Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales)

Detalhes bibliográficos
Autor(a) principal: Nakamura-Gouvea, Natalia
Data de Publicação: 2022
Outros Autores: Alves-Lima, Cicero, Benites, Luiz Felipe, Iha, Cintia, Maracaja-Coutinho, Vinicius, Aliaga-Tobar, Victor, Araujo Amaral Carneiro, Marcella, Yokoya, Nair S., Marinho-Soriano, Eliane, Graminha, Marcia A. S. [UNESP], Collén, Jonas, Oliveira, Mariana C., Setubal, Joao C., Colepicolo, Pio
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1111/jpy.13238
http://hdl.handle.net/11449/231635
Resumo: Gracilariales is a clade of florideophycean red macroalgae known for being the main source of agar. We present a de novo genome assembly and annotation of Gracilaria domingensis, an agarophyte alga with flattened thallus widely distributed along Central and South American Atlantic intertidal zones. In addition to structural analysis, an organizational comparison was done with other Rhodophyta genomes. The nuclear genome has 78 Mbp, with 11,437 predicted coding genes, 4,075 of which did not have hits in sequence databases. We also predicted 1,567 noncoding RNAs, distributed in 14 classes. The plastid and mitochondrion genome structures were also obtained. Genes related to agar synthesis were identified. Genes for type II galactose sulfurylases could not be found. Genes related to ascorbate synthesis were found. These results suggest an intricate connection of cell wall polysaccharide synthesis and the redox systems through the use of L-galactose in Rhodophyta. The genome of G. domingensis should be valuable to phycological and aquacultural research, as it is the first tropical and Western Atlantic red macroalgal genome to be sequenced.
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spelling Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales)agarascorbateGracilaria domingensisHGTncRNAsrhodophytasecondary metabolitesGracilariales is a clade of florideophycean red macroalgae known for being the main source of agar. We present a de novo genome assembly and annotation of Gracilaria domingensis, an agarophyte alga with flattened thallus widely distributed along Central and South American Atlantic intertidal zones. In addition to structural analysis, an organizational comparison was done with other Rhodophyta genomes. The nuclear genome has 78 Mbp, with 11,437 predicted coding genes, 4,075 of which did not have hits in sequence databases. We also predicted 1,567 noncoding RNAs, distributed in 14 classes. The plastid and mitochondrion genome structures were also obtained. Genes related to agar synthesis were identified. Genes for type II galactose sulfurylases could not be found. Genes related to ascorbate synthesis were found. These results suggest an intricate connection of cell wall polysaccharide synthesis and the redox systems through the use of L-galactose in Rhodophyta. The genome of G. domingensis should be valuable to phycological and aquacultural research, as it is the first tropical and Western Atlantic red macroalgal genome to be sequenced.Laboratory of Algal Biochemistry and Molecular Biology Department of Biochemistry Institute of Chemistry University of São Paulo, Av. Prof. Lineu, Prestes, 748, SPCNRS UMR 7232 Biologie Intégrative des Organismes Marins (BIOM) Sorbonne Université, Observatoire Océanologique - F-66650Department of Botany Institute of Biosciences University of São Paulo, R Matão 277, SPDepartamento de Bioquímica y Biología Molecular Facultad de Ciencias Químicas y Farmacéuticas Universidad de Chile Universidad de Chile - IndependenciaDepartment of Oceanography and Limnology Federal University of Rio Grande do Norte - Via Costeira, Praia de Mãe Luiza, s/n, RNPhycology Research Center Institute of Botany Secretary of Infrastructure and Environment of São Paulo State, Brazil - Av. Miguel Estefano, 3687, Água Funda, SPSchool of Pharmaceutical Sciences São Paulo State University (UNESP), Rod. Araraquara-Jaú km 1, Campus Ville, SPStation Biologique de Roscoff UMR 8227 Integrative Biology of Marine Models - CS 90074Department of Biochemistry Institute of Chemistry University of São Paulo, Av. Prof. Lineu Prestes, 748, SPSchool of Pharmaceutical Sciences São Paulo State University (UNESP), Rod. Araraquara-Jaú km 1, Campus Ville, SPUniversidade de São Paulo (USP)Sorbonne UniversitéUniversidad de Chile - IndependenciaFederal University of Rio Grande do Norte - Via CosteiraSecretary of Infrastructure and Environment of São Paulo StateUniversidade Estadual Paulista (UNESP)Integrative Biology of Marine Models - CS 90074Nakamura-Gouvea, NataliaAlves-Lima, CiceroBenites, Luiz FelipeIha, CintiaMaracaja-Coutinho, ViniciusAliaga-Tobar, VictorAraujo Amaral Carneiro, MarcellaYokoya, Nair S.Marinho-Soriano, ElianeGraminha, Marcia A. S. [UNESP]Collén, JonasOliveira, Mariana C.Setubal, Joao C.Colepicolo, Pio2022-04-29T08:46:41Z2022-04-29T08:46:41Z2022-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1111/jpy.13238Journal of Phycology.1529-88170022-3646http://hdl.handle.net/11449/23163510.1111/jpy.132382-s2.0-85126730886Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal of Phycologyinfo:eu-repo/semantics/openAccess2022-04-29T08:46:41Zoai:repositorio.unesp.br:11449/231635Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T17:57:48.374394Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales)
title Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales)
spellingShingle Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales)
Nakamura-Gouvea, Natalia
agar
ascorbate
Gracilaria domingensis
HGT
ncRNAs
rhodophyta
secondary metabolites
title_short Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales)
title_full Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales)
title_fullStr Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales)
title_full_unstemmed Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales)
title_sort Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales)
author Nakamura-Gouvea, Natalia
author_facet Nakamura-Gouvea, Natalia
Alves-Lima, Cicero
Benites, Luiz Felipe
Iha, Cintia
Maracaja-Coutinho, Vinicius
Aliaga-Tobar, Victor
Araujo Amaral Carneiro, Marcella
Yokoya, Nair S.
Marinho-Soriano, Eliane
Graminha, Marcia A. S. [UNESP]
Collén, Jonas
Oliveira, Mariana C.
Setubal, Joao C.
Colepicolo, Pio
author_role author
author2 Alves-Lima, Cicero
Benites, Luiz Felipe
Iha, Cintia
Maracaja-Coutinho, Vinicius
Aliaga-Tobar, Victor
Araujo Amaral Carneiro, Marcella
Yokoya, Nair S.
Marinho-Soriano, Eliane
Graminha, Marcia A. S. [UNESP]
Collén, Jonas
Oliveira, Mariana C.
Setubal, Joao C.
Colepicolo, Pio
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade de São Paulo (USP)
Sorbonne Université
Universidad de Chile - Independencia
Federal University of Rio Grande do Norte - Via Costeira
Secretary of Infrastructure and Environment of São Paulo State
Universidade Estadual Paulista (UNESP)
Integrative Biology of Marine Models - CS 90074
dc.contributor.author.fl_str_mv Nakamura-Gouvea, Natalia
Alves-Lima, Cicero
Benites, Luiz Felipe
Iha, Cintia
Maracaja-Coutinho, Vinicius
Aliaga-Tobar, Victor
Araujo Amaral Carneiro, Marcella
Yokoya, Nair S.
Marinho-Soriano, Eliane
Graminha, Marcia A. S. [UNESP]
Collén, Jonas
Oliveira, Mariana C.
Setubal, Joao C.
Colepicolo, Pio
dc.subject.por.fl_str_mv agar
ascorbate
Gracilaria domingensis
HGT
ncRNAs
rhodophyta
secondary metabolites
topic agar
ascorbate
Gracilaria domingensis
HGT
ncRNAs
rhodophyta
secondary metabolites
description Gracilariales is a clade of florideophycean red macroalgae known for being the main source of agar. We present a de novo genome assembly and annotation of Gracilaria domingensis, an agarophyte alga with flattened thallus widely distributed along Central and South American Atlantic intertidal zones. In addition to structural analysis, an organizational comparison was done with other Rhodophyta genomes. The nuclear genome has 78 Mbp, with 11,437 predicted coding genes, 4,075 of which did not have hits in sequence databases. We also predicted 1,567 noncoding RNAs, distributed in 14 classes. The plastid and mitochondrion genome structures were also obtained. Genes related to agar synthesis were identified. Genes for type II galactose sulfurylases could not be found. Genes related to ascorbate synthesis were found. These results suggest an intricate connection of cell wall polysaccharide synthesis and the redox systems through the use of L-galactose in Rhodophyta. The genome of G. domingensis should be valuable to phycological and aquacultural research, as it is the first tropical and Western Atlantic red macroalgal genome to be sequenced.
publishDate 2022
dc.date.none.fl_str_mv 2022-04-29T08:46:41Z
2022-04-29T08:46:41Z
2022-01-01
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/10.1111/jpy.13238
Journal of Phycology.
1529-8817
0022-3646
http://hdl.handle.net/11449/231635
10.1111/jpy.13238
2-s2.0-85126730886
url http://dx.doi.org/10.1111/jpy.13238
http://hdl.handle.net/11449/231635
identifier_str_mv Journal of Phycology.
1529-8817
0022-3646
10.1111/jpy.13238
2-s2.0-85126730886
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Journal of Phycology
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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