A highly contiguous genome assembly for the California quail (Callipepla californica).
A highly contiguous genome assembly for the California quail (Callipepla californica).
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DOI：
10.1093/jhered/esad008
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发表时间：
2023-06-22
期刊：
影响因子：
--
通讯作者：
Bowie RCK
中科院分区：
文献类型：
--
作者：
Benham PM;Cicero C;Escalona M;Beraut E;Marimuthu MPA;Nguyen O;Nachman MW;Bowie RCK
加州鹌鹑（Callipepla californica）是加州和墨西哥下半岛灌木丛和橡树林地的标志性原生鸟类。在这里，我们报告了从PacBio HiFi长读取和Omni-C染色质邻近测序数据生成的物种的参考组装草案，作为加州保护基因组学项目（CCGP）的一部分。将测序的读数组装到总共1.08Gb长度的321个支架中。组装度量表明高度连续和完整的组装，重叠群N50为5.5 Mb，支架N50为19.4 Mb，BUSCO完整性评分为96.5%。转座因子（TE）占基因组的16.5%，比以前的Odontophoridae鹌鹑组件，但在最近的长读组装的鸡和北京鸭TE含量的估计。这些指标一起表明，本组装比先前的参考组装产生的齿科鹌鹑更完整。这参考将作为一个重要的资源，对当地的适应性，生态地理学和保护遗传学的研究，在这个物种的重要生物和娱乐的兴趣。
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.
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影响因子：
46.9
作者：
Cheng, Haoyu;Jarvis, Erich D.;Fedrigo, Olivier;Koepfli, Klaus-Peter;Urban, Lara;Gemmell, Neil J.;Li, Heng
通讯作者：
Li, Heng
鸟类多样性的密集采样增强了比较基因组学的力量
影响因子：
64.8
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通讯作者：
Zhang G
影响因子：
2.6
作者：
Challis, Richard;Richards, Edward;Blaxter, Mark
通讯作者：
Blaxter, Mark
影响因子：
9.2
作者：
Korlach J;Gedman G;Kingan SB;Chin CS;Howard JT;Audet JN;Cantin L;Jarvis ED
通讯作者：
Jarvis ED
影响因子：
5.8
作者：
Guan, Dengfeng;McCarthy, Shane A.;Durbin, Richard
通讯作者：
Durbin, Richard