Aphelocoma coerulescens Genome sequencing

This project contains two versions of Aphelocoma coerulescens (Florida Scrub-Jay) genome assemblies: V. 2 (male) and V. 3 (female). V. 2 improves on V. 1 (GenBank assembly accession: GCA_013398375.1) via additional scaffolding with Hi-C data (HiRise pipeline from Dovetail Genomics) and confirmation with a preliminary framework linkage map (CRIMAP 2.507, Chromonomer v. 1.13, Juicer v. 1.5.6). RNA-seq data from liver, heart, kidney, and ovary tissues from one male and one female individual were used to generate the transcriptome and annotate genes. V. 2 was generated as part of a study examining short-term changes in allele frequencies in a pedigreed population of Florida Scrub-Jays as a result of sex-biased demography.V. 3 of the genome was sequenced with long-read technology (PacBio HiFi) and scaffolded with both Hi-C reads (Arima Genomics mapping pipeline, SALAS v. 2.3, Juicer v. 1.6) and the linkage map (ALLMAPS v. 1.3.7) described for V. 2. This genome was also annotated with the same RNA-seq dataset as V. 2. V. 3 was generated with the goal of creating a high quality, chromosome-level genome assembly of a female Florida Scrub-Jay for future studies. Please direct any questions about this project to Faye Romero ([e-mail]) or Nancy Chen ([e-mail]).