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Abstract BackgroundModern plant breeding strategies rely on the intensive use of advanced genomic tools to expedite the development of improved crop varieties. Genomic DNA extraction from crop seeds eliminates the need to grow plants in contrast to fresh leaf tissue; however, it can still be a bottleneck due to the presence of stored compounds and the complexity of the matrix. The interaction of environmentally benign choline-based ionic liquids (ILs) with DNA offers an innovative approach to enhance the quality of extracted DNA from seeds. While prior IL-based plant DNA extraction workflows have primarily supported polymerase chain reaction (PCR) and quantitative PCR-based applications, their suitability for high-throughput sequencing (HTS) remained largely unexplored. This study explores the efficacy of IL-assisted method for genomic DNA extraction from soybean (Glycine max) seeds, addressing the limited application of ILs in HTS. ResultsThe optimized DNA extraction method, utilizing 25% (w/v) choline formate, enabled the recovery of high-purity DNA with abundant fragment sizes > 20 kb, suitable for downstream applications including PCR, whole genome amplification (WGA), simple sequence repeat (SSR) amplification, and high-throughput Illumina sequencing. The IL-method was benchmarked against a silica-binding method using cetyltrimethylammonium bromide (CTAB) and sodium dodecyl sulfate (SDS) as lysis agents using a commercial plant DNA extraction kit in terms of DNA yield, purity, abundant DNA fragment size distribution, and integrity. In addition, DNA isolated from this method demonstrated successful PCR amplification of markers from both the nuclear and plastid genomes and yielded > 99% whole genome coverage with Illumina (PE150) sequencing reads. ConclusionsThis is the first known instance of a whole genome sequence generated from DNA extracted with ILs. These findings mark a significant milestone in establishing ILs as promising alternatives to conventional methods for seed DNA extraction, with potential utility in third generation (long-read) sequencing experiments. 

Abstract The genus Asparagus arose ∼9 to 15 million years ago (Ma), and transitions from hermaphroditism to dioecy (separate sexes) occurred ∼3 to 4 Ma. Roughly 27% of extant Asparagus species are dioecious, while the remaining are bisexual with monoclinous flowers. As such, Asparagus is an ideal model taxon for studying the early stages of dioecy and sex chromosome evolution in plants. Until now, however, understanding of diversification and shifts from hermaphroditism to dioecy in Asparagus has been hampered by the lack of robust species tree estimates for the genus. In this study, a genus-wide phylogenomic analysis including 1,726 nuclear loci and comprehensive species sampling supports two independent origins of dioecy in Asparagus—first in a widely distributed Eurasian clade and then in a clade restricted to the Mediterranean Basin. Modeling of ancestral biogeography indicates that both dioecy origins were associated with range expansion out of southern Africa. Our findings also reveal several bursts of diversification across the phylogeny, including an initial radiation in southern Africa that gave rise to 12 major clades in the genus, and more recent radiations that have resulted in paraphyly and polyphyly among closely related species, as expected given active speciation processes. Lastly, we report that the geographic origin of domesticated garden asparagus (Asparagus officinalis L.) was likely in western Asia near the Mediterranean Sea. The presented phylogenomic framework for Asparagus is foundational for ongoing genomic investigations of diversification and functional trait evolution in the genus and contributes to its utility for understanding the origin and early evolution of dioecy and sex chromosomes. 

PremiseApetaly is widespread across distantly related lineages of flowering plants and is associated with abiotic (or self‐) pollination. It is particularly prevalent in the carnation family, and the cosmopolitan genusStellariacontains many lineages that are hypothesized to have lost petals from showy petalous ancestors. But the pollination biology of apetalous species ofStellariaremains unclear. MethodsUsing a substantial species‐level sampling (~92% of known taxonomic diversity), we describe the pattern of petal evolution withinStellariausing ancestral character state reconstructions. To help shed light on the reproductive biology of apetalousStellaria, we conducted a field experiment at an alpine tundra site in the southern Rocky Mountains to test whether an apetalous species (S. irrigua) exhibits higher levels of selfing than a sympatric, showy petalous congener (S. longipes). ResultsAnalyses indicated that the ancestor ofStellariawas likely showy petalous and that repeated, parallel reductions of petals occurred in clades across much of the world, with uncommon reversal back to showy petals. Field experiments supported high rates of selfing in the apetalous species and high rates of outcrossing in the petalous species. ConclusionsPetal loss is rampant across major clades ofStellariaand is potentially linked with self‐pollination worldwide. Self‐pollination occurs within the buds inS. irrigua, and high propensities for this and other forms of selfing known in many other taxa of arctic‐alpine habitats may reflect erratic availability of pollinators.