Biology subjects

Willis, S. C.

Publications and source records attributed to Willis, S. C..

3 recordsLinked to original sources

bioRxiv2025

Genome assembly and diagnostic DNA markers for sex of the largest freshwater fish in North America, the white sturgeon (Acipenser transmontanus).

Sturgeon and paddlefish represent some of the most early diverging branches of ray-finned fishes and have undergone at least one global and several lineage-specific whole genome duplication events. White sturgeon (Acipenser transmontanus), the largest freshwater fish in North America, have experienced at least two rounds of whole genome duplication, and may exhibit both di- and multi-valent meiotic segregation. Moreover, they exhibit contemporary ploidy variants due to spontaneous autopolyploidy, particularly in aquaculture. Nonetheless, as a species with several population segments that exhibit chronic recruitment failure, conservation aquaculture is an important part of their management. To facilitate the development of genetic tools to aid white sturgeon conservation, as well as a basis to understand how ploidy changes and variation historically and contemporarily shape the evolution of this species, we present a genome assembly for a white sturgeon from the Snake River, Idaho, USA. Analysis of sequence data used for assembly indicated a haploid genome size of approximately 1.5Gbp, implying tetraploidy (4N), while analysis of heterozygous k-mers from 21 to 41 bp suggest the genome reflects both 4N and 8N variants. The final genome assembly, scaffolded using linkage maps constructed from Fraser River and Snake River F1 families, contained 6.26Gbp in 832,145 scaffolds, consistent with published genome size estimates. Conserved ortholog completeness for this genome (90.5%; 22.8% single-copy and 67.7% duplicated) was similar to the putatively diploid sterlet sturgeon, and the largest linkage map-based scaffold was 55.2Gbp, though the N50 for this assembly was only 416Kbp, indicating the assembly remains fragmented. We demonstrate the utility of this assembly by identifying genomic regions significantly associated with sex. Genetic markers, designed for inclusion in an amplicon genotyping panel, predicted sex 96.6% and 81.5% correctly in females and males, respectively, providing a strong overall association ({square}2 p-value < 2.7x10-37) with some variation by geographic region. Article summaryFunctional polysomes (more than two chromosomes that pair in meiosis) are rare among vertebrates. White sturgeon, the largest freshwater fish in North America, are tetraploid and occasionally hexaploid. Several populations of this species are stagnant or declining, requiring aquaculture to bolster reproduction. We analyzed whole genomic data and assembled the genome of an individual from the unique Snake River, Idaho, population. Results indicate most genetic variants are consistent with tetraploidy, and the genome assembly, while fragmented, is largely complete. We demonstrate its utility by designing genetic markers for sex for use in conservation and commercial aquaculture.

genomics↗

bioRxiv2020

Inference of ploidy by leveraging read depth from amplicon sequencing

Variation in ploidy occurs naturally in select plant and animal species. Ploidy variation can also occur spontaneously or be induced during artificial propagation of fish and shellfish. Studying species and systems that have variable ploidy requires techniques to infer ploidy of individuals. Massively parallel sequencing of biallelic SNPs has been used to infer ploidy, but existing techniques have several drawbacks. These include being limited to only comparing a fixed number of ploidies (diploidy, triploidy, and tetraploidy) and requiring that heterozygous genotypes in an individual be identified prior to ploidy inference. We describe a method of inferring ploidy from sequencing of biallelic SNPs based on beta-binomial mixture models. This method is generalized to apply to any ploidy and does not require prior identification of heterozygous genotypes. We demonstrate efficacy of this method for comparing ancestral octoploidy, decaploidy, and dodecaploidy (tetraploidy, pentaploidy, and hexaploidy for the sequenced SNPs) in white sturgeon and diploidy and triploidy in Chinook salmon with amplicon sequencing (GT-seq) data. Results indicated that ploidy could be reliably estimated for individuals based on distinct distribution of log-likelihood ratios (LLR) for known ploidy samples of both species that were tested. Confidence in ploidy estimates increased with sequencing depth. We encourage users to explore the sequencing depths and LLR critical values that provide reliable estimates of ploidy for a given organism and set of SNPs. We expect that the R package provided will empower studies of genetic variation and inheritance in organisms that vary in ploidy naturally or as a result of artificial propagation practices.

bioinformatics↗

bioRxiv2018

Osmoregulation in freshwaters: Gene expression in the gills of a Neotropical cichlid in contrasting pH and ionic environments

Freshwater habitats of the Neotropics exhibit a gradient from relatively neutral, ion-rich whitewater to acidic, ion-poor blackwater. Closely related species often show complementary distributions among ionic habitats, suggesting that adaptation to divergent osmoregulatory environments may be an important driver of Neotropical fish diversity. However, little is known about the evolutionary tradeoffs involved in ionoregulation across distinct freshwater environments. Here, we surveyed gill mRNA expression of Cichla ocellaris var. monoculus, a Neotropical cichlid, to examine cellular and physiological responses to experimental conditions mimicking whitewater and blackwater.\n\nGene ontology enrichment of expressed genes indicated that the gills were remodeled during both forms of environmental challenge, with changes biased towards the cellular membrane. We observed expression of signaling pathways from both the acute and extended response phases, including evidence that growth hormone (GH) may mediate osmoregulation in whitewater through paracrine expression of insulin-like growth factor I (IGF-I), but not through the GH receptor, which instead showed correlated up-regulation with the prolactin receptor and insulin-like growth factor II in blackwater.\n\nDifferential expression of genes related to paracellular tight junctions and transcellular ion transport showed responses similar to euryhaline fishes in fresh versus seawater, with some exceptions, suggesting that relaxed ion retention via the gills, possibly mediated by the GH/IGF-I axis, is a strong candidate for evolutionary modification in whitewater and blackwater endemic populations. In each osmoregulatory domain, we saw examples of contrasting differential expression of paralogs of genes that are single copy in most terrestrial vertebrates, indicating that adaption by fishes to diverse physicochemcial environments has capitalized on diversification of osmoregulatory gene families.

ecology↗