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ABSTRACT Weedy rice is a close relative of cultivated rice (Oryza sativa) that infests rice fields worldwide and drastically reduces yields. To combat this agricultural pest, rice farmers in the southern US began to grow herbicide‐resistant (HR) rice cultivars in the early 2000s, which permitted the application of herbicides that selectively targeted weedy rice without harming the crop. The widespread adoption of HR rice coincided with increased reliance on hybrid rice cultivars in place of traditional inbred varieties. Although both cultivated and weedy rice are predominantly self‐fertilising, the combined introductions of HR and hybrid rice dramatically altered the opportunities and selective pressure for crop‐weed hybridization and adaptive introgression. In this study, we generated genotyping‐by‐sequencing data for 178 weedy rice samples collected from across the rice growing region of the southern US; these were analysed together with previously published rice and weedy rice genome sequences to determine the recent genomic and population genetic consequences of adaptive introgression and selection for herbicide resistance in US weedy rice populations. We find a reshaped geographical structure of southern US weedy rice as well as purging of crop‐derived alleles in some weed strains of crop‐weed hybrid origin. Furthermore, we uncover evidence that related weedy rice strains have made use of different genetic mechanisms to respond to selection. Lastly, we identify widespread presence of HR alleles in both hybrid‐derived and nonadmixed samples, which further supports an overall picture of weedy rice evolution and adaptation through diverse genetic mechanisms. 

Abstract One of the common mechanisms to trigger plant innate immunity is recognition of pathogen avirulence gene products directly by products of major resistance (R) genes in a gene for gene manner. In the USA, theRgenes,Pik-s, PiKh/m, andPi-ta, Pi-39(t), andPtrgenes have been effectively deployed to prevent the infections ofM. oryzaeraces, IB49, and IC17 for some time.Pi-9is only recently being deployed to provide overlapped and complimentary resistance toMagnaporthe oryzaeraces IB49, IC17 and IE1k in the USA. Pi-ta, Pi-39(t), Pi9 are major nuclear binding site-leucine rich (NLR) proteins, and Ptr is an atypical R protein with 4 armadillo repeats. AlphaFold is an artificial intelligence system that predicts a protein 3D structure from its amino acid sequence. Here we report genome sequence analyses of the effectors and avirulence (AVR) genes,AVR-PitaandAVR-Pik, andAVR-Pi9, in 3 differentialM. oryzaeraces. Using AlphaFold 2 and 3 we find strong evidence of direct interactions of products of resistance genesPi-taandPikwithM. oryzaeavirulence (AVR) genes,AVR-PitaandAVR-Pikrespectively. We also found that AVR-Pita interacts with Pi-39(t) and Ptr, and Pi9 interacts with both AVR-Pi9 and AVR-Pik. Validation of direct interactions of two pairs of R and AVR proteins supported a direct interaction mechanism of plant innate immunity. Detecting interaction of both Ptr and Pi39(t) with AVR-Pita, and Pi-9 with both AVR-Pi9 and AVR-Pik, revealed a new insight into recognition of pathogen signaling molecules by these host R genes in triggering plant innate immunity. 

Abstract High reproductive compatibility between crops and their wild relatives can provide benefits for crop breeding but also poses risks for agricultural weed evolution. Weedy rice is a feral relative of rice that infests paddies and causes severe crop losses worldwide. In regions of tropical Asia where the wild progenitor of rice occurs, weedy rice could be influenced by hybridization with the wild species. Genomic analysis of this phenomenon has been very limited. Here we use whole genome sequence analyses of 217 wild, weedy and cultivated rice samples to show that wild rice hybridization has contributed substantially to the evolution of Southeast Asian weedy rice, with some strains acquiring weed-adaptive traits through introgression from the wild progenitor. Our study highlights how adaptive introgression from wild species can contribute to agricultural weed evolution, and it provides a case study of parallel evolution of weediness in independently-evolved strains of a weedy crop relative. 

Abstract Weedy rice is a close relative of cultivated rice that devastates rice productivity worldwide. In the southern United States, two distinct strains have been historically predominant, but the 21^stcentury introduction of hybrid rice and herbicide resistant rice technologies has dramatically altered the weedy rice selective landscape. Here, we use whole-genome sequences of 48 contemporary weedy rice accessions to investigate the genomic consequences of crop-weed hybridization and selection for herbicide resistance. We find that population dynamics have shifted such that most contemporary weeds are now crop-weed hybrid derivatives, and that their genomes have subsequently evolved to be more like their weedy ancestors. Haplotype analysis reveals extensive adaptive introgression of cultivated alleles at the resistance geneALS, but also uncovers evidence for convergent molecular evolution in accessions with no signs of hybrid origin. The results of this study suggest a new era of weedy rice evolution in the United States. 

Abstract White clover (Trifolium repens L.; Fabaceae) is an important forage and cover crop in agricultural pastures around the world and is increasingly used in evolutionary ecology and genetics to understand the genetic basis of adaptation. Historically, improvements in white clover breeding practices and assessments of genetic variation in nature have been hampered by a lack of high-quality genomic resources for this species, owing in part to its high heterozygosity and allotetraploid hybrid origin. Here, we use PacBio HiFi and chromosome conformation capture (Omni-C) technologies to generate a chromosome-level, haplotype-resolved genome assembly for white clover totaling 998 Mbp (scaffold N50 = 59.3 Mbp) and 1 Gbp (scaffold N50 = 58.6 Mbp) for haplotypes 1 and 2, respectively, with each haplotype arranged into 16 chromosomes (8 per subgenome). We additionally provide a functionally annotated haploid mapping assembly (968 Mbp, scaffold N50 = 59.9 Mbp), which drastically improves on the existing reference assembly in both contiguity and assembly accuracy. We annotated 78,174 protein-coding genes, resulting in protein BUSCO completeness scores of 99.6% and 99.3% against the embryophyta_odb10 and fabales_odb10 lineage datasets, respectively. 

Abstract There are two species of cultivated rice in the world— Oryza sativa L. from Asia and Oryza glaberrima Steud. from Africa. The former was domesticated from the wild progenitor Oryza rufipogon Griff. and the latter from the African wild rice species Oryza barthii A. Shiv. The first known center of rice cultivation in China generated the O. sativa subspecies japonica . The indica subspecies arose from the second center of domestication in the Ganges River plains of India. Variants of domesticated lines and the continuous hybridization between cultivated varieties and the wild progenitor(s) resulted in weedy rice types. Some weedy types resemble the wild ancestor, but the majority of weedy rices today bear close resemblance to cultivated rice. Weedy rice accompanies rice culture and has increased in occurrence with the global shift in rice establishment from transplanting to direct-seeded or dry-drill-seeded rice. Weedy rice ( Oryza spp.) is the most difficult weed to control in rice, causing as much as 90% yield loss or abandonment of severely infested fields. The gene flow continuum between cultivar and weedy rice or wild relative, crop de-domestication, and regionalized adaptation have resulted in a myriad of weedy rice types. The complex lineage of weedy rice has resulted in confusion of weedy rice nomenclature. Two names are generally used for weedy rice— Oryza sativa L. and Oryza sativa f. spontanea . Genomic data show that O. sativa L. applies to weedy rice populations derived from cultivated O. sativa , whereas O. sativa f. spontanea applies only to weedy types that primarily descended from O. rufipogon . Neither of these names applies to African weedy rice, which is of African wild rice or O. glaberrima lineage. Therefore, unless the lineage of the weedy population in question is known, the proper name to use is the generalized name Oryza spp.