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Master's Dissertation
DOI
https://doi.org/10.11606/D.95.2022.tde-21032022-114006
Document
Author
Full name
Natalia Nakamura Gouvea
Institute/School/College
Knowledge Area
Date of Defense
Published
São Paulo, 2022
Supervisor
Committee
Setubal, João Carlos (President)
Almeida Junior, Nalvo Franco de
Fujita, André
Varani, Alessandro de Mello
Title in Portuguese
O genoma da alga vermelha Gracilaria domingensis (Rhodophyta, Gracilariales)
Keywords in Portuguese
Agar
Alga
Anotação
Descontaminação
Genoma
Genômica
Gracilaria domingensis
Macroalga
Montagem
Rodófita
Abstract in Portuguese
A alga vermelha multicelular Gracilaria domingensis pode ser encontrada ao longo de toda a costa brasileira, e apresenta grande potencial de cultivo e exploração para extração de compostos de interesse industrial. Além disso, as algas vermelhas, que compõem o filo Rhodophyta, são um grupo com papel importante no histórico evolutivo da multicelularidade e fotossíntese, assim como na manutenção de ecossistemas marinhos. No entanto, ainda são poucos os genomas de Rhodophyta publicados. Obter e descrever um genoma inédito é um grande passo para esclarecer seu potencial metabólico e relações evolutivas, além de servir de base para outros estudos analíticos e experimentais. Neste trabalho, o genoma de Gracilaria domingensis foi obtido através da montagem e anotação automática por métodos computacionais, a partir do seu sequenciamento pela plataforma PacBio. O sequenciamento da Gracilaria domingensis gerou 6.011.680 leituras longas, resultando na montagem de 3.332 contigs, totalizando 212 Mpb. Após a montagem foi feito o processo de descontaminação in silico dos contigs, resultando em uma montagem limpa de 78 Mpb, distribuídos em 684 scaffolds, com N50 de 180.332 pb. A anotação estrutural e funcional dos genes foi feita com o uso de diversos softwares e bancos de dados públicos. Foram identificados 11.437 genes codificantes de proteínas, dos quais 38% (4.075) não obtiveram correspondência no banco de dados NCBI-nr, sugerindo se tratarem de proteínas potencialmente desconhecidas. Somada à anotação automática, foram identificados genes relacionados a importantes processos biológicos e produção de metabólitos com interesse industrial, apenas com a anotação in silico do genoma, através de buscas por BLAST. Os resultados da montagens e anotação estrutural e funcional do genoma foram comparados com os de outros genomas de Rhodophyta já publicados, os quais foram reanotados neste trabalho utilizando a mesma metodologia, na tentativa de evitar vieses metodológicos que poderiam impactar as análises comparativas.
Title in English
Genome of the red alga Gracilaria domingensis
Keywords in English
Agar
Alga
Annotation
Assembly
Decontamination
Genome
Genomics
Gracilaria domingensis
Rhodophyta
Abstract in English
The multicellular red alga Gracilaria domingensis can be found along all of the Brazillian coast, and shows a large potencial for cultivation and exploration for the extraction of compounds of industrial interest. Furthermore, red algae, which make up the Rhodophyta phylum, are a group with an important role in the evolutionary history of multicellularity and photosynthesis, as well as in the maintenance of marine ecosystems. However, there are still few Rhodophyta genomes published. To obtain and describe a novel genome is a great step to clarify its metabolical potential and evolutionary relationships, in addition to serving as a basis for further analytical and experimental studies. In this work, the genome of Gracilaria domingensis was obtained through the assembly and automatic annotation with computational methods, from its sequencing by PacBio platform. The sequencing of Gracilaria domingensis produced 6,011,680 long reads, resulting in the assembly of 3,332 contigs, and a total of 212 Mbp. After assembly, followed the process of in silico decontamination, resulting in a clean assembly of 78 Mbp, distributed in 684 scaffolds, with an N50 of 180,332 bp. The structural and functional annotation of genes was performed with the use of various softwares and public databases. We identified 11,437 protein coding genes, of which 38% (4,075) did not have matches in the NCBI-nr sequence database, suggesting them to be potential novel proteins. In addition to the automatic annotation, we identified genes related to important biological processes and biosynthesis of metabolites of industrial interest, from only the in silico annotation of the genome, through BLAST searchs. The results from the assembly and structural and functional annotation were compared to the ones from the other published Rhodophyta genomes, which were reannotated in this work with the same methodology, in the attempt to avoid methodological biases that could impact the comparative analysis.
 
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Publishing Date
2022-05-19
 
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