Dynamic evolution of NBS-LRR genes in bread wheat and its progenitors

A chromosome-scale genome assembly of the Mongolian oak (Quercus mongolica)

Mongolian oak (Quercus mongolica Fisch.) is an ecologically and economically important white oak species native to and widespread in the temperate zone of East Asia. Here, we present a chromosome-scale reference genome assembly of Q. mongolica, a representative white oak species, by combining Illumina and PacBio data with Hi-C mapping technologies that is the first reference genome created for an Asian oak. Our results showed that the PacBio draft genome size was 809.84 Mb, with a BUSCO complete gene percentage of 92.71%. Hi-C scaffolding anchored 774.59 Mb contigs (95.65% of draft assembly) onto 12 pseudochromosomes. The contig N50 and scaffold N50 were 2.64 Mb and 66.74 Mb, respectively. Of the 36,553 protein-coding genes predicted in the study, approximately 95% had functional annotations in public databases. A total of 435.34 Mb (53.75% of the genome) of repetitive sequences were predicted in the assembled genome. Genome evolution analysis showed that Q. mongolica is closely related to Q. robur from Europe, and they shared a common ancestor ~11.8 million years ago. Gene family evolution analysis of Q. mongolica revealed that the nucleotide-binding site (NBS)-encoding gene family related to disease resistance was significantly contracted, whereas the ECERIFERUM 1 (CER1) homologous genes related to cuticular wax biosynthesis was significantly expanded. This pioneering Asian oak genome resource represents an important supplement to the oak genomics community and will improve our understanding of Asian white oak biology and evolution.

A Cluster of Nucleotide-Binding Site-Leucine-Rich Repeat Genes Resides in a Barley Powdery Mildew Resistance Quantitative Trait Loci on 7HL

Powdery mildew causes severe yield losses in barley production worldwide. Although many resistance genes have been described, only a few have already been cloned. A strong QTL (quantitative trait locus) conferring resistance to a wide array of powdery mildew isolates was identified in a Spanish barley landrace on the long arm of chromosome 7H. Previous studies narrowed down the QTL position, but were unable to identify candidate genes or physically locate the resistance. In this study, the exome of three recombinant lines from a high-resolution mapping population was sequenced and analyzed, narrowing the position of the resistance down to a single physical contig. Closer inspection of the region revealed a cluster of closely related NBS-LRR (nucleotide-binding site-leucine-rich repeat containing protein) genes. Large differences were found between the resistant lines and the reference genome of cultivar Morex, in the form of PAV (presence-absence variation) in the composition of the NBS-LRR cluster. Finally, a template-guided assembly was performed and subsequent expression analysis revealed that one of the new assembled candidate genes is transcribed. In summary, the results suggest that NBS-LRR genes, absent from the reference and the susceptible genotypes, could be functional and responsible for the powdery mildew resistance. The procedure followed is an example of the use of NGS (next-generation sequencing) tools to tackle the challenges of gene cloning when the target gene is absent from the reference genome.