• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

重测序和光学作图揭示了假结核棒状杆菌基因组中的错误组装和真实倒位。

Re-sequencing and optical mapping reveals misassemblies and real inversions on Corynebacterium pseudotuberculosis genomes.

机构信息

Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.

National Reference Laboratory for Aquatic Animal Diseases (AQUACEN) of Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.

出版信息

Sci Rep. 2019 Nov 8;9(1):16387. doi: 10.1038/s41598-019-52695-4.

DOI:10.1038/s41598-019-52695-4
PMID:31705053
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6841979/
Abstract

The number of draft genomes deposited in Genbank from the National Center for Biotechnology Information (NCBI) is higher than the complete ones. Draft genomes are assemblies that contain fragments of misassembled regions (gaps). Such draft genomes present a hindrance to the complete understanding of the biology and evolution of the organism since they lack genomic information. To overcome this problem, strategies to improve the assembly process are developed continuously. Also, the greatest challenge to the assembly progress is the presence of repetitive DNA regions. This article highlights the use of optical mapping, to detect and correct assembly errors in Corynebacterium pseudotuberculosis. We also demonstrate that choosing a reference genome should be done with caution to avoid assembly errors and loss of genetic information.

摘要

美国国家生物技术信息中心（NCBI）在 Genbank 中提交的基因组草案数量高于完整基因组。基因组草案是包含组装错误区域（缺口）片段的组装。由于缺乏基因组信息，这些基因组草案阻碍了对生物体生物学和进化的全面理解。为了克服这个问题，不断开发改进组装过程的策略。此外，组装过程中最大的挑战是重复 DNA 区域的存在。本文重点介绍了使用光学图谱来检测和纠正类鼻疽伯克霍尔德氏菌的组装错误。我们还表明，选择参考基因组时应谨慎，以避免组装错误和遗传信息丢失。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4d2/6841979/e31ccada10cf/41598_2019_52695_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4d2/6841979/42a869e3bec9/41598_2019_52695_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4d2/6841979/5ffe959f7665/41598_2019_52695_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4d2/6841979/590a591c1b51/41598_2019_52695_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4d2/6841979/e93c32cfc38e/41598_2019_52695_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4d2/6841979/35f79f588088/41598_2019_52695_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4d2/6841979/e31ccada10cf/41598_2019_52695_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4d2/6841979/42a869e3bec9/41598_2019_52695_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4d2/6841979/5ffe959f7665/41598_2019_52695_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4d2/6841979/590a591c1b51/41598_2019_52695_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4d2/6841979/e93c32cfc38e/41598_2019_52695_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4d2/6841979/35f79f588088/41598_2019_52695_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b4d2/6841979/e31ccada10cf/41598_2019_52695_Fig6_HTML.jpg

相似文献

1
Re-sequencing and optical mapping reveals misassemblies and real inversions on Corynebacterium pseudotuberculosis genomes.重测序和光学作图揭示了假结核棒状杆菌基因组中的错误组装和真实倒位。
Sci Rep. 2019 Nov 8;9(1):16387. doi: 10.1038/s41598-019-52695-4.
2
Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002.全基因组光学图谱揭示了伪结核棒状杆菌1002菌株两个rRNA操纵子之间的错误组装。
BMC Genomics. 2016 Apr 30;17:315. doi: 10.1186/s12864-016-2673-7.
3
Complete genome sequences of Corynebacterium pseudotuberculosis strains 3/99-5 and 42/02-A, isolated from sheep in Scotland and Australia, respectively.分别从苏格兰和澳大利亚的绵羊中分离到的 Corynebacterium pseudotuberculosis 菌株 3/99-5 和 42/02-A 的完整基因组序列。
J Bacteriol. 2012 Sep;194(17):4736-7. doi: 10.1128/JB.00918-12.
4
Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study.仅使用短读长进行快速混合从头组装微生物基因组：以 Corynebacterium pseudotuberculosis I19 为例。
J Microbiol Methods. 2011 Aug;86(2):218-23. doi: 10.1016/j.mimet.2011.05.008. Epub 2011 May 18.
5
Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer.使用半导体测序仪组装耻垢分枝杆菌基因组的技巧和窍门。
Microb Biotechnol. 2013 Mar;6(2):150-6. doi: 10.1111/1751-7915.12006. Epub 2012 Dec 2.
6
Scaffolding and validation of bacterial genome assemblies using optical restriction maps.利用光学限制图谱对细菌基因组组装进行支架构建和验证。
Bioinformatics. 2008 May 15;24(10):1229-35. doi: 10.1093/bioinformatics/btn102. Epub 2008 Mar 20.
7
Construction and partial characterization of a Corynebacterium pseudotuberculosis bacterial artificial chromosome library through genomic survey sequencing.通过基因组调查测序构建假结核棒状杆菌细菌人工染色体文库并进行部分特征分析。
Genet Mol Res. 2006 Nov 30;5(4):653-63.
8
Complete genome sequence of Corynebacterium pseudotuberculosis Cp31, isolated from an Egyptian buffalo.埃及水牛源假结核棒状杆菌 CP31 的全基因组序列
J Bacteriol. 2012 Dec;194(23):6663-4. doi: 10.1128/JB.01782-12.
9
Survey of genome organization and gene content of Corynebacterium pseudotuberculosis. Corynebacterium pseudotuberculosis 基因组结构与基因组成的调查。
Microbiol Res. 2010 May 30;165(4):312-20. doi: 10.1016/j.micres.2009.05.009. Epub 2009 Aug 31.
10
Complete genome sequence of Corynebacterium pseudotuberculosis I19, a strain isolated from a cow in Israel with bovine mastitis.豚鼠气单胞菌 I19 全基因组序列，该菌株分离自以色列患有乳腺炎的奶牛。
J Bacteriol. 2011 Jan;193(1):323-4. doi: 10.1128/JB.01211-10. Epub 2010 Oct 29.

引用本文的文献

1
In silico analysis of Ffp1, an ancestral Porphyromonas spp. fimbrillin, shows differences with Fim and Mfa.对祖先卟啉单胞菌属菌毛蛋白Ffp1的计算机模拟分析显示，其与菌毛蛋白（Fim）和微纤毛蛋白（Mfa）存在差异。
Access Microbiol. 2024 Jul 11;6(7). doi: 10.1099/acmi.0.000771.v3. eCollection 2024.
2
Resequencing and characterization of the first genome isolated from camel.从骆驼中分离出的首个基因组的重测序与特征分析。
PeerJ. 2024 Jan 30;12:e16513. doi: 10.7717/peerj.16513. eCollection 2024.
3
Molecular Characterization of Isolated over a 15-Year Period in Switzerland.

本文引用的文献

1
riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions.riboSeed：利用原核基因组结构跨越核糖体区域进行组装。
Nucleic Acids Res. 2018 Jun 20;46(11):e68. doi: 10.1093/nar/gky212.
2
Insight of Genus : Ascertaining the Role of Pathogenic and Non-pathogenic Species.属的洞察：确定致病和非致病物种的作用。
Front Microbiol. 2017 Oct 12;8:1937. doi: 10.3389/fmicb.2017.01937. eCollection 2017.
3
Applications of optical DNA mapping in microbiology.光学DNA图谱在微生物学中的应用。
瑞士15年间分离株的分子特征分析
Vet Sci. 2021 Jul 30;8(8):151. doi: 10.3390/vetsci8080151.
4
Cell wall glycolipids from Corynebacterium pseudotuberculosis strains with different virulences differ in terms of composition and immune recognition.不同毒力的假结核棒状杆菌细胞壁糖脂在组成和免疫识别方面存在差异。
Braz J Microbiol. 2020 Dec;51(4):2101-2110. doi: 10.1007/s42770-020-00343-9. Epub 2020 Jul 25.
5
Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum.改良的染色体 12 重建和比较分析以纠正陆地棉的错误组装。
BMC Genomics. 2020 Jul 8;21(1):470. doi: 10.1186/s12864-020-06814-5.
Biotechniques. 2017 Jun 1;62(6):255-267. doi: 10.2144/000114555.
4
Comparative genomic analysis between Corynebacterium pseudotuberculosis strains isolated from buffalo.从水牛分离出的伪结核棒状杆菌菌株之间的比较基因组分析。
PLoS One. 2017 Apr 26;12(4):e0176347. doi: 10.1371/journal.pone.0176347. eCollection 2017.
5
The hidden perils of read mapping as a quality assessment tool in genome sequencing.作为基因组测序中质量评估工具的读映射的潜在危险。
Sci Rep. 2017 Feb 22;7:43149. doi: 10.1038/srep43149.
6
Genomic analysis of four strains of bv. Equi isolated from horses showing distinct signs of infection.对从表现出明显感染症状的马匹中分离出的四株马鼻疽生物变种进行基因组分析。
Stand Genomic Sci. 2017 Jan 31;12:16. doi: 10.1186/s40793-017-0234-6. eCollection 2017.
7
Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics.通过比较基因组学评估马伪结核棒状杆菌生物变种菌株之间的基因型差异。
PLoS One. 2017 Jan 26;12(1):e0170676. doi: 10.1371/journal.pone.0170676. eCollection 2017.
8
SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.SIMBA：一种用于管理由Ion PGM测序技术生成的细菌基因组组装的网络工具。
BMC Bioinformatics. 2016 Dec 15;17(Suppl 18):456. doi: 10.1186/s12859-016-1344-7.
9
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community.牛津纳米孔MinION测序仪：将纳米孔测序技术带给基因组学界。
Genome Biol. 2016 Nov 25;17(1):239. doi: 10.1186/s13059-016-1103-0.
10
Complete Genome Sequence of the Attenuated Corynebacterium pseudotuberculosis Strain T1.减毒伪结核棒状杆菌菌株T1的全基因组序列
Genome Announc. 2016 Sep 8;4(5):e00947-16. doi: 10.1128/genomeA.00947-16.