Lewis flax (Linum lewisii) is widely distributed across western North America and is currently used in native ecosystem restoration. There is also growing interest in de novo domestication of Lewis flax as a perennial oilseed crop. To better understand this species and facilitate both restoration and domestication, we used common gardens to assess bio-geographical variation in a variety of seed and growth traits from 37 flax accessions, consisting of 35 wild populations from the Intermountain West region, the pre-variety germplasm Maple Grove (L. lewisii) and the cultivar ‘Appar’ (L. perenne) and related this variation to collection site geography and climate. Results from linear mixed models suggest there is extensive phenotypic variation among populations of Lewis flax within the Intermountain West. Using a multivariate approach, we identify a key suite of traits that are related to latitude and climate and may facilitate adaptation, including flowering indeterminacy, seed mass, and stem number. These traits should be taken into account when considering the release of new germplasm for restoration efforts. We also find that Lewis flax seed contains desirably high amounts of alpha-linolenic acid and is otherwise mostly indistinguishable in fatty acid composition from oil-type varieties of domesticated flax (L. usitatissimum), making it a strong candidate for domestication. This study provides fundamental knowledge for future research into the ecology and evolution of Lewis flax, which will inform its use in both restoration and agriculture.

Hirundo is the most species-rich genus of the passerine swallow family (Hirundinidae) and has a cosmopolitan distribution. Here we report the complete, annotated mitochondrial genomes for 25 individuals from 10 of the 14 extant Hirundo species; these include representatives from four subspecies of the barn swallow, H. rustica. Mitogenomes were conserved in size, ranging from 18,500 to 18,700 base pairs. They all contained 13 protein-coding regions, 22 tRNAs, a control region, and large and small ribosomal subunits. Phylogenetic analysis resolved most of the relationships between the studied species and subspecies which were largely consistent with previously published trees. Several new relationships were observed within the phylogeny that could have only been discovered with the increased amount of genetic material. This study represents the largest Hirundo mitochondrial phylogeny to date, and could serve as a vital tool for other studies focusing on the evolution of the Hirundo genus.

Regulation of gene expression is a critical link between genotype and phenotype explaining substantial heritable variation within species. However, we are only beginning to understand the ways that specific gene regulatory mechanisms contribute to adaptive divergence of populations. Alternative splicing (AS) is a post-transcriptional regulatory mechanism in eukaryotes that generates multiple different transcripts (isoforms) from a single gene and thus may provide a source of evolutionary novelty. In plants, AS a compelling potential target of natural selection because it plays important roles in both development and abiotic stress response. We investigated whether variation in alternative splicing and gene expression levels might contribute to adaptation and incipient speciation of dune-adapted prairie sunflowers in Great Sand Dunes National Park, Colorado, USA. We conducted a common garden experiment to assess transcriptomic variation between ecotypes and analyzed differential expression, differential splicing, and gene coexpression. We show that individual genes are strongly differentiated for both transcript level and alternative isoform proportions, and that gene coexpression networks are disrupted between ecotypes. Furthermore, we examined how genome-wide patterns of sequence divergence correspond to divergence in transcript levels and isoform proportions and find evidence for a substantial contribution of trans-regulation. Genes that show significant differential expression and/or differential splicing are enriched for functions involving seed development, abiotic stress response, nutrient acquisition, and photosynthesis, some of which relate to known adaptive traits. Our results emphasize that alternative splicing has been underappreciated as a mechanism providing variation for natural selection to act upon at short time scales.

Cannabinoid production is a key attribute of the plant Cannabis sativa and characterizing the genes involved is an essential first step to develop tools for their optimization. We used bioinformatic approaches to annotate and explore variation in the genes coding for enzymes comprising the cannabinoid pathway: olivetol synthase (OLS), olivetolic acid cyclase (OAC), cannabigerolic acid synthase (CBGAS), and the cannabinoid oxidocyclases (THCAS, CBDAS, CBCAS) in multiple C. sativa genome assemblies from diverse lineages. The former three enzymes generate the precursor molecules for the oxidocyclases to produce cannabinoids THC and CBD. We show that duplications of OLS and OAC are consistent across varieties, and that OAC has the least amount of sequence diversity based on phylogenetic comparisons. We also found that one CBGAS-like gene exhibits copy number variation among varieties. We discuss implications of these genes existing on separate chromosomes (with homologs of each found in close proximity), and the significance of CBGAS being located on the X chromosome for cannabinoid production in female plants. This study provides valuable insight on the genomic identity and variation of cannabinoid biosynthesis genes that will benefit future research on the origin and evolution of this pathway, a driver of economic, social, and medicinal value.

Cannabinoid production is one of the key attributes of the plant Cannabis sativa and the characterization of the genes involved is an essential first step to develop tools for their optimization. We used bioinformatic approaches to annotate and explore variation in the coding genes for critical enzymes comprising the cannabinoid pathway: Olivetol Synthase (OLS), Olivetolic Acid Cyclase (OAC), and Cannabigerolic Acid Synthase (CBGAS), in multiple C. sativa genomes. These upstream genes of the Cannabinoid Oxidocyclase Genes THCAS, CBDAS, and CBCAS generate the necessary precursor molecules to produce the cannabinoids THC and CBD. We found that these genes vary in copy number and confirm that OLS, OAC, CBGAS, and the Cannabinoid Oxidocyclases are on separate chromosomes, while homologs are found in proximity. CBGAS, located on Chromosome X, suggests potential dosage effects in female plants. Except for the Cannabinoid Oxidocyclase genes, the other genes have multiple exons, up to 10 in CBGAS. Through differential exon usage explorations in CBGAS we found evidence for potential regulatory differences. This study provides valuable insight on the genomic identity and variation of cannabinoid biosynthesis genes that will benefit future research on the origin and evolution of this pathway, driver of economic, social, and medicinal value.