Reprint of: Sequencing and assembling the genome of Przewalski's horse in the classroom

IF 1.3 3区 农林科学 Q2 VETERINARY SCIENCES
Christopher Faulk
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引用次数: 0

Abstract

Sequencing a genome by students has now become practical as we demonstrated with our recent publication of the Przewalski's horse (Equus ferus przewalskii) genome. In this review, I describe my experience teaching genome assembly in the classroom. In my course, students sequenced, assembled, and published a high-quality genome for Przewalski's horse using Oxford Nanopore long-read sequencing with only $4000 of materials. Along with the genome, we assembled the mitochondrial genome, sequence variants, predicted gene annotations, and DNA methylation levels. Our genome statistics far exceeded the previous Przewalski's horse assembly and is on par the domestic horse genome, EquCab3.0. Methods were streamlined, simplified, and conveyed in markdown for complete recording and use in the classroom. All students were authors on the resulting manuscript. By bringing genome assembly into the classroom, we provide both new reference genomes and new genomics expertise to the scientific community at the same time.
转载:在课堂上对普氏野马的基因组进行测序和组装
通过我们最近发表的普氏野马(Equus ferus Przewalski)基因组,我们可以证明,由学生进行基因组测序现在已经变得可行。在这篇综述中,我描述了我在课堂上教授基因组组装的经验。在我的课程中,学生们对普氏野马的基因组进行了测序、组装并发表了高质量的基因组,使用的是牛津纳米孔长读测序技术,所用材料仅为4000美元。除了基因组,我们还组装了线粒体基因组、序列变异、预测基因注释和DNA甲基化水平。我们的基因组统计数据远远超过了之前的普氏野马组合,与国产马基因组EquCab3.0相当。方法精简,简化,并在markdown传达完整的记录和在课堂上使用。所有学生都是最终手稿的作者。通过将基因组组装带入课堂,我们同时为科学界提供了新的参考基因组和新的基因组学专业知识。
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来源期刊
Journal of Equine Veterinary Science
Journal of Equine Veterinary Science 农林科学-兽医学
CiteScore
2.70
自引率
7.70%
发文量
249
审稿时长
77 days
期刊介绍: Journal of Equine Veterinary Science (JEVS) is an international publication designed for the practicing equine veterinarian, equine researcher, and other equine health care specialist. Published monthly, each issue of JEVS includes original research, reviews, case reports, short communications, and clinical techniques from leaders in the equine veterinary field, covering such topics as laminitis, reproduction, infectious disease, parasitology, behavior, podology, internal medicine, surgery and nutrition.
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