Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Ever since Darwin's pioneering research, the evolution of self-fertilisation (selfing) has been regarded as one of the most prevalent evolutionary transitions in flowering plants. A major mechanism to prevent selfing is the self-incompatibility (SI) recognition system, which consists of male and female specificity genes at the S-locus and SI modifier genes. Under conditions that favour selfing, mutations disabling the male recognition component are predicted to enjoy a relative advantage over those disabling the female component, because male mutations would increase through both pollen and seeds whereas female mutations would increase only through seeds. Despite many studies on the genetic basis of loss of SI in the predominantly selfing plant Arabidopsis thaliana, it remains unknown whether selfing arose through mutations in the female specificity gene (S-receptor kinase, SRK), male specificity gene (S-locus cysteine-rich protein, SCR; also known as S-locus protein 11, SP11) or modifier genes, and whether any of them rose to high frequency across large geographic regions. Here we report that a disruptive 213-base-pair (bp) inversion in the SCR gene (or its derivative haplotypes with deletions encompassing the entire SCR-A and a large portion of SRK-A) is found in 95% of European accessions, which contrasts with the genome-wide pattern of polymorphism in European A. thaliana. Importantly, interspecific crossings using Arabidopsis halleri as a pollen donor reveal that some A. thaliana accessions, including Wei-1, retain the female SI reaction, suggesting that all female components including SRK are still functional. Moreover, when the 213-bp inversion in SCR was inverted and expressed in transgenic Wei-1 plants, the functional SCR restored the SI reaction. The inversion within SCR is the first mutation disrupting SI shown to be nearly fixed in geographically wide samples, and its prevalence is consistent with theoretical predictions regarding the evolutionary advantage of mutations in male components.

Self-incompatibility (SI) systems in flowering plants distinguish self-and non-self pollen to prevent inbreeding. While other SI systems rely on the self-recognition between specific male-and femaledeterminants, the Solanaceae family has a non-self recognition system resulting in the detoxification of female-determinants of S-ribonucleases (S-RNases), expressed in pistils, by multiple male-determinants of S-locus F-box proteins (SLFs), expressed in pollen. It is not known how many SLF components of this non-self recognition system there are in Solanaceae species, or how they evolved. We identified 16-20 SLFs in each S-haplotype in SI Petunia, from a total of 168 SLF sequences using large-scale nextgeneration sequencing and genomic polymerase chain reaction (PCR) techniques. We predicted the target S-RNases of SLFs by assuming that a particular S-allele must not have a conserved SLF that recognizes its own S-RNase, and validated these predictions by transformation experiments. A simple mathematical model confirmed that 16-20 SLF sequences would be adequate to recognize the vast majority of target S-RNases. We found evidence of gene conversion events, which we suggest are essential to the constitution of a non-self recognition system and also contribute to self-compatible mutations. Self-incompatibility (SI) systems in flowering plants distinguish self and non-self pollen to prevent inbreeding. While all other SI systems studied to date rely on the self-recognition between each single male-and female-determinants, the Solanaceae plants has a non-self recognition system that functions through the detoxification of non-self female-determinants of S-ribonucleases (S-RNases), expressed in pistils, by multiple male-determinants of S-locus F-box proteins (SLFs), expressed in pollen.However, little is known about how many SLF components constitute such a non-self recognition system and how they evolve. Here we conducted large-scale next-generation sequencing and genomic PCR and identified 16-20 SLFs in each S-haplotype in SI Petunia, for a total of 168 SLF sequences. We predicted the target S-RNases of SLFs by assuming that a particular S-allele must not have a conserved SLF that recognizes its own S-RNase, and validated them by transformation experiments. A simple mathematical model showed that 16-20 SLF sequences would be adequate to recognize the vast majority of target S-RNases. We found evidence of gene conversion events, which we suggest are essential to constitute a non-self recognition system and as well as contributed to self-compatible mutations.SI is a genetically controlled reproductive barrier in angiosperms that allows the pistil to reject self (genetically-related) pollen and accept non-self (genetically-unrelated) pollen [1][2][3][4] . In most cases, this self/non-self discrimination is controlled by male-and

Polyploidization, or genome duplication, has played a critical role in the diversification of animals, fungi and plants. Little is known about the population structure and multiple origins of polyploid species because of the difficulty in identifying multiple homeologous nuclear genes. The allotetraploid species Arabidopsis kamchatica is closely related to the model species Arabidopsis thaliana and is distributed in a broader climatic niche than its parental species. Here, we performed direct sequencing of homeologous pairs of the low-copy nuclear genes WER and CHS by designing homeolog-specific primers, and obtained also chloroplast and ribosomal internal transcribed spacer sequences. Phylogenetic analysis showed that 50 individuals covering the distribution range including North America are allopolyploids derived from Arabidopsis lyrata and Arabidopsis halleri. Three major clusters within A. kamchatica were detected using Bayesian clustering. One cluster has widespread distribution. The other two are restricted to the southern part of the distribution range including Japan, where the parent A. lyrata is not currently distributed. This suggests that the mountains in Central Honshu and surrounding areas in Japan served as refugia during glacial-interglacial cycles and retained this diversity. We also found that multiple haplotypes of nuclear and chloroplast sequences of A. kamchatica are identical to those of their parental species. This indicates that multiple diploid individuals contributed to the origin of A. kamchatica. The haplotypes of low-copy nuclear genes in Japan suggest independent polyploidization events rather than introgression. Our findings suggest that self-compatibility and gene silencing occurred independently in different origins.

Genome duplication with hybridization, or allopolyploidization, occurs commonly in plants, and is considered to be a strong force for generating new species. However, genome-wide quantification of homeolog expression ratios was technically hindered because of the high homology between homeologous gene pairs. To quantify the homeolog expression ratio using RNA-seq obtained from polyploids, a new method named HomeoRoq was developed, in which the genomic origin of sequencing reads was estimated using mismatches between the read and each parental genome. To verify this method, we first assembled the two diploid parental genomes of Arabidopsis halleri subsp. gemmifera and Arabidopsis lyrata subsp. petraea (Arabidopsis petraea subsp. umbrosa), then generated a synthetic allotetraploid, mimicking the natural allopolyploid Arabidopsis kamchatica. The quantified ratios corresponded well to those obtained by Pyrosequencing. We found that the ratios of homeologs before and after cold stress treatment were highly correlated (r = 0.870). This highlights the presence of nonstochastic polyploid gene regulation despite previous research identifying stochastic variation in expression. Moreover, our new statistical test incorporating overdispersion identified 226 homeologs (1.11% of 20 369 expressed homeologs) with significant ratio changes, many of which were related to stress responses. HomeoRoq would contribute to the study of the genes responsible for polyploid-specific environmental responses.