Biology subjects

Innes, P. A.

Publications and source records attributed to Innes, P. A..

3 recordsLinked to original sources

bioRxiv2023

Chromosome-scale Genome Assembly of Lewis Flax (Linum lewisii Pursh.)

The shift from self-incompatibility to self-compatibility is a frequent evolutionary transition in flowering plants with numerous ecological and evolutionary consequences. It is also an advantageous transition for domestication of new crop plants, as self-compatibility makes it considerably easier to drive adaptively important alleles to fixation. In the flax genus, Linum, self-incompatibility is linked to the floral polymorphism known as heterostyly, where plants exhibit distinct floral morphs with different positioning of male and female reproductive organs. Heterostyly has been lost multiple times independently across the flax genus, leading to homostyly and self-compatibility, but the genetic causes of this transition are not fully understood. Here, we present a near telomere-to-telomere genome assembly of "Maple Grove" Lewis flax (Linum lewisii, 2n = 2x = 18), a homostylous wild blue flax species native to North America. By comparison to the genome of close heterostylous relative L. perenne, we found that the coding sequence of heterostyly candidate gene TSS1 is deleted in the Lewis flax genome, which could underlie its transition from heterostyly to homostyly. Analysis of chromosomal synteny between Lewis flax and common flax (L. usitatissimum) further revealed a striking amount of chromosomal rearrangements, which will complicate the use of comparative genomics to accelerate domestication of Lewis flax as a new perennial oilseed crop. The final, primary haplotype was 845 Mb in length and comprised 9 pseudochromosomes and 324 unplaced scaffolds with a contig N50 of 17.9 Mb. Annotation of the assembly revealed 19,593 protein-coding genes. This genomic resource will inform ongoing breeding efforts and will support its use in native ecosystem restoration and in other native plantings across western North America.

genomics↗

bioRxiv2023

Gene expression and alternative splicing contribute to adaptive divergence of ecotypes

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. In plants, the post-transcriptional regulatory mechanism of alternative splicing (AS) plays an important role in both development and abiotic stress response, making it a compelling potential target of natural selection. AS allows organisms to generate multiple different transcripts/proteins from a single gene and thus may provide a source of evolutionary novelty. Here we examine 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 among 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, even when grown in a common environment, 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 both cis and trans-regulation. Together our results emphasize that alternative splicing has been an underappreciated mechanism providing source material for natural selection at micro-evolutionary time scales.

evolutionary biology↗

bioRxiv2022

Genomic description of critical upstream cannabinoid biosynthesis genes

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.

genomics↗