Biology subjects

Kauwe, A. N.

Publications and source records attributed to Kauwe, A. N..

4 recordsLinked to original sources

bioRxiv2026

Chromosome-level genome assembly of the Olympia oyster (Ostrea lurida), the only oyster species native to the West Coast of North America

The Olympia oyster (Ostrea lurida) was once a major food source and a key component of coastal marine ecosystems and culture on the US West Coast. Overfishing and habitat contamination in the early to mid-20th century severely depleted populations of Olympia oysters, and the species is currently considered a species of concern. Although multiple restoration efforts are underway, progress understanding the species biology and recovery potential has been limited by the historical lack of genomic resources. Here, we report a chromosome-level assembly of the Olympia oyster. The assembly was built using Oxford Nanopore reads and Hi-C to obtain a highly contiguous 1.03 Gb-assembly consisting of 10 chromosomes. RNA from gills, mantle, adductor muscle, and a mix of brooding eggs and larvae were also sequenced as 150 nt long paired-end reads which were used to guide the genome annotation. Over 52 K genes were predicted in the genome, of which 34K were protein-coding. A BUSCO analysis on the assembly showed 98.9% of the mollusca_odb12 gene set were complete (with 2.1% duplicated, and 0.8% missing). The short RNA reads were also used to identify tissue-level gene expression signatures in adductor muscles, egg and brooding larvae, and mantle. Development-related genes were highly expressed in eggs and brooding larvae whereas many xenobiotic metabolism genes were present in mantle tissues, highlighting mantles role in the interaction of the oyster with external environments. This new genomic resource will greatly advance our understanding of this keystone mollusk and provide a critical tool for guiding restoration efforts and the development of sustainable commercial production.

genomics↗

bioRxiv2026

Chromosome-level genome assembly of the Erythrina Gall Wasp, Quadrastichus erythrinae (Hymenoptera: Eulophidae)

The erythrina gall wasp, Quadrastichus erythrinae, is an invasive gall-inducing chalcidoid wasp and a major pest of the endemic wiliwili tree (Erythrina sandwicensis) in Hawai{square}i. As a foundation to associated research, we generated a chromosome-level genome assembly from a wild-collected female measuring <2 mm. The final assembly consists of five scaffolds representing the five autosomes totaling 399 Mb (N50 = 75.6 Mb) and one unplaced 16 kb contig. BUSCO analysis recovers 91.1% of conserved Hymenoptera orthologs, representing the first chromosome-scale genome for the genus Quadrastichus. Comparative genomic analyses reveal syntenic conservation across Hymenoptera despite deep evolutionary divergence, with strongest collinearity to the chalcidoid Nasonia vitripennis. Genome size variation is largely explained by repeat content, and Q. erythrinae exhibits high proportions of unclassified transposable elements similar to the cynipid gall inducer. We also assembled a complete genome of its endosymbiont, Wolbachia pipientis. Together, these genomic resources provide a foundation for comparative, evolutionary, and applied research aimed at managing this invasive pest.

genomics↗

bioRxiv2024

The genetic basis of the black pupae phenotype in tephritid fruit flies

The remarkable diversity of insect pigmentation offers a captivating avenue for exploring evolution and genetics. In tephritid fruit flies, decoding the molecular pathways underlying pigmentation traits also plays a central role in applied entomology. Mutant phenotypes like the black pupae (bp) have long been used as a component of genetic sexing strains, allowing male-only release in tephritid sterile insect technique applications. However, the genetic basis of bp remains largely unknown. Here, we present independent evidence from classical and modern genetics showing that the bp phenotype in the GUA10 strain of the Mexican fruit fly, Anastrepha ludens, is caused by a large deletion at the ebony locus resulting in the removal of the entire protein-coding region of the gene. Targeted knockout of ebony induced analogous bp phenotypes across six tephritid species spanning over 50 million years of divergent evolution. This functionally validated our findings and allowed for a deeper investigation into the role of Ebony in pigmentation and development in these species. Our study offers fundamental knowledge for developing new sexing strains based on the bp marker and for future evolutionary developmental biology studies in tephritid fruit flies.

genomics↗

bioRxiv2023

Chromosome-scale Genome Assembly of the West Indian Fruit Fly Anastrepha obliqua (Diptera: Tephritidae)

The West Indian fruit fly, Anastrepha obliqua, is a major pest of mango in Central and South America and attacks more than 60 species of host fruits. To support current genetic and genomic research on A. obliqua, we sequenced the genome using high-fidelity (HiFi) long-read sequencing. This resulted in a highly contiguous contig assembly with 90% of the genome in 10 contigs. The contig assembly was placed in a chromosomal context using synteny with a closely related species, A. ludens, as both are members of the A. fraterculus group. The resulting assembly represents the five autosomes and the X chromosome which represents 95.9% of the genome, and 199 unplaced contigs representing the remaining 4.1%. Orthology analysis across the structural annotation sets of high quality tephritid genomes demonstrates the gene annotations are robust, and identified genes unique to Anastrepha species that may help define their pestiferous nature that can be used as a starting point for comparative genomics. This genome assembly represents the first of this species and will serve as a foundation for future genetic and genomic research in support of its management as an agricultural pest.

genomics↗