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Abstract PremisePectocarya recurvata(Boraginaceae, subfamily Cynoglossoideae), a species native to the Sonoran Desert (North America), has served as a model system for a suite of ecological and evolutionary studies. However, no reference genomes are currently available in Cynoglossoideae. A high‐quality reference genome forP. recurvatawould be valuable for addressing questions in this system and across broader taxonomic scales. MethodsUsing PacBio HiFi sequencing, we assembled a reference genome forP. recurvataand annotated coding regions with full‐length transcripts from an Iso‐Seq library. We assessed genome completeness with BUSCO andk‐mer analysis, and estimated the genome size of six individuals using flow cytometry. ResultsThe chromosome‐scale genome assembly forP. recurvatawas 216.0 Mbp long (N50 = 12.1 Mbp). Previous observations indicatedP. recurvatais 2n = 24. Our assembly included 12 primary contigs (158.3 Mbp) containing 30,655 genes with telomeres at 23 out of 24 ends. Flow cytometry measurements from the same population included two plants with 1C = 196.9 Mbp, the smallest measured for Boraginaceae, and four with 1C = 385.8 Mbp, which is consistent with tetraploidy in this population. DiscussionTheP. recurvatagenome assembly and annotation provide a high‐quality genomic resource in a sparsely represented area of the angiosperm phylogeny. This new reference genome will facilitate answering open questions in ecophysiology, biogeography, and systematics. 

Abstract PremiseThe extraction of high‐quality RNA is the critical first step for the analysis of gene expression and gene space. This remains particularly challenging in plants, and especially in ferns, where the disruption of the cell wall and separation of organic compounds from nucleic acids is not trivial. MethodsWe developed a cetyltrimethylammonium bromide (CTAB)‐based RNA extraction protocol that consistently performs well across a large phylogenetic breadth of ferns—a lineage of plants high in secondary compounds—and in an array of tissue types. Two alternative options (precipitation vs. clean‐up without intermediate precipitation) are presented, both of which yield high‐quality RNA extracts with optical density (OD) ratios of OD 260/280 = 1.9–2.1 and OD 260/230 > 1.6, and RNA integrity numbers >7. ConclusionsThis study presents an efficient protocol for the extraction of high‐quality RNA from multiple tissues and across the fern phylogeny, a clade of plants that still lags behind other major lineages in the development of genomic resources. We hope that this method can be used to help facilitate the closing of this gap. 

Abstract PremiseReticulate evolution, often accompanied by polyploidy, is prevalent in plants, and particularly in the ferns. Resolving the resulting non‐bifurcating histories remains a major challenge for plant phylogenetics. Here, we present a phylogenomic investigation into the complex evolutionary history of the vining ferns,Lygodium(Lygodiaceae, Schizaeales). MethodsUsing a targeted enrichment approach with theGoFlag 408flagellate land plant probe set, we generated large nuclear and plastid sequence datasets for nearly all taxa in the genus and constructed the most comprehensive phylogeny of the family to date using concatenated maximum likelihood and coalescence approaches. We integrated this phylogeny with cytological and spore data to explore karyotype evolution and generate hypotheses about the origins of putative polyploids and hybrids. ResultsOur data and analyses support the origins of several putative allopolyploids (e.g.,L. cubense, L. heterodoxum) and hybrids (e.g.,L.×fayae) and also highlight the potential prevalence of autopolyploidy in this clade (e.g.,L. articulatum, L. flexuosum, andL. longifolium). ConclusionsOur robust phylogenetic framework provides valuable insights into dynamic reticulate evolution in this clade and demonstrates the utility of target‐capture data for resolving these complex relationships. 

Abstract Premise The functional annotation of genes is a crucial component of genomic analyses. A common way to summarize functional annotations is with hierarchical gene ontologies, such as the Gene Ontology (GO) Resource. GO includes information about the cellular location, molecular function(s), and products/processes that genes produce or are involved in. For a set of genes, summarizing GO annotations using pre‐defined, higher‐order terms (GO slims) is often desirable in order to characterize the overall function of the data set, and it is impractical to do this manually. Methods and Results The GOgetter pipeline consists of bash and Python scripts. From an input FASTA file of nucleotide gene sequences, it outputs text and image files that list (1) the best hit for each input gene in a set of reference gene models, (2) all GO terms and annotations associated with those hits, and (3) a summary and visualization of GO slim categories for the data set. These output files can be queried further and analyzed statistically, depending on the downstream need(s). Conclusions GO annotations are a widely used “universal language” for describing gene functions and products. GOgetter is a fast and easy‐to‐implement pipeline for obtaining, summarizing, and visualizing GO slim categories associated with a set of genes. 

Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree–species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored. 

Abstract Octocorals are conspicuous members of coral reefs and deep-sea ecosystems. Yet, species boundaries and taxonomic relationships within this group remain poorly understood, hindering our understanding of this essential component of the marine fauna. We used a multifaceted approach to revisit the systematics of the Caribbean octocorals Plexaura homomalla and Plexaura kükenthali , two taxa that have a long history of taxonomic revisions. We integrated morphological and reproductive analyses with high-throughput sequencing technology to clarify the relationship between these common gorgonians. Although size and shape of the sclerites are significantly different, there is overlap in the distributions making identification based on sclerites alone difficult. Differences in reproductive timing and mode of larval development were detected, suggesting possible mechanisms of pre-zygotic isolation. Furthermore, there are substantial genetic differences and clear separation of the two species in nuclear introns and single-nucleotide polymorphisms obtained from de novo assembled transcriptomes. Despite these differences, analyses with SNPs suggest that hybridization is still possible between the two groups. The two nascent species also differed in their symbiont communities (genus Breviolum ) across multiple sampling sites in the Caribbean. Despite a complicated history of taxonomic revisions, our results support the differentiation of P. homomalla and P. kükenthali, emphasizing that integrative approaches are essential for Anthozoan systematics.