Genetic diversity and SNP's from the chloroplast coding regions of virus-infected cassava
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.7717/peerj.8632 http://hdl.handle.net/11449/198749 |
Resumo: | Cassava is a staple food crop in sub-Saharan Africa; it is a rich source of carbohydrates and proteins which currently supports livelihoods of more than 800 million people worldwide. However, its continued production is at stake due to vector-transmitted diseases such as Cassava mosaic disease and Cassava brown streak disease. Currently, the management and control of viral diseases in cassava relies mainly on virus-resistant cultivars of cassava. Thus, the discovery of new target genes for plant virus resistance is essential for the development of more cassava varieties by conventional breeding or genetic engineering. The chloroplast is a common target for plant viruses propagation and is also a potential source for discovering new resistant genes for plant breeding. Non-infected and infected cassava leaf samples were obtained from different locations of East Africa in Tanzania, Kenya and Mozambique. RNA extraction followed by cDNA library preparation and Illumina sequencing was performed. Assembling and mapping of the reads were carried out and 33 partial chloroplast genomes were obtained. Bayesian phylogenetic analysis from 55 chloroplast protein-coding genes of a dataset with 39 taxa was performed and the single nucleotide polymorphisms for the chloroplast dataset were identified. Phylogenetic analysis revealed considerable genetic diversity present in chloroplast partial genome among cultivated cassava of East Africa. The results obtained may supplement data of previously selected resistant materials and aid breeding programs to find diversity and achieve resistance for new cassava varieties. |
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Genetic diversity and SNP's from the chloroplast coding regions of virus-infected cassavaCassava brown streak diseaseCassava mosaic diseaseEast AfricaKenyaManihot esculentaMozambiqueTanzaniaCassava is a staple food crop in sub-Saharan Africa; it is a rich source of carbohydrates and proteins which currently supports livelihoods of more than 800 million people worldwide. However, its continued production is at stake due to vector-transmitted diseases such as Cassava mosaic disease and Cassava brown streak disease. Currently, the management and control of viral diseases in cassava relies mainly on virus-resistant cultivars of cassava. Thus, the discovery of new target genes for plant virus resistance is essential for the development of more cassava varieties by conventional breeding or genetic engineering. The chloroplast is a common target for plant viruses propagation and is also a potential source for discovering new resistant genes for plant breeding. Non-infected and infected cassava leaf samples were obtained from different locations of East Africa in Tanzania, Kenya and Mozambique. RNA extraction followed by cDNA library preparation and Illumina sequencing was performed. Assembling and mapping of the reads were carried out and 33 partial chloroplast genomes were obtained. Bayesian phylogenetic analysis from 55 chloroplast protein-coding genes of a dataset with 39 taxa was performed and the single nucleotide polymorphisms for the chloroplast dataset were identified. Phylogenetic analysis revealed considerable genetic diversity present in chloroplast partial genome among cultivated cassava of East Africa. The results obtained may supplement data of previously selected resistant materials and aid breeding programs to find diversity and achieve resistance for new cassava varieties.Australian GovernmentGovernment of Western AustraliaGulf Coast Research and Education Center University of FloridaSchool of Molecular Sciences Australian Research Council Centre of Excellence in Plant Energy Biology University of Western AustraliaDepartment of Plant Protection UNESP - Universidade Estadual Paulista Julio de Mesquita Filho FCAMikocheni Agricultural Research InstituteDepartment of Primary Industries and Regional Development Diagnostic Laboratory ServiceDepartment of Horticulture Jomo Kenyatta University of Agriculture and TechnologyMozambique Agricultural Research InstituteDepartment of Plant Protection UNESP - Universidade Estadual Paulista Julio de Mesquita Filho FCAUniversity of FloridaUniversity of Western AustraliaUniversidade Estadual Paulista (Unesp)Mikocheni Agricultural Research InstituteDiagnostic Laboratory ServiceJomo Kenyatta University of Agriculture and TechnologyMozambique Agricultural Research InstituteDe Marchi, Bruno Rossitto [UNESP]Kinene, TonnyKrause-Sakate, Renate [UNESP]Boykin, Laura M.Ndunguru, JosephKehoe, MonicaAteka, ElijahTairo, FredAmisse, JamisseSseruwagi, Peter2020-12-12T01:21:04Z2020-12-12T01:21:04Z2020-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.7717/peerj.8632PeerJ, v. 2020, n. 3, 2020.2167-8359http://hdl.handle.net/11449/19874910.7717/peerj.86322-s2.0-85083523293Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengPeerJinfo:eu-repo/semantics/openAccess2021-10-22T20:11:14Zoai:repositorio.unesp.br:11449/198749Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T20:03:59.714632Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Genetic diversity and SNP's from the chloroplast coding regions of virus-infected cassava |
title |
Genetic diversity and SNP's from the chloroplast coding regions of virus-infected cassava |
spellingShingle |
Genetic diversity and SNP's from the chloroplast coding regions of virus-infected cassava De Marchi, Bruno Rossitto [UNESP] Cassava brown streak disease Cassava mosaic disease East Africa Kenya Manihot esculenta Mozambique Tanzania |
title_short |
Genetic diversity and SNP's from the chloroplast coding regions of virus-infected cassava |
title_full |
Genetic diversity and SNP's from the chloroplast coding regions of virus-infected cassava |
title_fullStr |
Genetic diversity and SNP's from the chloroplast coding regions of virus-infected cassava |
title_full_unstemmed |
Genetic diversity and SNP's from the chloroplast coding regions of virus-infected cassava |
title_sort |
Genetic diversity and SNP's from the chloroplast coding regions of virus-infected cassava |
author |
De Marchi, Bruno Rossitto [UNESP] |
author_facet |
De Marchi, Bruno Rossitto [UNESP] Kinene, Tonny Krause-Sakate, Renate [UNESP] Boykin, Laura M. Ndunguru, Joseph Kehoe, Monica Ateka, Elijah Tairo, Fred Amisse, Jamisse Sseruwagi, Peter |
author_role |
author |
author2 |
Kinene, Tonny Krause-Sakate, Renate [UNESP] Boykin, Laura M. Ndunguru, Joseph Kehoe, Monica Ateka, Elijah Tairo, Fred Amisse, Jamisse Sseruwagi, Peter |
author2_role |
author author author author author author author author author |
dc.contributor.none.fl_str_mv |
University of Florida University of Western Australia Universidade Estadual Paulista (Unesp) Mikocheni Agricultural Research Institute Diagnostic Laboratory Service Jomo Kenyatta University of Agriculture and Technology Mozambique Agricultural Research Institute |
dc.contributor.author.fl_str_mv |
De Marchi, Bruno Rossitto [UNESP] Kinene, Tonny Krause-Sakate, Renate [UNESP] Boykin, Laura M. Ndunguru, Joseph Kehoe, Monica Ateka, Elijah Tairo, Fred Amisse, Jamisse Sseruwagi, Peter |
dc.subject.por.fl_str_mv |
Cassava brown streak disease Cassava mosaic disease East Africa Kenya Manihot esculenta Mozambique Tanzania |
topic |
Cassava brown streak disease Cassava mosaic disease East Africa Kenya Manihot esculenta Mozambique Tanzania |
description |
Cassava is a staple food crop in sub-Saharan Africa; it is a rich source of carbohydrates and proteins which currently supports livelihoods of more than 800 million people worldwide. However, its continued production is at stake due to vector-transmitted diseases such as Cassava mosaic disease and Cassava brown streak disease. Currently, the management and control of viral diseases in cassava relies mainly on virus-resistant cultivars of cassava. Thus, the discovery of new target genes for plant virus resistance is essential for the development of more cassava varieties by conventional breeding or genetic engineering. The chloroplast is a common target for plant viruses propagation and is also a potential source for discovering new resistant genes for plant breeding. Non-infected and infected cassava leaf samples were obtained from different locations of East Africa in Tanzania, Kenya and Mozambique. RNA extraction followed by cDNA library preparation and Illumina sequencing was performed. Assembling and mapping of the reads were carried out and 33 partial chloroplast genomes were obtained. Bayesian phylogenetic analysis from 55 chloroplast protein-coding genes of a dataset with 39 taxa was performed and the single nucleotide polymorphisms for the chloroplast dataset were identified. Phylogenetic analysis revealed considerable genetic diversity present in chloroplast partial genome among cultivated cassava of East Africa. The results obtained may supplement data of previously selected resistant materials and aid breeding programs to find diversity and achieve resistance for new cassava varieties. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-12-12T01:21:04Z 2020-12-12T01:21:04Z 2020-01-01 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.7717/peerj.8632 PeerJ, v. 2020, n. 3, 2020. 2167-8359 http://hdl.handle.net/11449/198749 10.7717/peerj.8632 2-s2.0-85083523293 |
url |
http://dx.doi.org/10.7717/peerj.8632 http://hdl.handle.net/11449/198749 |
identifier_str_mv |
PeerJ, v. 2020, n. 3, 2020. 2167-8359 10.7717/peerj.8632 2-s2.0-85083523293 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
PeerJ |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
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1808129156370661376 |