Molecular mechanisms underlying sugarcane response to aluminum stress by rna-seq
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/10.3390/ijms21217934 http://hdl.handle.net/11449/205392 |
Resumo: | Some metals are beneficial to plants and contribute to critical physiological processes. Some metals, however, are not. The presence of aluminum ions (Al3+ ) can be very toxic, especially in acidic soils. Considerable parts of the world’s arable land are acidic in nature; mechanistically elucidating a plant’s response to aluminum stress is critical to mitigating this stress and improving the quality of plants. To identify the genes involved in sugarcane response to aluminum stress, we generated 372 million paired-end RNA sequencing reads from the roots of CTC-2 and RB855453, which are two contrasting cultivars. Data normalization resulted in 162,161 contigs (contiguous sequences) and 97,335 genes from a de novo transcriptome assembly (trinity genes). A total of 4858 and 1307 differently expressed genes (DEGs) for treatment versus control were identified for the CTC-2 and RB855453 cultivars, respectively. The DEGs were annotated into 34 functional categories. The majority of the genes were upregulated in the CTC-2 (tolerant cultivar) and downregulated in RB855453 (sensitive cultivar). Here, we present the first root transcriptome of sugarcane under aluminum stress. The results and conclusions of this study are a crucial launch pad for future genetic and genomic studies of sugarcane. The transcriptome analysis shows that sugarcane tolerance to aluminum may be explained by an efficient detoxification mechanism combined with lateral root formation and activation of redox enzymes. We also present a hypothetical model for aluminum tolerance in the CTC-2 cultivar. |
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Molecular mechanisms underlying sugarcane response to aluminum stress by rna-seqAluminum ions (Al3+ )Auxin signalingDetoxificationSaccharumSome metals are beneficial to plants and contribute to critical physiological processes. Some metals, however, are not. The presence of aluminum ions (Al3+ ) can be very toxic, especially in acidic soils. Considerable parts of the world’s arable land are acidic in nature; mechanistically elucidating a plant’s response to aluminum stress is critical to mitigating this stress and improving the quality of plants. To identify the genes involved in sugarcane response to aluminum stress, we generated 372 million paired-end RNA sequencing reads from the roots of CTC-2 and RB855453, which are two contrasting cultivars. Data normalization resulted in 162,161 contigs (contiguous sequences) and 97,335 genes from a de novo transcriptome assembly (trinity genes). A total of 4858 and 1307 differently expressed genes (DEGs) for treatment versus control were identified for the CTC-2 and RB855453 cultivars, respectively. The DEGs were annotated into 34 functional categories. The majority of the genes were upregulated in the CTC-2 (tolerant cultivar) and downregulated in RB855453 (sensitive cultivar). Here, we present the first root transcriptome of sugarcane under aluminum stress. The results and conclusions of this study are a crucial launch pad for future genetic and genomic studies of sugarcane. The transcriptome analysis shows that sugarcane tolerance to aluminum may be explained by an efficient detoxification mechanism combined with lateral root formation and activation of redox enzymes. We also present a hypothetical model for aluminum tolerance in the CTC-2 cultivar.Functional Genomics Lab Biotechnology Department University of Ribeirão PretoSchool of Agricultural and Veterinarian Sciences São Paulo State University (UNESP)Center for Biotechnology and Genomics Texas Tech UniversityHartwell Center St. Jude Children’s Research HospitalAUA College of Medicine, Jabberwock Rd., P.O. Box 1451, OsbournSchool of Agricultural and Veterinarian Sciences São Paulo State University (UNESP)University of Ribeirão PretoUniversidade Estadual Paulista (Unesp)Texas Tech UniversitySt. Jude Children’s Research HospitalAUA College of MedicineRosa-Santos, Thiago Mateusda Silva, Renan Gonçalves [UNESP]Kumar, PoornasreeKottapalli, PratibhaCrasto, ChiquitoKottapalli, Kameswara RaoFrança, Suzelei CastroZingaretti, Sonia Marli [UNESP]2021-06-25T10:14:32Z2021-06-25T10:14:32Z2020-11-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article1-17http://dx.doi.org/10.3390/ijms21217934International Journal of Molecular Sciences, v. 21, n. 21, p. 1-17, 2020.1422-00671661-6596http://hdl.handle.net/11449/20539210.3390/ijms212179342-s2.0-85094176298Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengInternational Journal of Molecular Sciencesinfo:eu-repo/semantics/openAccess2021-10-23T12:40:01Zoai:repositorio.unesp.br:11449/205392Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T23:37:35.450958Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Molecular mechanisms underlying sugarcane response to aluminum stress by rna-seq |
title |
Molecular mechanisms underlying sugarcane response to aluminum stress by rna-seq |
spellingShingle |
Molecular mechanisms underlying sugarcane response to aluminum stress by rna-seq Rosa-Santos, Thiago Mateus Aluminum ions (Al3+ ) Auxin signaling Detoxification Saccharum |
title_short |
Molecular mechanisms underlying sugarcane response to aluminum stress by rna-seq |
title_full |
Molecular mechanisms underlying sugarcane response to aluminum stress by rna-seq |
title_fullStr |
Molecular mechanisms underlying sugarcane response to aluminum stress by rna-seq |
title_full_unstemmed |
Molecular mechanisms underlying sugarcane response to aluminum stress by rna-seq |
title_sort |
Molecular mechanisms underlying sugarcane response to aluminum stress by rna-seq |
author |
Rosa-Santos, Thiago Mateus |
author_facet |
Rosa-Santos, Thiago Mateus da Silva, Renan Gonçalves [UNESP] Kumar, Poornasree Kottapalli, Pratibha Crasto, Chiquito Kottapalli, Kameswara Rao França, Suzelei Castro Zingaretti, Sonia Marli [UNESP] |
author_role |
author |
author2 |
da Silva, Renan Gonçalves [UNESP] Kumar, Poornasree Kottapalli, Pratibha Crasto, Chiquito Kottapalli, Kameswara Rao França, Suzelei Castro Zingaretti, Sonia Marli [UNESP] |
author2_role |
author author author author author author author |
dc.contributor.none.fl_str_mv |
University of Ribeirão Preto Universidade Estadual Paulista (Unesp) Texas Tech University St. Jude Children’s Research Hospital AUA College of Medicine |
dc.contributor.author.fl_str_mv |
Rosa-Santos, Thiago Mateus da Silva, Renan Gonçalves [UNESP] Kumar, Poornasree Kottapalli, Pratibha Crasto, Chiquito Kottapalli, Kameswara Rao França, Suzelei Castro Zingaretti, Sonia Marli [UNESP] |
dc.subject.por.fl_str_mv |
Aluminum ions (Al3+ ) Auxin signaling Detoxification Saccharum |
topic |
Aluminum ions (Al3+ ) Auxin signaling Detoxification Saccharum |
description |
Some metals are beneficial to plants and contribute to critical physiological processes. Some metals, however, are not. The presence of aluminum ions (Al3+ ) can be very toxic, especially in acidic soils. Considerable parts of the world’s arable land are acidic in nature; mechanistically elucidating a plant’s response to aluminum stress is critical to mitigating this stress and improving the quality of plants. To identify the genes involved in sugarcane response to aluminum stress, we generated 372 million paired-end RNA sequencing reads from the roots of CTC-2 and RB855453, which are two contrasting cultivars. Data normalization resulted in 162,161 contigs (contiguous sequences) and 97,335 genes from a de novo transcriptome assembly (trinity genes). A total of 4858 and 1307 differently expressed genes (DEGs) for treatment versus control were identified for the CTC-2 and RB855453 cultivars, respectively. The DEGs were annotated into 34 functional categories. The majority of the genes were upregulated in the CTC-2 (tolerant cultivar) and downregulated in RB855453 (sensitive cultivar). Here, we present the first root transcriptome of sugarcane under aluminum stress. The results and conclusions of this study are a crucial launch pad for future genetic and genomic studies of sugarcane. The transcriptome analysis shows that sugarcane tolerance to aluminum may be explained by an efficient detoxification mechanism combined with lateral root formation and activation of redox enzymes. We also present a hypothetical model for aluminum tolerance in the CTC-2 cultivar. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-11-01 2021-06-25T10:14:32Z 2021-06-25T10:14:32Z |
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/10.3390/ijms21217934 International Journal of Molecular Sciences, v. 21, n. 21, p. 1-17, 2020. 1422-0067 1661-6596 http://hdl.handle.net/11449/205392 10.3390/ijms21217934 2-s2.0-85094176298 |
url |
http://dx.doi.org/10.3390/ijms21217934 http://hdl.handle.net/11449/205392 |
identifier_str_mv |
International Journal of Molecular Sciences, v. 21, n. 21, p. 1-17, 2020. 1422-0067 1661-6596 10.3390/ijms21217934 2-s2.0-85094176298 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
International Journal of Molecular Sciences |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
1-17 |
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 |
|
_version_ |
1808129537616117760 |