Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States.
Department of Integrative Biology, University of California Berkeley, Berkeley, CA, United States.
J Hered. 2023 Jun 22;114(4):418-427. doi: 10.1093/jhered/esad008.
The California quail (Callipepla californica) is an iconic native bird of scrub and oak woodlands in California and the Baja Peninsula of Mexico. Here, we report a draft reference assembly for the species generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 321 scaffolds totaling 1.08 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 5.5 Mb, scaffold N50 of 19.4 Mb, and BUSCO completeness score of 96.5%. Transposable elements (TEs) occupy 16.5% of the genome, more than previous Odontophoridae quail assemblies but in line with estimates of TE content for recent long-read assemblies of chicken and Peking duck. Together these metrics indicate that the present assembly is more complete than prior reference assemblies generated for Odontophoridae quail. This reference will serve as an essential resource for studies on local adaptation, phylogeography, and conservation genetics in this species of significant biological and recreational interest.
加利福尼亚鹌鹑（Callipepla californica）是加利福尼亚州灌丛和橡树林以及墨西哥下加利福尼亚半岛的标志性本土鸟类。在这里，我们报告了一个由加利福尼亚保护基因组计划（CCGP）的 PacBio HiFi 长读和 Omni-C 染色质接近测序数据生成的物种的草案参考组装。测序reads 被组装成 321 个支架，总长度为 10.8GB。组装指标表明组装具有高度连续和完整的特性，其 contig N50 为 5.5Mb，scaffold N50 为 19.4Mb，BUSCO 完整性得分达到 96.5%。转座元件（TEs）占据基因组的 16.5%，超过了先前的 Odontophoridae 鹌鹑组装，但与最近对鸡和北京鸭的长读组装的 TEs 含量估计相符。这些指标表明，与先前为 Odontophoridae 鹌鹑生成的参考组装相比，本次组装更为完整。该参考资源将为该物种的局部适应、系统地理学和保护遗传学研究提供重要资源，该物种具有重要的生物学和娱乐价值。
