South African bread wheat (Triticum aestivum) cultivar
 Kariega by combining high-fidelity long reads, optical mapping, and
 chromosome conformation capture. The resulting assembly is an order of
 magnitude more contiguous than previous wheat assemblies. Kariega shows
 durable resistance against the devastating fungal stripe rust disease. We
 identified the race-specific disease resistance gene Yr27, encoding an
 intracellular immune receptor, as a major contributor to this resistance.
 Yr27 is allelic to the leaf rust resistance gene Lr13, with the Yr27 and
 Lr13 proteins sharing 97% sequence identity. Our results thus demonstrate
 the feasibility of generating chromosome-scale wheat assemblies to clone
 genes and also exemplify that highly similar alleles of a single-copy gene
 can confer resistance to different pathogens, which might provide a basis
 for engineering Yr27 alleles with multiple recognition specificities in
 future.
description: The folder 'Kariega_v1_pseudomolecules.tar.gz' contains
 DNA sequence file and masked sequences in FASTA format for chromosomal
 pseudomolecules of bread wheat (Triticum aestivum) cv. Kariega. Primary
 contig assembly from PacBio Hifi reads was done with HiFiAsm. Contigs were
 scaffolded with Bionano data and arranged into chromosomal pseudomolecules
 with Omni-C data using the Juicer / 3D-DNA / Juicebox pipeline. An AGP
 file specifying the placement of sequence scaffolds in the pseudomolecules
 is provided. <br> The folder
 'Kariega_v1_annotations.tar.gz' holds the structural gene
 annotation based on evidences derived from protein homology, RNAseq and
 IsoSeq datasets, as well as ab initio gene prediction incorporating TE
 annotations: gene models in GFF3 format, their functional descriptions as
 well as coding and protein sequences of high- and low-confidence genes. De
 novo annotations were subject of a confidence classification step, which
 includes homology to existing proteins, robustness of functional
 assessment and results in high- (HC) and low- (LC) confidence genes. A
 fixed cut-off threshold was applied for protein homology and functional
 assessment was carried out using an Interproscan pipeline and was not
 manually curated.<br> A GFF file containing the NLR genes predicted
 with NLR-Annotator pipeline. It contains also the GFF files specifying the
 positions of transposable elements and a fasta file with a transposable
 elements library annotated with EDTA software. <br> The Yr27 CDS and
 genomic sequences are present in FASTA format.
 <br> Provided in these folders:<br> - Umasked and
 Masked DNA sequences<br> - Annotation in gff3 format including
 isoforms, UTRs and description line putative functional
 assignments<br> - separate gff3 files for high- (HC)/ low- (LC)
 confidence genes and transposable elements (TE)<br> - CDS and
 protein sequences<br> - Transposable elements library<br> -
 NLR annotation<br> - Yr27 CDS and genomic sequences
 <br> Detailed list of files in '.tar.gz'
 folders:<br> Kariega_v1_pseudomolecules.tar.gz<br> --&gt;
 Kariega_v1.fasta (Unmasked pseudomolecules)<br> --&gt;
 Kariega_v1-masked.fasta (masked pseudomolecules)<br> --&gt;
 Kariega_v1.agp (scaffold order in each pseudomolecules)<br>
 --&gt; Kariega_v1.length (pseudomolecule size)
 <br> Kariega_v1_annotations.tar.gz<br> (High- and
 Low-confidence gene models)<br> --&gt; Kariega_v1.gff3<br>
 --&gt; Kariega_v1-cds.fasta<br> --&gt;
 Kariega_v1-prot.fasta (High-confidence gene
 models)<br> --&gt; Kariega_v1_HC.gff3<br> --&gt;
 Kariega_v1_HC-cds.fasta<br> --&gt;
 Kariega_v1_HC-prot.fasta (Low-confidence gene
 models)<br> --&gt; Kariega_v1_LC.gff3<br> --&gt;
 Kariega_v1_LC-cds.fasta<br> --&gt;
 Kariega_v1_LC-prot.fasta (NLR gene
 prediction)<br> --&gt; Kariega_v1_NLR.gff3
 (Transposable elements)<br> --&gt;
 Kariega_v1_TE-intact.gff3<br> --&gt;
 Kariega_v1_TE-lib.fasta