Romero Faye G, Beaudry Felix E G, Hovmand Warner Eyvind, Nguyen Tram N, Fitzpatrick John W, Chen Nancy
Department of Biology, University of Rochester, Rochester, NY 14620, USA.
Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
G3 (Bethesda). 2024 Sep 27;14(12). doi: 10.1093/g3journal/jkae232.
The Florida Scrub-Jay (Aphelocoma coerulescens), a Federally Threatened, cooperatively-breeding bird, is an emerging model system in evolutionary biology and ecology. Extensive individual-based monitoring and genetic sampling for decades has yielded a wealth of data, allowing for the detailed study of social behavior, demography, and population genetics of this natural population. Here, we report a linkage map and a chromosome-level genome assembly and annotation for a female Florida Scrub-Jay made with long-read sequencing technology, chromatin conformation data, and the linkage map. We constructed a linkage map comprising 4,468 SNPs that had 34 linkage groups and a total sex-averaged autosomal genetic map length of 2446.78 cM. The new genome assembly is 1.33 Gb in length, consisting of 33 complete or near-complete autosomes and the sex chromosomes (ZW). This highly contiguous assembly has an NG50 of 68 Mb and a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 97.1% with respect to the Aves database. The annotated gene set has a BUSCO transcriptome completeness score of 95.5% and 17,964 identified protein-coding genes, 92.5% of which have associated functional annotations. This new, high-quality genome assembly and linkage map of the Florida Scrub-Jay provides valuable tools for future research into the evolutionary dynamics of small, natural populations of conservation concern.
佛罗里达灌丛鸦（Aphelocoma coerulescens）是一种受到联邦政府威胁的合作繁殖鸟类，是进化生物学和生态学中一个新兴的模型系统。几十年来广泛的基于个体的监测和基因采样产生了大量数据，使得对这个自然种群的社会行为、种群统计学和种群遗传学进行详细研究成为可能。在此，我们报告了一张连锁图谱以及一个基于长读长测序技术、染色质构象数据和连锁图谱构建的雌性佛罗里达灌丛鸦的染色体水平基因组组装和注释。我们构建了一张包含4468个单核苷酸多态性（SNP）的连锁图谱，该图谱有34个连锁群，性平均常染色体遗传图谱总长度为2446.78厘摩（cM）。新的基因组组装长度为1.33千兆碱基（Gb），由33条完整或近乎完整的常染色体以及性染色体（ZW）组成。这个高度连续的组装体的N50为68兆碱基（Mb），相对于鸟类数据库，基准通用单拷贝直系同源基因（BUSCO）完整性得分97.1%。注释的基因集的BUSCO转录组完整性得分95.5%，共鉴定出17964个蛋白质编码基因，其中92.5%具有相关的功能注释。佛罗里达灌丛鸦这个新的、高质量的基因组组装和连锁图谱为未来研究具有保护意义的小型自然种群的进化动态提供了有价值的工具。
