Scrub-Jay (Aphelocoma) Pangenome Project

The Scrub-Jay pangenome project is a study comparing three species of North American Scrub-Jays - Florida (Aphelocoma coerulescens), Island (A. insularis) and Woodhouse's (A. woodhouseii) - to understand the abundance, distribution and fitness effects structural variation. The study sequenced 44 individual Scrub-Jays, one outgroup species (Yucatan Jay, Cyanocorax yucatanicus) and two additional Florida birds (total = 47 individuals) to high coverage with PacBio HiFi technology. We then used pangenome tools, including PGGB, minigraph and others to characterize the landscape of structural variants, leveraging the drastic differences in effective population size among the three species to understand the selective forces influencing structural variant diversity and distribution. The data set was also useful for understanding the landscape of repetitive elements, including satellite DNA, and telomere variation among individuals. A variety of statistical and bioinformatics tools were used to characterize copy number variants of genes, as well as inversions and chromosomal fissions. Gene expression data from multiple tissues was collected for the 15 A. woodhouseii birds, and whole blood transcriptomes were generated from the 14 A. coerulescens individuals. The data from A. woodhouseii individuals is linked to voucher specimens in the Museum of Comparative Zoology, Harvard University.