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De novo assembly of Vriesea carinata leaf transcriptome to identify candidate cysteine-proteases

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dc.contributor.author Eguiluz, M.
dc.contributor.author Kulcheski, F. R.
dc.contributor.author Margis, R.
dc.contributor.author Guzman, F.
dc.date.accessioned 2019-07-04T16:59:27Z
dc.date.available 2019-07-04T16:59:27Z
dc.date.issued 2019
dc.identifier.uri https://hdl.handle.net/20.500.12866/6761
dc.description.abstract Vriesea carinata is an endemic bromeliad from the Brazilian Atlantic Forest. It has trichome and tank system in their leaves which allows to absorb water and nutrients. It belongs to Bromeliaceae family, which includes several species highly enriched of cysteine-proteases (CysPs). These proteolytic enzymes regulate processes as senescence, cell differentiation, pathogen-linked programmed cell death and mobilization of proteins. Although, their biological importance, there are not genomic resources in V. carinata that can help to identify and understand their molecular mechanisms involved in different biological processes. Thus high-throughput transcriptome sequencing of V. carinata is necessary to generate sequences for the purpose of gene discovery and functional genomic studies. In the present study, we sequenced and assembled the V. carinata transcriptome to the identification of CysPs. A total of 43,232 contigs were assembled for the leaf tissue. BLAST analysis indicated that 23,803 contigs exhibited similarity to non-redundant Viridiplantae proteins. 28.24% of the contigs were classified into the COG database, and gene ontology categorized them into 61 functional groups. A metabolic pathway analysis with KEGG revealed 9679 contigs assigned to 31 metabolic pathways. Among 16 full-length CysPs identified, 11 were evaluated in respect to their expression patterns in the leaf apex, base and inflorescence tissues. The results showed differential expression levels of legumain, metacaspase, pyroglutamyl and papain-like CysPs depending of the leaf region. These results provide a global overview of V. carinata gene functions and expression activities of CysPs in those tissues. en_US
dc.language.iso eng
dc.publisher Elsevier
dc.relation.ispartofseries Gene
dc.rights info:eu-repo/semantics/restrictedAccess
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject Transcriptome en_US
dc.subject High-Throughput Nucleotide Sequencing en_US
dc.subject Molecular Sequence Annotation en_US
dc.subject Multigene Family en_US
dc.subject Sequence Analysis, RNA en_US
dc.subject Bromeliaceae en_US
dc.subject Bromeliaceae/genetics en_US
dc.subject Contig Mapping/methods en_US
dc.subject Cysteine Proteases/genetics en_US
dc.subject Cysteine-protease en_US
dc.subject Gene Expression Profiling/methods en_US
dc.subject Gene Expression Regulation, Plant en_US
dc.subject Metabolic Networks and Pathways en_US
dc.subject Plant Leaves/genetics en_US
dc.subject Plant Proteins/genetics en_US
dc.subject V.carinata en_US
dc.title De novo assembly of Vriesea carinata leaf transcriptome to identify candidate cysteine-proteases en_US
dc.type info:eu-repo/semantics/article
dc.identifier.doi https://doi.org/10.1016/j.gene.2018.12.053
dc.subject.ocde https://purl.org/pe-repo/ocde/ford#1.06.07
dc.relation.issn 1879-0038


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