Corneous beta-proteins (CBPs; historically known as beta-keratins) are major structural proteins of sauropsid epidermal appendages, including feathers, claws, and scales, yet CBP gene nomenclature and annotation remain inconsistent across genome assemblies and species. Using modern broiler and layer chicken reference genomes, we identified 271 protein-coding CBP genes. Comparative analyses revealed substantial variation among CBP groups in gene redundancy, annotation concordance, and protein sequence diversity. These differences were particularly pronounced in feather-associated CBP loci, including a chromosome 27 region exhibiting reduced local synteny and extensive assembly-specific gene annotations. Despite these challenges, phylogenetic analyses consistently resolved eight major CBP families and supported development of a standardized phylogeny-informed nomenclature system. Application of this framework to turkey and zebra finch demonstrated that phylogeny-informed classification can be extended across birds and avoids problems associated with expression- and morphology-based naming systems, which are used inconsistently across species. In the genomic regions examined, chicken-derived gene names could be assigned to 67 of 78 (87.2%) turkey CBPs and 34 of 40 (85.0%) zebra finch CBPs. Together, these findings establish a phylogeny-informed nomenclature for chicken CBP genes and demonstrate its applicability across avian species, providing a foundation for consistent gene naming and comparative studies of CBP evolution in birds.
Advances and accessibility to next-generation technology provide opportunities to sequence non-model organisms. Despite this increase in whole-genome sequencing data, annotation and the production of reference genomes remain limited. Reference genomes are a critical tool for a variety of studies in evolutionary biology, functional genomics, and conservation genetics. Tiger beetles (Carabidae, Cicindelinae) are a diverse and globally distributed subfamily of beetles that serve as bioindicator taxa and flagship species for insect conservation. Here, we report highly complete (average BUSCO % C: ∼95.95%), contiguous (average N50: 15.33 Mbp; average L50: 23.75), and annotated genome assemblies (average OrthoDB AA annotation completeness: 94%) representing draft reference genomes for three species of tiger beetle spanning the phylogeny. These draft reference genomes are for Audouin’s night-stalking tiger beetle, Omus audouini (k-mer genome size estimate: 938 Megabases (Mb)); the montane giant tiger beetle, Amblycheila baroni (k-mer genome size estimate: 1086 Mb); and the western red-bellied tiger beetle, Cicindelidia sedecimpunctata (k-mer genome size estimate: 819 Mb). These annotated reference genomes will address important resource gaps and support future tiger beetle research endeavors.
Abstract Ubiquitination is a highly regulated post-translational modification that controls protein stability, activity, localization, and interactions, and its disruption process contributes to a broad range of human diseases, including cancer, neurodegeneration, and immune dysfunction. The genetic model organism Drosophila melanogaster offers powerful in vivo tools for studying ubiquitination, including the GAL4/UAS, Split-GAL4, GeneSwitch, and MARCM system, which can be combined with imaging and biochemical approaches to achieve precise spatial and temporal analyses. Realizing this potential, however, requires epitope-tagged UAS-Ubiquitin transgenes—both unmodified and chain-restricted—that behave like endogenous ubiquitin. Here we report a screen to generate and validate such a panel. We first defined the endogenous ubiquitination pattern at larval neuromuscular junctions (NMJs) as a bench mark, then compared it with a series of transgenically expressed, tagged ubiquitin in muscle and neurons. His-Myc-, HA-, and His-Biotin-tagged ubiquitins reproduced endogenous postsynaptic ubiquitination pattern and, by anti-tag immunoprecipitation followed by anti-ubiquitin immunoblotting, were shown to be covalently incorporated into ubiquitin conjugates in vivo. In contrast, a larger NTAP-tagged ubiquitin failed to conjugate at the postsynaptic density. Expression of the validated transgenes did not alter NMJ bouton number. We describe the practical uses of the validated transgenes for tissue-specific imaging and affinity purification, together with their limitations, to help investigators select appropriate tools for studying ubiquitination across diverse cellular and developmental contexts.
Abstract In Scots pine (Pinus sylvestris L.), long generation intervals limit genetic gain, but mature progeny trials may provide reference populations for genomic selection. We combined repeated phenotypes from two German trials established in 1990 with single-nucleotide polymorphism (SNP) genotypes, parentage auditing, duplicate filtering, and empirically calibrated forward simulations. Of 1,986 phenotype-matched genotyped trees, 1,651 remained after quality control. Across 14 trait-by-age combinations, genomic best linear unbiased prediction (GBLUP) gave modest but consistent improvements in predictive ability for diameter and volume from age 20 onwards. For volume at age 20 (V20), repeated leave-progeny-out predictive ability increased from 0.233 with pedigree-based additive best linear unbiased prediction (ABLUP) to 0.268 with GBLUP, and GBLUP exceeded ABLUP in all 20 matched partitions. Paired jackknife intervals did not establish systematic differences in narrow-sense heritability. ABLUP and GBLUP rankings were highly correlated, but only 75.9% of the top 10% V20 candidates overlapped. Simulations calibrated to empirical V20 variance components and family relationships compared phenotypic selection, ABLUP, progeny testing, direct genomic selection, and genomic selection followed by phenotypic thinning. After five cycles, progeny testing produced the greatest cumulative additive genetic gain (163.3%), whereas direct genomic selection produced the greatest annual gain (1.208% yr−1) because of shorter cycles. Faster genomic pathways accumulated more kinship, and a kinship-aware penalty reduced relatedness with pathway-specific effects on gain. These results support staged genomic implementation with continual reference-population updating, field validation, and explicit coancestry management.
Abstract Canine inherited ocular diseases exhibit significant genetic heterogeneity, mirroring many human ophthalmic conditions. This study conducted an extensive screening of 90 OMIA-listed disease-associated variants across 192 affected dogs from 71 breeds to evaluate diagnostic utility and identify novel disease models. This screening identified previously reported variants in 35% of cases, while most cases remained unexplained, prompting whole-genome sequencing of a variant-negative case. This led to the identification of a novel candidate duplication c.442dupC in the X-linked Retinoschisin 1 (RS1) gene, located in the conserved discoidin domain of RS1. If validated, this variant may establish the first spontaneous canine model for human X-linked retinoschisis that may provide a new model for studying pathogenesis and therapeutic approaches. Our analysis also supported the expansion of the known breed distributions for several variants, including progressive retinal atrophy (PRA) variant IFT122 c.3176G>A in Finnish Lapphunds, PRA variant PDE6A c.1847del in Pomeranians, glaucoma variant ADAMTS10 c.1981G>A in East Siberian Laikas, and microphthalmia variant RBP4 c.90_92del in Jack Russell Terriers. The RPGRIP1 c.142_143ins[A[29]; GGAAGCAACAGGATG] PRA variant was observed in four new breeds; however, the reported phenotype was not sufficient to confirm the causative nature. Additionally, our data reclassified the JPH2 c.452A>C PRA variant as a common, benign polymorphism rather than a causal variant in Shih Tzus, emphasizing the need for large-scale genomic validation of published markers. Collectively, these results illustrate the extensive genetic heterogeneity underlying canine eye diseases and underscore the potential for identifying novel preclinical models that advance both veterinary medicine and human vision research.
