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Lindera benzoin is a dioecious understory shrub native to eastern North America. Northern spicebush is a beautiful shrub with a natural round shrub shape, golden-yellow fall foliage, attractive bright red drupes, and precocious yellow flowers in early spring; however, its market value as an ornamental value has been overlooked. To improve the ornamental values of this under-cultivated nursery crop, breeding for a better compact form, larger leaves, enlarged flower clusters and fruit, and increased stress tolerances could all be beneficial. Polyploidy manipulation is a valuable method to improve such traits for many ornamental plants. This study established the genome doubling method by oryzalin-infused solid agar treatment on young northern spicebush seedlings. The seedlings of two wild populations in North Carolina were collected and used. A total of 288 seedlings were treated with solid agar containing 150 µM oryzalin for 24, 72, and 120 h. The results were sporadic in their survival ratios and tetraploid conversion ratios between different treatments; however, a total of 16 tetraploid L. benzoin plants were produced in this study. The 24-h treatment showed the optimal result, with 7.1% of total treated seedlings or 15.2% of surviving seedlings converted into tetraploids. Tetraploid plants had visible differences in leaf morphology, a statistically significant enlarged stomata size, and reduced stomatal density compared to diploid plants. This research provides ploidy manipulation information for all future breeding processes of L. benzoin and related species. [ABSTRACT FROM AUTHOR]

Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research, including evolution, genetics, genomics, ecology, agriculture, forestry, and global climate. To investigate which plant conserves best the core eudicots common ancestor genome, we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant families. The genomes of Davidia involucrata (a known living fossil), Camptotheca acuminata and Nyssa sinensis, one per existent genus of Nyssaceae, were performed comparative genomic analysis. We found that Nyssaceae originated from a single Nyssaceae common tetraploidization event (NCT)– autotetraploidization 28–31 Mya after the core eudicot common hexaploidization (ECH). We identified Nyssaceae orthologous and paralogous genes, determined its chromosomal evolutionary trajectory, and reconstructed the Nyssaceae most recent ancestor genome. D. involucrata genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant families. Combing both its high retention of paleochromosomes and its low mutation rate, D. involucrata provides the best case in conservation of the core eudicot paleogenome.

Lindera benzoin is a dioecious understory shrub native to eastern North America. Northern spicebush is a beautiful shrub with a natural round shrub shape, golden-yellow fall foliage, attractive bright red drupes, and precocious yellow flowers in early spring; however, its market value as an ornamental value has been overlooked. To improve the ornamental values of this under-cultivated nursery crop, breeding for a better compact form, larger leaves, enlarged flower clusters and fruit, and increased stress tolerances could all be beneficial. Polyploidy manipulation is a valuable method to improve such traits for many ornamental plants. This study established the genome doubling method by oryzalin-infused solid agar treatment on young northern spicebush seedlings. The seedlings of two wild populations in North Carolina were collected and used. A total of 288 seedlings were treated with solid agar containing 150 µM oryzalin for 24, 72, and 120 h. The results were sporadic in their survival ratios and tetraploid conversion ratios between different treatments; however, a total of 16 tetraploid L. benzoin plants were produced in this study. The 24-h treatment showed the optimal result, with 7.1% of total treated seedlings or 15.2% of surviving seedlings converted into tetraploids. Tetraploid plants had visible differences in leaf morphology, a statistically significant enlarged stomata size, and reduced stomatal density compared to diploid plants. This research provides ploidy manipulation information for all future breeding processes of L. benzoin and related species.

Chinese mahogany (Toona sinensis) is of considerable medical and economic importance, and its genome has been deciphered. However, the process underlying its polyploidy is unclear, and the chromosomal evolutionary trajectory is poorly understood. Here, by reanalysing the T. sinensis genome, we found evidence of a tetraploidization event (T. sinensis special tetraploidization, TST) that occurred approximately 15–17 million years ago (MYA) after the core eudicot-common hexaploidization (ECH or gamma) event. We characterized the synonymous nucleotide substitution rates (Ks values) of collinear genes and found that T. sinensis genes affected by the TST evolve at a slower rate than Acer yangbiense genes. Furthermore, we identified homologous genes related to polyploidization and speciation and constructed multiple alignments with different reference genomes. Notably, the significant balance of gene retention and loss characterized in the two TST-derived subgenomes suggests an autopolyploid nature of the TST. Moreover, we deduced the chromosomal karyotypes of the two subgenomes and identified 7 chromosomal fusions that have shaped the T. sinensis genome; more information is available on a newly constructed karyotype platform (http://www.cgrpoee.top/Toona_sinensis/index.html). The T. sinensis genome preserves the ancestral chromosome structure of dicotyledons well and could serve as a good reference for understanding genomic changes in other Meliaceae and Sapindales plants. In addition, we verified that tandem duplication and the ECH have promoted the expansion of terpene synthase (TPS) genes; conversely, the TST seems to have inhibited expansion of these genes. This present effort has clarified the polyploidy events of the T. sinensis genome, filled gaps in the history of karyotype evolution, and laid a solid foundation for further genomic studies in the Meliaceae research community and beyond.

Background: The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification are often temporally separated from WGD. Salmonid fish, whose ancestor underwent WGD by autotetraploidization ~95 million years ago, fit such a 'time-lag' model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model, 'lineage-specific ohnologue resolution' (LORe), to address the consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event., Results: Using cross-species sequence capture, phylogenomics and genome-wide analyses of ohnologue expression divergence, we demonstrate the major impact of LORe on salmonid evolution. One-quarter of each salmonid genome, harbouring at least 4550 ohnologues, has evolved under LORe, with rediploidization and functional divergence occurring on multiple independent occasions >50 million years post-WGD. We demonstrate the existence and regulatory divergence of many LORe ohnologues with functions in lineage-specific physiological adaptations that potentially facilitated salmonid species radiation. We show that LORe ohnologues are enriched for different functions than 'older' ohnologues that began diverging in the salmonid ancestor., Conclusions: LORe has unappreciated significance as a nested component of post-WGD divergence that impacts the functional properties of genes, whilst providing ohnologues available solely for lineage-specific adaptation. Under LORe, which is predicted following many WGD events, the functional outcomes of WGD need not appear 'explosively', but can arise gradually over tens of millions of years, promoting lineage-specific diversification regimes under prevailing ecological pressures.