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 Carya 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 4 haplotypes. The haplotype A assembly spans 600.4 Mb, comprises 55.0% repetitive sequences, and contains 30,947 protein-coding genes, with a Benchmarking Universal Single-Copy Orthologs (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 3 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 4 haplotypes of C. glabra and the published genomes of 3 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. We also provide a phylogenomic tree for Carya based on numerous nuclear genes, showing that C. glabra forms a clade with other North American tetraploid species. 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.