A new high-quality genome assembly and annotation for the threatened Florida Scrub-Jay (Aphelocoma coerulescens).

IF 2.1 3区生物学 Q3 GENETICS & HEREDITY G3: Genes|Genomes|Genetics Pub Date : 2024-09-27 DOI:10.1093/g3journal/jkae232

Faye G Romero, Felix E G Beaudry, Eyvind Hovmand Warner, Tram N Nguyen, John W Fitzpatrick, Nancy Chen

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Abstract

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.

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为濒危的佛罗里达鸦雀（Aphelocoma coerulescens）进行新的高质量基因组组装和注释。

佛罗里达灌丛鸦雀（Aphelocoma coerulescens）是一种受联邦威胁的合作繁殖鸟类，是进化生物学和生态学的新兴模型系统。几十年来，基于个体的广泛监测和遗传采样已经产生了大量数据，从而可以对这一自然种群的社会行为、人口统计学和种群遗传学进行详细研究。在此，我们报告了利用长线程测序技术、染色质构象数据和连接图绘制的雌性佛罗里达恙螨的连接图和染色体水平的基因组组装与注释。我们构建了一个由 4468 个 SNPs 组成的连锁图谱，其中有 34 个连锁群，性别平均常染色体遗传图谱总长度为 2446.78 cM。新的基因组装配长度为 1.33 Gb，由 33 条完整或接近完整的常染色体和性染色体（ZW）组成。这个高度连续的组装体的 NG50 为 68 Mb，与 Aves 数据库相比，Benchmarking Universal Single-Copy Orthologs (BUSCO) 的完整性得分为 97.1%。注释基因集的 BUSCO 转录组完整性得分为 95.5%，鉴定出 17,964 个蛋白编码基因，其中 92.5%有相关的功能注释。这一新的、高质量的佛罗里达灌丛松鸦基因组组装和连接图为未来研究受保护的小型自然种群的进化动态提供了宝贵的工具。

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来源期刊

G3: Genes|Genomes|Genetics GENETICS & HEREDITY-

CiteScore

5.10

自引率

3.80%

发文量

305

审稿时长

3-8 weeks

期刊介绍： G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights. G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.