Biology subjects

Swanson, L.

Publications and source records attributed to Swanson, L..

3 recordsLinked to original sources

bioRxiv2025

A haplotype-resolved, chromosome-scale genome assembly and annotation for Carya glabra (pignut hickory; Juglandaceae)

Carya glabra (2n = 4x = 64), also known as pignut hickory, is a widely distributed species in the walnut family (Juglandaceae). Native to the central and eastern United States and southeastern Canada, C. glabra plays an important ecological role as a common upland forest species; it is closely related to several economically valuable nut trees, including C. illinoinensis (pecan). A deeper understanding of the genetics of C. glabra is essential for studying its evolutionary history and biology, with potential implications for agricultural improvement of pecan. Here, we present the first nuclear genome assembly and annotation of C. glabra. The assembly is chromosome-level and phased, representing the first assembled polyploid genome in the genus Carya. A total of 64 pseudochromosomes were assembled and phased into four haplotypes. The haplotype A assembly spans 600.4 Mb, comprises 55.0% repetitive sequences, and contains 30,947 protein-coding genes, with a BUSCO completeness score of 97.7%. Functional annotation assigned 94.3% of haplotype A genes to gene families, and 79.7% and 86.3% of genes were annotated with Gene Ontology terms and protein domains, respectively; 635 putative plant disease resistance genes were found in haplotype A. The other three haplotypes exhibited similarly high-quality annotation metrics. Our genomic analyses also suggest that C. glabra is an autotetraploid. Comparative genomic analyses revealed high collinearity among the four haplotypes of C. glabra and the published genomes of three other Carya species, although structural variation among the genomes of these species was identified. In addition, we provide an improved chloroplast genome assembly and the first mitochondrial genome for C. glabra. Importantly, most members of the research team are undergraduate students; the sequenced individual is located in McCarty Woods, a Conservation Area on the University of Florida campus. This work highlights the value of genome assembly efforts as powerful tools for teaching genomics and supporting conservation initiatives. This first high-quality reference genome for C. glabra provides a valuable resource for studying Carya, a genus of significant ecological and economic importance. Article summaryCarya glabra (pignut hickory) is a common upland forest species in North America. This species is a member of the walnut family (Juglandaceae), which includes many economically important nut trees. Here, we present the first nuclear genome assembly and annotation of C. glabra. The assembly is chromosome-level and phased. The haplotype A assembly contains 30,947 protein-coding genes, with a BUSCO completeness score of 97.7%. Our genomic analyses suggest that C. glabra is an autopolyploid. We also provide chloroplast and mitochondrial genome assemblies. This nuclear genome provides a valuable resource for studying Carya, a genus of significant ecological and economic importance.

genomics↗

bioRxiv2023

Systematic review of residual toxicity studies of pesticides to bees and comparison to language on pesticide labels using data from studies and the Environmental Protection Agency.

BACKGROUNDResidues of pesticides on crops can result in mortality to foraging bees. The likelihood of mortality can be mitigated by applying pesticides in the evening so that their residues dissipate by the following morning when bees resume foraging. The dissipation rates of different pesticides, or their residual toxicity, is captured in a public-facing database compiled by the U.S. Environmental Protection Agency (EPA), but the database includes only a fraction pesticides bees are likely to encounter in the environment. Pesticide applicators in the U.S. encounter a Pollinating Insect Hazard Statement on pesticide labels, which coarsely indicate which products dissipate over the course of an evening. There is reason to suspect that these statements may not align with residual toxicity data, given previous findings of significant misalignment from published data discovered on the acute toxicity section of the Pollinating Insect Hazard Statement. Without a complete database of residual toxicity estimates, however, it is not possible to determine whether the residual toxicity components of the Pollinating Insect Hazard Statement similarly diverge from published studies. RESULTSWe compiled 48 studies and calculated the residual time to 25% mortality (RT25) of each assay for three different bee species (Apis mellifera, Nomia melanderi, and Megachile rotundata). Our findings were compared to the EPA published database of RT25 values. Of the RT25 values that we could compare, we found that over 90% of the values support a similar conclusion to EPA: that the active ingredient has extended residual toxicity (i.e., residues cause greater than 25% mortality for eight hours or more). Next, we compared our values and the EPAs values to the Pollinating Insect Hazard Statement in the Environmental Hazards sections of 155 EPA registered product labels. Of these labels, a little less than a third (27%) presented their residual toxicity in a manner inconsistent with their calculated RT25 and current EPA labeling guidelines. Moreover, over a third (33%) of labels contained an active ingredient which was neither listed under EPAs RT25 database nor had a published study to estimate this value. CONCLUSIONResidual toxicity of pesticides is a key parameter used by pesticide applicators to reduce impacts of their applications to bees. We provide the first evidence that many pesticide labels may convey residual toxicity information to applicators that is not correct and could lead to bees being exposed to toxic residues on plants. We also show large gaps in the availability of contemporary residual toxicity study for many pesticides, suggesting either researchers should conduct studies to estimate RT25 values for these products, or EPA should make data from registrants more readily available. Finally, our analysis identified significant variation found between RT25 values among different bee species tested, and different formulations of the same active ingredient, suggesting these factors should be incorporated into future bee residual toxicity studies.

ecology↗

bioRxiv2017

Guanine-nucleotide Exchange Modulator, GIV/Girdin, Serves as a Tunable Valve for Growth Factor-Stimulated Cyclic AMP Signals

Cellular levels of the versatile second messenger, cyclic-(c)AMP are regulated by the antagonistic actions of the canonical G protein[->]adenylyl cyclase pathway that is initiated by G-protein-coupled receptors (GPCRs) and by phosphodiesterases (PDEs); dysregulated cAMP signaling drives many diseases, including cancers. Recently, an alternative paradigm for cAMP signaling has emerged, in which growth factor-receptor tyrosine kinases (RTKs; e.g., EGFR) access and modulate G proteins via cytosolic guanine-nucleotide exchange modulator (GEM), GIV/Girdin; dysregulation of this pathway is frequently encountered in cancers. Here we present a comprehensive network-based compartmental model for the paradigm of GEM-dependent signaling that reveals unforeseen crosstalk and network dynamics between upstream events and the various feedback-loops that fine-tune the GEM action of GIV, and captures the experimentally determined dynamics of cAMP. The model also reveals that GIV acts a tunable control-valve within the RTK[->]cAMP pathway; hence, it modulates cAMP via mechanisms distinct from the two most-often targeted classes of cAMP modulators, GPCRs and PDEs.

systems biology↗