全基因组测序的未映射短读序列表明德国黑皮安格斯牛中存在潜在的传染性病原体。
Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in german black Pied cattle.
机构信息
Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.
Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany.
出版信息
Vet Res. 2023 Oct 18;54(1):95. doi: 10.1186/s13567-023-01227-0.
Abstract
When resequencing animal genomes, some short reads cannot be mapped to the reference genome and are usually discarded. In this study, unmapped reads from 302 German Black Pied cattle were analyzed to identify potential pathogenic DNA. These unmapped reads were assembled and blasted against NCBI's database to identify bacterial and viral sequences. The results provided evidence for the presence of pathogens. We found sequences of Bovine parvovirus 3 and Mycoplasma species. These findings emphasize the information content of unmapped reads for gaining insight into bacterial and viral infections, which is important for veterinarians and epidemiologists.
摘要
当对动物基因组进行重测序时，一些短读段无法映射到参考基因组，通常会被丢弃。在这项研究中，分析了 302 头德国黑皮牛的未映射读段，以鉴定潜在的致病 DNA。这些未映射的读段被组装并与 NCBI 的数据库进行比对，以鉴定细菌和病毒序列。结果提供了病原体存在的证据。我们发现了牛细小病毒 3 和支原体属的序列。这些发现强调了未映射读段对于了解细菌和病毒感染的信息含量，这对兽医和流行病学家很重要。
相似文献
1
Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in german black Pied cattle.全基因组测序的未映射短读序列表明德国黑皮安格斯牛中存在潜在的传染性病原体。
Vet Res. 2023 Oct 18;54(1):95. doi: 10.1186/s13567-023-01227-0.
2
Unmapped reads from cattle RNAseq data: A source for missing and misassembled sequences in the reference assemblies and for detection of pathogens in the host.来自牛RNA测序数据的未映射 reads：参考基因组组装中缺失和错误组装序列的来源以及宿主中病原体检测的来源。
Genomics. 2017 Jan;109(1):36-42. doi: 10.1016/j.ygeno.2016.11.009. Epub 2016 Nov 29.
3
Exploring the unmapped DNA and RNA reads in a songbird genome.探索鸣禽基因组中的未映射 DNA 和 RNA 读数。
BMC Genomics. 2019 Jan 8;20(1):19. doi: 10.1186/s12864-018-5378-2.
4
What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual.你的下一代测序数据中有什么？对来自牛参考个体的未映射DNA和RNA序列读数的探索。
BMC Genomics. 2015 Dec 29;16:1114. doi: 10.1186/s12864-015-2313-7.
5
Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing.基于全基因组测序的濒危德国黑 pied 牛（DSN）与其他 68 个牛品种的基因组多样性及亲缘关系分析。
Front Genet. 2023 Jan 4;13:993959. doi: 10.3389/fgene.2022.993959. eCollection 2022.
6
Another lesson from unmapped reads: in-depth analysis of RNA-Seq reads from various horse tissues.另一个来自未映射reads 的教训：对来自不同马组织的 RNA-Seq reads 的深度分析。
J Appl Genet. 2022 Sep;63(3):571-581. doi: 10.1007/s13353-022-00705-z. Epub 2022 Jun 7.
7
From trash to treasure: detecting unexpected contamination in unmapped NGS data.从垃圾到宝藏：检测未映射 NGS 数据中的意外污染。
BMC Bioinformatics. 2019 Apr 18;20(Suppl 4):168. doi: 10.1186/s12859-019-2684-x.
8
The Genomic Scrapheap Challenge; Extracting Relevant Data from Unmapped Whole Genome Sequencing Reads, Including Strain Specific Genomic Segments, in Rats.基因组垃圾堆挑战：从大鼠未映射的全基因组测序读数（包括菌株特异性基因组片段）中提取相关数据
PLoS One. 2016 Aug 8;11(8):e0160036. doi: 10.1371/journal.pone.0160036. eCollection 2016.
9
DNA Sequence Variants and Protein Haplotypes of Casein Genes in German Black Pied Cattle (DSN).德国黑 pied 牛（DSN）中酪蛋白基因的 DNA 序列变异和蛋白质单倍型
Front Genet. 2019 Nov 8;10:1129. doi: 10.3389/fgene.2019.01129. eCollection 2019.
10
Detection of viral pathogens in high grade gliomas from unmapped next-generation sequencing data.从无图谱的下一代测序数据中检测高级别神经胶质瘤中的病毒病原体。
Exp Mol Pathol. 2014 Jun;96(3):310-5. doi: 10.1016/j.yexmp.2014.03.010. Epub 2014 Apr 1.
引用本文的文献
1
Advantages of Mutant Generation by Genome Rearrangements of Non-Conventional Yeast via Direct Nuclease Transfection.通过直接核酸酶转染对非常规酵母进行基因组重排产生突变体的优势。
Genes Cells. 2025 Mar;30(2):e70010. doi: 10.1111/gtc.70010.
本文引用的文献
1
The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species.牛泛基因组联盟：为全球牛品种和其他牛种的基因组组装提供民主化的生产和获取途径。
Genome Biol. 2023 Jun 19;24(1):139. doi: 10.1186/s13059-023-02975-0.
2
In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants.从长远考虑：利用长读测序技术在畜牧业中进行结构变异的群体规模研究的观点。
Genet Sel Evol. 2023 Jan 31;55(1):9. doi: 10.1186/s12711-023-00783-5.
3
Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing.基于全基因组测序的濒危德国黑 pied 牛（DSN）与其他 68 个牛品种的基因组多样性及亲缘关系分析。
Front Genet. 2023 Jan 4;13:993959. doi: 10.3389/fgene.2022.993959. eCollection 2022.
4
Apparent prevalence of , and bovine leukemia virus in Wisconsin and Michigan dairy cattle herds.威斯康星州和密歇根州奶牛群中 以及牛白血病病毒的表观流行率。
（注：原文中“Apparent prevalence of ”后面似乎缺失了具体内容）
JDS Commun. 2021 Jan 22;2(2):61-66. doi: 10.3168/jdsc.2020-0033. eCollection 2021 Mar.
5
Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history.组装全球牛的泛基因组揭示了缺失的序列和新的结构变异，为它们的多样性和进化历史提供了新的见解。
Genome Res. 2022 Aug 25;32(8):1585-1601. doi: 10.1101/gr.276550.122.
6
Metagenomic analysis reveals presence of different animal viruses in commercial fetal bovine serum and trypsin.元基因组分析揭示了商业胎牛血清和胰蛋白酶中存在不同的动物病毒。
Zool Res. 2022 Sep 18;43(5):756-766. doi: 10.24272/j.issn.2095-8137.2022.093.
7
Mastitis.乳腺炎
Curr Res Microb Sci. 2022 Feb 24;3:100123. doi: 10.1016/j.crmicr.2022.100123. eCollection 2022.
8
Genetic characterization of upper respiratory tract virome from nonvaccinated Egyptian cow-calf operations.非免疫埃及牛犊养殖场上呼吸道病毒组的遗传特征。
PLoS One. 2022 May 5;17(5):e0267036. doi: 10.1371/journal.pone.0267036. eCollection 2022.
9
A cattle graph genome incorporating global breed diversity.一个纳入全球品种多样性的牛基因组图谱。
Nat Commun. 2022 Feb 17;13(1):910. doi: 10.1038/s41467-022-28605-0.
10
Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN).专为濒危的德国黑皮牛（DSN）开发的 200k SNP 牛芯片的设计和性能。
BMC Genomics. 2021 Dec 18;22(1):905. doi: 10.1186/s12864-021-08237-2.
Zotero 插件