Metagenomic Analysis of Plant Virus Occurrence in Common Bean (Phaseolus vulgaris) in Central Kenya
Two closely related potyviruses, bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV), are regarded as major constraints on production of common bean (Phaseolus vulgaris L.) in Eastern and Central Africa, where this crop provides a high proportion of dietary protein as well...
Main Authors: | , , , , , , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Frontiers Media S.A.
2018-12-01
|
Series: | Frontiers in Microbiology |
Subjects: | |
Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2018.02939/full |
id |
doaj-cc0074b883d945fbafc915c089db5a6d |
---|---|
record_format |
Article |
spelling |
doaj-cc0074b883d945fbafc915c089db5a6d2020-11-25T02:44:54ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-12-01910.3389/fmicb.2018.02939412707Metagenomic Analysis of Plant Virus Occurrence in Common Bean (Phaseolus vulgaris) in Central KenyaJ. Musembi Mutuku0J. Musembi Mutuku1Francis O. Wamonje2Gerardine Mukeshimana3Joyce Njuguna4Mark Wamalwa5Seung-Kook Choi6Seung-Kook Choi7Trisna Tungadi8Appolinaire Djikeng9Krys Kelly10Jean-Baka Domelevo Entfellner11Sita R. Ghimire12Hodeba D. Mignouna13John P. Carr14Jagger J. W. Harvey15Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, KenyaDepartment of Plant Sciences, University of Cambridge, Cambridge, United KingdomDepartment of Plant Sciences, University of Cambridge, Cambridge, United KingdomBiosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, KenyaBiosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, KenyaBiotechnology Department, Kenyatta University, Nairobi, KenyaDepartment of Plant Sciences, University of Cambridge, Cambridge, United KingdomDepartment of Vegetable Research, National Institute of Horticultural and Herbal Science, Rural Development Agency, Wanju County, South KoreaDepartment of Plant Sciences, University of Cambridge, Cambridge, United KingdomBiosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, KenyaDepartment of Plant Sciences, University of Cambridge, Cambridge, United KingdomBiosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, KenyaBiosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, KenyaBiosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, KenyaDepartment of Plant Sciences, University of Cambridge, Cambridge, United KingdomBiosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, KenyaTwo closely related potyviruses, bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV), are regarded as major constraints on production of common bean (Phaseolus vulgaris L.) in Eastern and Central Africa, where this crop provides a high proportion of dietary protein as well as other nutritional, agronomic, and economic benefits. Previous studies using antibody-based assays and indicator plants indicated that BCMV and BCMNV are both prevalent in bean fields in the region but these approaches cannot distinguish between these potyviruses or detect other viruses that may threaten the crop. In this study, we utilized next generation shotgun sequencing for a metagenomic examination of viruses present in bean plants growing at two locations in Kenya: the University of Nairobi Research Farm in Nairobi's Kabete district and at sites in Kirinyaga County. RNA was extracted from leaves of bean plants exhibiting apparent viral symptoms and sequenced on the Illumina MiSeq platform. We detected BCMNV, cucumber mosaic virus (CMV), and Phaseolus vulgaris alphaendornaviruses 1 and 2 (PvEV1 and 2), with CMV present in the Kirinyaga samples. The CMV strain detected in this study was most closely related to Asian strains, which suggests that it may be a recent introduction to the region. Surprisingly, and in contrast to previous surveys, BCMV was not detected in plants at either location. Some plants were infected with PvEV1 and 2. The detection of PvEV1 and 2 suggests these seed transmitted viruses may be more prevalent in Eastern African bean germplasm than previously thought.https://www.frontiersin.org/article/10.3389/fmicb.2018.02939/fullviral metagenomicsplant-virus interactionsinsect vectorsvertical transmissionendornaviruscucumovirus |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
J. Musembi Mutuku J. Musembi Mutuku Francis O. Wamonje Gerardine Mukeshimana Joyce Njuguna Mark Wamalwa Seung-Kook Choi Seung-Kook Choi Trisna Tungadi Appolinaire Djikeng Krys Kelly Jean-Baka Domelevo Entfellner Sita R. Ghimire Hodeba D. Mignouna John P. Carr Jagger J. W. Harvey |
spellingShingle |
J. Musembi Mutuku J. Musembi Mutuku Francis O. Wamonje Gerardine Mukeshimana Joyce Njuguna Mark Wamalwa Seung-Kook Choi Seung-Kook Choi Trisna Tungadi Appolinaire Djikeng Krys Kelly Jean-Baka Domelevo Entfellner Sita R. Ghimire Hodeba D. Mignouna John P. Carr Jagger J. W. Harvey Metagenomic Analysis of Plant Virus Occurrence in Common Bean (Phaseolus vulgaris) in Central Kenya Frontiers in Microbiology viral metagenomics plant-virus interactions insect vectors vertical transmission endornavirus cucumovirus |
author_facet |
J. Musembi Mutuku J. Musembi Mutuku Francis O. Wamonje Gerardine Mukeshimana Joyce Njuguna Mark Wamalwa Seung-Kook Choi Seung-Kook Choi Trisna Tungadi Appolinaire Djikeng Krys Kelly Jean-Baka Domelevo Entfellner Sita R. Ghimire Hodeba D. Mignouna John P. Carr Jagger J. W. Harvey |
author_sort |
J. Musembi Mutuku |
title |
Metagenomic Analysis of Plant Virus Occurrence in Common Bean (Phaseolus vulgaris) in Central Kenya |
title_short |
Metagenomic Analysis of Plant Virus Occurrence in Common Bean (Phaseolus vulgaris) in Central Kenya |
title_full |
Metagenomic Analysis of Plant Virus Occurrence in Common Bean (Phaseolus vulgaris) in Central Kenya |
title_fullStr |
Metagenomic Analysis of Plant Virus Occurrence in Common Bean (Phaseolus vulgaris) in Central Kenya |
title_full_unstemmed |
Metagenomic Analysis of Plant Virus Occurrence in Common Bean (Phaseolus vulgaris) in Central Kenya |
title_sort |
metagenomic analysis of plant virus occurrence in common bean (phaseolus vulgaris) in central kenya |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2018-12-01 |
description |
Two closely related potyviruses, bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV), are regarded as major constraints on production of common bean (Phaseolus vulgaris L.) in Eastern and Central Africa, where this crop provides a high proportion of dietary protein as well as other nutritional, agronomic, and economic benefits. Previous studies using antibody-based assays and indicator plants indicated that BCMV and BCMNV are both prevalent in bean fields in the region but these approaches cannot distinguish between these potyviruses or detect other viruses that may threaten the crop. In this study, we utilized next generation shotgun sequencing for a metagenomic examination of viruses present in bean plants growing at two locations in Kenya: the University of Nairobi Research Farm in Nairobi's Kabete district and at sites in Kirinyaga County. RNA was extracted from leaves of bean plants exhibiting apparent viral symptoms and sequenced on the Illumina MiSeq platform. We detected BCMNV, cucumber mosaic virus (CMV), and Phaseolus vulgaris alphaendornaviruses 1 and 2 (PvEV1 and 2), with CMV present in the Kirinyaga samples. The CMV strain detected in this study was most closely related to Asian strains, which suggests that it may be a recent introduction to the region. Surprisingly, and in contrast to previous surveys, BCMV was not detected in plants at either location. Some plants were infected with PvEV1 and 2. The detection of PvEV1 and 2 suggests these seed transmitted viruses may be more prevalent in Eastern African bean germplasm than previously thought. |
topic |
viral metagenomics plant-virus interactions insect vectors vertical transmission endornavirus cucumovirus |
url |
https://www.frontiersin.org/article/10.3389/fmicb.2018.02939/full |
work_keys_str_mv |
AT jmusembimutuku metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya AT jmusembimutuku metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya AT francisowamonje metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya AT gerardinemukeshimana metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya AT joycenjuguna metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya AT markwamalwa metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya AT seungkookchoi metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya AT seungkookchoi metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya AT trisnatungadi metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya AT appolinairedjikeng metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya AT kryskelly metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya AT jeanbakadomelevoentfellner metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya AT sitarghimire metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya AT hodebadmignouna metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya AT johnpcarr metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya AT jaggerjwharvey metagenomicanalysisofplantvirusoccurrenceincommonbeanphaseolusvulgarisincentralkenya |
_version_ |
1724765322485956608 |