Weimin Dai

Horsenettle (Solanum carolinense L.) is a noxious weed widely distributed across North America and increasingly invasive in other regions. Its strong environmental adaptability, complex defense strategies, and distinctive reproductive traits make it an important model for studying plant–herbivore coevolution. However, the absence of high-quality genomic resources has limited deeper investigation into its adaptive evolutionary mechanisms. In this study, we generated a chromosome-level reference genome assembly for S. carolinense using an integrated approach combining PacBio HiFi long-read sequencing, Illumina second-generation sequencing, and Hi-C chromatin interaction scaffolding. The final genome assembly had a total length of 915.40 Mb, with a contig N50 of 51.06 Mb and a scaffold N50 of 73.17 Mb; 96.05% of the sequences were successfully anchored onto 12 pseudochromosomes. The genome was characterized by a high proportion of repetitive sequences (73.64%) and substantial heterozygosity (1.13%), consistent with a highly repetitive and moderately high heterozygous genome. BUSCO analysis indicated that the chromosome-level genome assembly of S. carolinense reached a completeness score of 94.8%. A total of 32,206 protein-coding genes were annotated, of which 97.95% received functional annotations. The evaluation of the annotated protein-coding gene set returned a completeness value of 94.9%. This reference genome provides a valuable resource for advancing research on the adaptive evolution of weedy Solanaceae species, supports the development of more effective management strategies for this troublesome species, and offers a technical reference for assembling other highly heterozygous weed genomes.

Solidago canadensis L. is a regulated invasive alien species in China and was first recorded in the wild in Jiangsu Province. Despite widespread concern regarding its distribution and ecological associations, province-wide information on its current invasion status and associated plant community patterns in Jiangsu remains limited. To fill this gap, we conducted field surveys at 165 sites across Jiangsu Province and combined hierarchical clustering, plant-community diversity analysis, species-level analysis of accompanying-plant composition, redundancy analysis, and MaxEnt modeling to evaluate invasion-intensity patterns, associated environmental and anthropogenic factors, and plant-community responses in invaded communities. Solidago canadensis was recorded throughout the province, but invasion intensity was highest in southern Jiangsu. Hierarchical clustering classified the 165 sampling sites into three invasion-intensity groups. Group A (74 sites), concentrated in southern Jiangsu, was classified as the severe invasion group and showed generally lower plant diversity within the invaded-site dataset. Group B (60 sites) represented moderate invasion. Group C (31 sites), mainly distributed in northern and coastal Jiangsu, represented light invasion and retained relatively higher accompanying-plant diversity. Within S. canadensis-invaded communities, we documented 183 accompanying plant species from 43 families. Asteraceae and Poaceae were the most species-rich families, and annual or biennial herbs were the dominant life-form category. Species-level analysis further showed that accompanying-plant composition varied significantly along the invasion-intensity gradient (PERMANOVA, R² = 0.035), suggesting that differences in S. canadensis dominance were associated with detectable shifts in local plant assemblages. Redundancy analysis indicated latitude, transportation route density, and floating population density were closely associated with variation in S. canadensis invasion indicators and associated community variables, with soil pH, precipitation of the driest month, GDP, and motor vehicle ownership also contributing to the observed pattern. MaxEnt modeling identified southern and central Jiangsu as the main climatically suitable areas. This pattern was broadly consistent with the concentration of higher invasion intensity in southern Jiangsu. Nevertheless, field records in northern Jiangsu suggest that areas with lower predicted climatic suitability should also remain under continued monitoring. These findings suggest the need for coordinated management, particularly along major transportation corridors and in highly disturbed urban habitats. Control efforts should combine zoning management, source control, repeated removal, and habitat restoration tailored to local conditions.

(1) Background: Horsenettle (Solanum carolinense) is a noxious weed widely distributed across North America and increasingly invasive in other regions. Its strong environmental adaptability, complex defense strategies, and distinctive reproductive traits make it an important model for studying plant-herbivore coevolution. However, the absence of high-quality genomic resources has limited deeper investigation into its adaptive evolutionary mechanisms. (2) Methods: In this study we generated a chromosome-level reference genome assembly for S. carolinense using an integrated approach combining PacBio HiFi long-read sequencing, Illumina second-generation sequencing, and Hi-C chromosome-mapping; (3) The final genome assembly has a total length of 915.40 Mb, with a contig N50 of 51.06 Mb and a scaffold N50 of 73.17 Mb; 96.05% of the sequences were successfully mapped to 12 pseudo-chromosomes. The genome is characterized by a high proportion of repetitive sequences (73.64%) and substantial heterozygosity (1.13%), consistent with a highly repetitive and highly heterozygous genome. BUSCO analysis indicates a completeness of 94.7%. A total of 32,206 protein-coding genes were annotated, of which 97.95% received functional annotations; (4) Conclusions: This reference genome provides a valuable resource for advancing research on the adaptive evolution of Solanaceae weeds, supports the development of more effective management strategies for this troublesome species, and offers a technical reference for assembling other highly heterozygous weed genomes.

Introduction: Bidirectional gene flow via pollen between transgenic rice and weedy rice could occur in natural fields. Gene flow from transgenic rice to weedy rice has been confirmed in many studies, and thus results showed that F₁ hybrids could persist in natural agroecosystems due to their unimpaired reproductive ability. However, the reverse gene flow from weedy rice to transgenic rice is rarely reported.Method: We quantified reverse gene flow from three weedy rice accessions to transgenic rice line T1c-19 with cry1C*/bar. In field trials with alternating layout of cultivating transgenic rice and weedy rice accessions and adjacent layout cultivating them in a close vicinity, the reverse gene flow was detected. And the fitness of reverse F₁ (RF₁) hybrids obtained by manual pollination using T1c-19 as maternal plants and weedy rice as paternal plants was evaluated in field.Result: No gene flow from WRTZ was observed, while gene flows from WRMM were observed at 0.0508% and 0.0808%, respectively, and those from WRYY were 0.0692% and 0.1008%, respectively. RF₁ plants exhibited significantly higher composite fitness compared to their weedy rice counterparts, due to enhanced fecundity-related traits observed under both insect pressure and no-insect pressure conditions. However, the impact of reverse gene flow may be limited because RF₁ hybrid seeds presented lower seed shattering, and therefore most of it would be harvested by combine harvester.Discussion: Our study revealed that gene flow from three weedy rice accessions to T1c-19 could produce RF₁ hybrids with greater composite fitness. Any loss of seeds into agroecosystem may result in a greater risk of RF1 hybrids due to their morphological similarity and high fitness.

Weedy rice, also known as red rice, mainly originates from the de-domestication of cultivated rice and is a vicious weed in paddy fields around the world. Its red seeds are rich in oxidized proanthocyanidins (OPAs). This study investigates whether OPA content varies among different weedy rice strains, whether these variations are possibly related to their adaptation to the local environment, and whether the change in OPA content could affect seed germination. A total of 202 weedy rice accessions from 69 populations across China were collected. Their OPA content, Rc/Rd genotypes, and seed germination percentage on the second, third, and seventh day were detected, respectively. Using bivariate Pearson’s two-tailed correlation analysis and generalized linear mixed models, our results showed that the content of OPAs varied widely among the different strains of weedy rice and were significantly correlated with local environment (latitude) and Rc/Rd genotypes but not with seed germination percentage on the second, third, and seventh day. Thus, the content of OPAs in Chinese weedy rice seeds is closely related to its ecological adaptability. These findings provide insights into the effect of OPA content on the ecological adaptability of weedy rice, which is beneficial to the control and germplasm resource utilization of weedy rice.

With the scarcity of fresh water resources and the increase in labor prices, rice cultivation is changing from transplanting to direct seeding. Weedy rice is a malignant weed with strong drought tolerance in seed germination in direct-seeding rice fields. As the same species of cultivated rice (Oryza sativa L.), weedy rice (Oryza sativa f. spontanea) has the potential of domestication into direct-seeding rice with strong drought tolerance in seed germination by changing a few unfavorable traits. The red pericarp, one of the harmful traits of weedy rice, seriously affects the quality and commercial value of cultivated rice. The recently developed CRISPR/Cas9 (Clustered Regular Interspaced Short Palindromic Repeats) technology can accurately edit the function of genes, providing a possibility for the directed evolution. Weedy rice (WRL-162) with red pericarp was used as a mutant material. Two mutation sites, upstream and downstream of the 14 bp differential fragment of exon 6 of Rc gene, were designed using the CRISPR-Cas9 gene-editing technique. Consequently, three mutant types in T1 generation weedy rice with CRISPR-Cas9 vector changed from red to white pericarp. One mutant type in T1 generation weedy rice with CRISPR-Cas9 vector maintained red pericarp. Comparing the wild type of weedy rice and rice variety control (Nipponbare), mutant types in T3 generation weedy rice without CRISPR-Cas9 vector significantly improved the drought resistance in seed germination. In addition, there was no significant difference in panicle number, seed setting rate per plant, grain length and width between wild type and T3 generation mutant weedy rice without CRISPR-Cas9 vector. Comparing the wild type, some mutant types in T3 generation weedy rice without CRISPR-Cas9 vector significantly decreased plant height, decreased spikelet number per main panicle, decreased plump seed number per main panicle, and increased 1000-grain weight. Our results showed that the Rc gene editing using CRISPR/Cas9 technology can not only remove the harmful pericarp character of weedy rice, but also improve drought tolerance in seed germination. This study might provide new insights for the utilization of weedy rice as germplasm resources for direct-seeding rice by precisely editing genes to remove unfavorable traits.

Increasing resistance to aging is conducive to seed storage and germination rate of crop. Meanwhile, the resistance to aging is one of the important adaptive mechanisms of weed to thrive in farmland. Weedy rice (Oryza sativa f. spontanea) and cultivated rice (Oryza sativa L.) provide a unique pair demonstrating a weed and conspecific model crop that can be used to study the aging resistance of plants across a diverse geographical range. Chinese weedy rice derived from de-domestication of cultivated rice has rapidly risen to malignant weeds, though the hazard has only been reported for about 20 years. Whether weedy rice rapidly evolves higher seed aging resistance than cultivated rice during the process of dedomestication, which is conducive to its persistence in rice fields, is still unclear. In this experiment, the seeds of weed rice populations and their co-existing rice varieties were collected from 61 regions of China and germinated under normal and high temperatures for consecutive four years (2013–2016). Our study found that the aging resistance of weedy rice was higher than that of the co-existing rice cultivars, and weedy rice may have evolved a different aging resistance mechanism than rice cultivars and could be used as a germplasm resource to cultivate aging-resistant rice. The indica-type has strong aging resistance and no dormancy, while the japonica type has weak aging resistance and a little weak dormancy. Thus, by introducing indica-type aging-resistant alleles into japonica rice, cultivation of aging-resistant japonica rice could be possible.

The mechanisms by which weedy rice (Oryza sativa f. spontanea) has adapted to endure low‐temperature stress in northern latitudes remain unresolved. In this study, we assessed cold tolerance of 100 rice varieties and 100 co‐occurring weedy rice populations, which were sampled across a broad range of climates in China. A parallel pattern of latitude‐dependent variation in cold tolerance was detected in cultivated rice and weedy rice. At the molecular level, differential cold tolerance was strongly correlated with relative expression levels of CBF cold response pathway genes and with methylation levels in the promoter region of OsICE1, a regulator of this pathway. Among all methylated cytosine sites of the OsICE1 promoter, levels of CHG and CHH methylation were found to be significantly correlated with cold tolerance among accessions. Furthermore, within many of the collection locales, weedy rice shared identical or near‐identical OsICE1 methylation patterns with co‐occurring cultivated rice. These findings provide new insights on the possible roles that methylation variation in the OsICE1 promoter may play in cold tolerance, and they suggest that weedy rice can rapidly acquire cold tolerance via methylation patterns that are shared with co‐occurring rice cultivars.