利用Illumina测序方法对6个高粱(高粱双色)品种的种子内生菌群进行分析

IF 10 1区 生物学 Q1 MYCOLOGY Mycosphere Pub Date : 2019-01-01 DOI:10.5943/mycosphere/10/1/16
T. Kinge
{"title":"利用Illumina测序方法对6个高粱(高粱双色)品种的种子内生菌群进行分析","authors":"T. Kinge","doi":"10.5943/mycosphere/10/1/16","DOIUrl":null,"url":null,"abstract":"Pathogen-free seeds are important for the establishment of young seedlings, prevention of health problems upon consumption by animals and livestock, and inadvertent movement of pathogens into and out of countries. However, testing for the presence of fungi, including pathogens from seeds is a time consuming and difficult process. In this study, we characterized the seed fungal microbiome (mycobiome) of six commercial sorghum cultivars from South Africa using a deep amplicon next generation sequencing approach based on the Internal Transcribed Spacer (ITS) region of the ribosomal operon. Sorghum is the fifth most important crop in the world, and widely used by African farmers. We found that the fungi present in each of the seedlots were similar to those reported by cultural studies. By comparing phylotypes of certain key families and genera to phylotypes used in established phylogenies and reputed sequences from public databases, the diagnostic value of the NGS method was also investigated. We showed that a number of molecular operational taxonomic units (MOTUs) could be identified at the species level and established that certain known pathogens are not present in the tested seeds, for instance in the Aspergillus group. Other groups could not be identified, not even to genus level. While acknowledging the shortcomings of using partial ITS data, we demonstrated that deep amplicon sequencing is a valuable diagnostic tool for seed disease control and prevention in some cases.","PeriodicalId":48718,"journal":{"name":"Mycosphere","volume":"1 1","pages":""},"PeriodicalIF":10.0000,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"11","resultStr":"{\"title\":\"Endophytic seed mycobiome of six sorghum (Sorghum bicolor) cultivars from commercial seedlots using an Illumina sequencing approach\",\"authors\":\"T. Kinge\",\"doi\":\"10.5943/mycosphere/10/1/16\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Pathogen-free seeds are important for the establishment of young seedlings, prevention of health problems upon consumption by animals and livestock, and inadvertent movement of pathogens into and out of countries. However, testing for the presence of fungi, including pathogens from seeds is a time consuming and difficult process. In this study, we characterized the seed fungal microbiome (mycobiome) of six commercial sorghum cultivars from South Africa using a deep amplicon next generation sequencing approach based on the Internal Transcribed Spacer (ITS) region of the ribosomal operon. Sorghum is the fifth most important crop in the world, and widely used by African farmers. We found that the fungi present in each of the seedlots were similar to those reported by cultural studies. By comparing phylotypes of certain key families and genera to phylotypes used in established phylogenies and reputed sequences from public databases, the diagnostic value of the NGS method was also investigated. We showed that a number of molecular operational taxonomic units (MOTUs) could be identified at the species level and established that certain known pathogens are not present in the tested seeds, for instance in the Aspergillus group. Other groups could not be identified, not even to genus level. While acknowledging the shortcomings of using partial ITS data, we demonstrated that deep amplicon sequencing is a valuable diagnostic tool for seed disease control and prevention in some cases.\",\"PeriodicalId\":48718,\"journal\":{\"name\":\"Mycosphere\",\"volume\":\"1 1\",\"pages\":\"\"},\"PeriodicalIF\":10.0000,\"publicationDate\":\"2019-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"11\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Mycosphere\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.5943/mycosphere/10/1/16\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"MYCOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Mycosphere","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.5943/mycosphere/10/1/16","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MYCOLOGY","Score":null,"Total":0}
引用次数: 11

摘要

无病原体种子对于培育幼苗、防止动物和牲畜食用后出现健康问题以及防止病原体在无意中进出各国都很重要。然而,检测真菌(包括种子中的病原体)的存在是一个耗时且困难的过程。在这项研究中,我们利用基于核糖体操纵子内部转录间隔区(ITS)区域的深度扩增子下一代测序方法,对来自南非的6个商业高粱品种的种子真菌微生物组(mycobiome)进行了表征。高粱是世界上第五大作物,被非洲农民广泛使用。我们发现每个苗区中存在的真菌与培养研究报告的真菌相似。通过将某些关键家族和属的种型与已建立的系统发生学和公共数据库中知名序列的种型进行比较,研究了NGS方法的诊断价值。我们发现许多分子操作分类单位(MOTUs)可以在物种水平上被识别,并确定某些已知的病原体不存在于测试的种子中,例如曲霉组。其他类群无法识别,甚至无法达到属水平。虽然承认使用部分ITS数据的缺点,但我们证明了深度扩增子测序在某些情况下是一种有价值的种子疾病控制和预防诊断工具。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
Endophytic seed mycobiome of six sorghum (Sorghum bicolor) cultivars from commercial seedlots using an Illumina sequencing approach
Pathogen-free seeds are important for the establishment of young seedlings, prevention of health problems upon consumption by animals and livestock, and inadvertent movement of pathogens into and out of countries. However, testing for the presence of fungi, including pathogens from seeds is a time consuming and difficult process. In this study, we characterized the seed fungal microbiome (mycobiome) of six commercial sorghum cultivars from South Africa using a deep amplicon next generation sequencing approach based on the Internal Transcribed Spacer (ITS) region of the ribosomal operon. Sorghum is the fifth most important crop in the world, and widely used by African farmers. We found that the fungi present in each of the seedlots were similar to those reported by cultural studies. By comparing phylotypes of certain key families and genera to phylotypes used in established phylogenies and reputed sequences from public databases, the diagnostic value of the NGS method was also investigated. We showed that a number of molecular operational taxonomic units (MOTUs) could be identified at the species level and established that certain known pathogens are not present in the tested seeds, for instance in the Aspergillus group. Other groups could not be identified, not even to genus level. While acknowledging the shortcomings of using partial ITS data, we demonstrated that deep amplicon sequencing is a valuable diagnostic tool for seed disease control and prevention in some cases.
求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Mycosphere
Mycosphere MYCOLOGY-
CiteScore
30.00
自引率
8.20%
发文量
9
审稿时长
4 weeks
期刊介绍: Mycosphere stands as an international, peer-reviewed journal committed to the rapid dissemination of high-quality papers on fungal biology. Embracing an open-access approach, Mycosphere serves as a dedicated platform for the mycology community, ensuring swift publication of their valuable contributions. All submitted manuscripts undergo a thorough peer-review process before acceptance, with authors retaining copyright. Key highlights of Mycosphere's publication include: - Peer-reviewed manuscripts and monographs - Open access, fostering accessibility and dissemination of knowledge - Swift turnaround, facilitating timely sharing of research findings - For information regarding open access charges, refer to the instructions for authors - Special volumes, offering a platform for thematic collections and focused contributions. Mycosphere is dedicated to promoting the accessibility and advancement of fungal biology through its inclusive and efficient publishing process.
期刊最新文献
Endophytic fungi in green manure crops; friends or foe? Phylogenomics and diversification of Sordariomycetes An updated taxonomic framework of Hymenochaetales (Agaricomycetes, Basidiomycota) Culturable mycota on bats in central and southern Yunnan Province, China Finding correct names for economically important chanterelles (Cantharellus, Hydnaceae, Cantharellales) in southwestern China: a plea for third party annotation of sequences in GenBank
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1