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1. SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses

Author

Luan Pinto Rabelo, Davidson Sodré, Rodrigo Petry Corrêa de Sousa, Luciana Watanabe, Grazielle Gomes, Iracilda Sampaio, and Marcelo Vallinoto

Subjects
Genomic data, Genbank, Bioinformatics, Synonymous names, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background The reconstruction of the evolutionary history of organisms has been greatly influenced by the advent of molecular techniques, leading to a significant increase in studies utilizing genomic data from different species. However, the lack of standardization in gene nomenclature poses a challenge in database searches and evolutionary analyses, impacting the accuracy of results obtained. Results To address this issue, a Python class for standardizing gene nomenclatures, SynGenes, has been developed. It automatically recognizes and converts different nomenclature variations into a standardized form, facilitating comprehensive and accurate searches. Additionally, SynGenes offers a web form for individual searches using different names associated with the same gene. The SynGenes database contains a total of 545 gene name variations for mitochondrial and 2485 for chloroplasts genes, providing a valuable resource for researchers. Conclusions The SynGenes platform offers a solution for standardizing gene nomenclatures of mitochondrial and chloroplast genes and providing a standardized search solution for specific markers in GenBank. Evaluation of SynGenes effectiveness through research conducted on GenBank and PubMedCentral demonstrated its ability to yield a greater number of outcomes compared to conventional searches, ensuring more comprehensive and accurate results. This tool is crucial for accurate database searches, and consequently, evolutionary analyses, addressing the challenges posed by non-standardized gene nomenclature. Graphical abstract

Published
2024
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2. Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species

Author

Valdemiro Muhala, Aurycéia Guimarães-Costa, Adam Rick Bessa-Silva, Luan Pinto Rabelo, Jeferson Carneiro, Isadola Eusébio Macate, Luciana Watanabe, Oscar David Balcázar, Grazielle Evangelista Gomes, Marcelo Vallinoto, and Iracilda Sampaio

Subjects
Medicine, Science
Abstract

Abstract Fish mitochondrial genome have been largely studied worldwide for evolutionary and other genetic purposes and the structure and gene organization are commonly conservative. However, several studies have demonstrated that this scenario may present variations in some taxa, showing differentiation on the gene rearrangement. In this study, the complete mitogenome of terrestrial fish Boleophthalmus dussumieri was generated and compared with other species of the Exudercidae fishes. The newly complete mitogenome generated is circular and 16,685 bp of length, and it contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA genes (tRNAs), and one control region (CR), with high conservative structure, like other Mudskippers. Most of the PCG showed similar codon usage bias. The gene length was found to be different specially for the CR, 12S rRNA gene and ND5 gene in some taxon. All the Boleophthalmus species showed a gene duplication in the CR, except for B. dussumieri, and they presented a long intergenic spacer specially on the tRNA-Pro/ OH Tandem duplication/random loss (TDRL) and dimer-mitogenome and nonrandom loss (DMNL) are suitable to explain the mitogenome rearrangement observed in this study. The phylogenetic analysis well supported the monophyly of all mudskipper species and the analysis positioned the Periophthalmus clade as the most basal of the terrestrial fishes. This finding provides basis and brings insights for gene variation, gene rearrangements and replications showing evidence for variety of mitochondrial structure diversity within mudskippers.

Published
2024
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3. DNA barcoding for the assessment of marine and coastal fish diversity from the Coast of Mozambique.

Author

Valdemiro Muhala, Aurycéia Guimarães-Costa, Isadola Eusébio Macate, Luan Pinto Rabelo, Adam Rick Bessa-Silva, Luciana Watanabe, Gisele Damasceno Dos Santos, Luísa Sambora, Marcelo Vallinoto, and Iracilda Sampaio

Subjects
Medicine, Science
Abstract

The ichthyological provinces of Mozambique are understudied hotspots of global fish diversity. In this study, we applied DNA barcoding to identify the composition of the fish fauna from the coast of Mozambique. A total of 143 species belonging to 104 genera, 59 families, and 30 orders were identified. The overall K2P distance of the COI sequences within species ranged from 0.00% to 1.51%, while interspecific distances ranged from 3.64% to 24.49%. Moreover, the study revealed 15 threatened species according to the IUCN Red List of Threatened Species, with elasmobranchs being the most represented group. Additionally, the study also uncovered four new species that were not previously recorded in this geographic area, including Boleophthalmus dussumieri, Maculabatis gerrardi, Hippocampus kelloggi, and Lethrinus miniatus. This study represents the first instance of utilizing molecular references to explore the fish fauna along the Mozambican coast. Our results indicate that DNA barcoding is a dependable technique for the identification and delineation of fish species in the waters of Mozambique. The DNA barcoding library established in this research will be an invaluable asset for advancing the understanding of fish diversity and guiding future conservation initiatives.

Published
2024
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4. Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing.

Author

Fátima Gomes, Luciana Watanabe, João Vianez, Márcio Nunes, Jedson Cardoso, Clayton Lima, Horacio Schneider, and Iracilda Sampaio

Subjects
Medicine, Science
Abstract

BackgroundThe C. macropomum is a characiform fish from the Amazon basin that has been hybridized with other pacu species to produce commercial hybrids, such as the tambacu. However, little is known of the functional genomics of the parental species or these hybrid forms. The transcriptome of C. macropomum and tambacu were sequenced using 454 Roche platform (pyrosequencing) techniques to characterize the domains of Gene Ontology (GO) and to evaluate the levels of gene expression in the two organisms.ResultsThe 8,188,945 reads were assembled into 400,845 contigs. A total of 58,322 contigs were annotated with a predominance of biological processes for both organisms, as determined by Gene Ontology (GO). Similar numbers of metabolic pathways were identified in both the C. macropomum and the tambacu, with the metabolism category presenting the largest number of transcripts. The BUSCO analysis indicated that our assembly was more than 40% complete. We identified 21,986 genes for the two fishes. The P and Log2FC values indicated significant differences in the levels of gene expression, with a total of 600 up-regulated genes.ConclusionIn spite of the lack of a reference genome, the functional annotation was successful, and confirmed a considerable difference in the specificity and levels of gene expression between the two organisms. This report provides a comprehensive baseline for the genetic management of these commercially important fishes, in particular for the identification of specific genes that may represent markers involved in the immunity, growth, and fertility of these organisms, with potential practical applications in aquaculture management.

Published
2019
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5. De novo transcriptome based on next-generation sequencing reveals candidate genes with sex-specific expression in Arapaima gigas (Schinz, 1822), an ancient Amazonian freshwater fish.

Author

Luciana Watanabe, Fátima Gomes, João Vianez, Márcio Nunes, Jedson Cardoso, Clayton Lima, Horacio Schneider, and Iracilda Sampaio

Subjects
Medicine, Science
Abstract

BACKGROUND:The Arapaima (Arapaima gigas) is one of the world's largest freshwater bony fish, and is found in the rivers of the Amazon basin. This species is a potential aquaculture resource, although reproductive management in captivity is limited in particular due to the lack of external sexual dimorphism. In this study, using the 454 Roche platform (pyrosequencing) techniques, we evaluated a major portion of the transcriptome of this important Amazonian species. RESULTS:Four libraries obtained from the liver and skin tissue of juvenile specimens (representing males and females separately) were sequenced, yielding 5,453,919 high-quality reads. The de novo transcriptome assembly resulted in 175,792 contigs, with 51,057 significant blast hits. A total of 38,586 transcripts were mapped by Gene Ontology using Blast2GO. We identified 20,219 genes in the total transcriptome (9,551 in the liver and 16,818 in the skin). The gene expression analyses indicated 105 genes in the liver and 204 in the skin with differentiated expression profiles, with 95 being over-expressed in the females and 214 in the males. The log2 Fold Change and heatmap based on Reads Per Kilobase per Million mapped reads (RPKM) revealed that the gene expression in the skin is highly differentiated between male and female arapaima, while the levels of expression in the liver are similar between the sexes. CONCLUSION:Transcriptome analysis based on pyrosequencing proved to be a reliable tool for the identification of genes with differentiated expression profiles between male and female arapaima. These results provide useful insights into the molecular pathways of sexual dimorphism in this important Amazonian species, and for comparative analyses with other teleosts.

Published
2018
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6. Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing

Author

Horacio Schneider, Iracilda Sampaio, João L.S.G. Vianez, Jedson Ferreira Cardoso, Márcio Roberto Teixeira Nunes, Clayton Pereira Silva de Lima, Luciana Watanabe, and Fátima Gomes

Subjects
0106 biological sciences, Fish species, Ontologia Gen?tica, Gene Expression, Muscle Proteins, Aquaculture, Tambaqui, Biochemistry, 01 natural sciences, Transcriptome, Caraciformes / gen?tica, Medicine and Health Sciences, Musculoskeletal System, Colossoma macropomum, 0303 health sciences, Multidisciplinary, Gene Ontologies, Muscles, High-Throughput Nucleotide Sequencing, Agriculture, Genomics, Peixes / gen?tica, Medicine, Fish Farming, Metabolic Pathways, Anatomy, Characiformes, Manejo de Esp?cimes, Transcriptome Analysis, Research Article, Fish farming, Science, Muscle Tissue, Fisheries, Biology, 010603 evolutionary biology, DNA sequencing, 03 medical and health sciences, Genetics, Animals, 030304 developmental biology, Biology and Life Sciences, Computational Biology, Proteins, Genome Analysis, biology.organism_classification, Fishery, Aquicultura, Biological Tissue, Metabolism, Skeletal Muscles
Abstract

Center of Technological Innovation (CIT), Evandro Chagas Institute (IEC) and National Council of Scientific and Technological Development (CNPq) (Bionorte Project: 550939/2010-5). Universidade Federal do Par? - Campus de Bragan?a. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragan?a, PA, Brazil. Universidade Federal do Par? - Campus de Bragan?a. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragan?a, PA, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Programa de P?s-Gradua??o em Virologia. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Universidade Federal do Par? - Campus de Bragan?a. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragan?a, PA, Brazil. Universidade Federal do Par? - Campus de Bragan?a. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragan?a, PA, Brazil. BACKGROUND: The C. macropomum is a characiform fish from the Amazon basin that has been hybridized with other pacu species to produce commercial hybrids, such as the tambacu. However, little is known of the functional genomics of the parental species or these hybrid forms. The transcriptome of C. macropomum and tambacu were sequenced using 454 Roche platform (pyrosequencing) techniques to characterize the domains of Gene Ontology (GO) and to evaluate the levels of gene expression in the two organisms. RESULTS: The 8,188,945 reads were assembled into 400,845 contigs. A total of 58,322 contigs were annotated with a predominance of biological processes for both organisms, as determined by Gene Ontology (GO). Similar numbers of metabolic pathways were identified in both the C. macropomum and the tambacu, with the metabolism category presenting the largest number of transcripts. The BUSCO analysis indicated that our assembly was more than 40% complete. We identified 21,986 genes for the two fishes. The P and Log2FC values indicated significant differences in the levels of gene expression, with a total of 600 up-regulated genes. CONCLUSION: In spite of the lack of a reference genome, the functional annotation was successful, and confirmed a considerable difference in the specificity and levels of gene expression between the two organisms. This report provides a comprehensive baseline for the genetic management of these commercially important fishes, in particular for the identification of specific genes that may represent markers involved in the immunity, growth, and fertility of these organisms, with potential practical applications in aquaculture management.

Published
2019

7. De novo transcriptome based on next-generation sequencing reveals candidate genes with sex-specific expression in Arapaima gigas (Schinz, 1822), an ancient Amazonian freshwater fish

Author

Clayton Pereira Silva de Lima, Fátima Gomes, Iracilda Sampaio, Jedson Ferreira Cardoso, Luciana Watanabe, João L.S.G. Vianez, Márcio Roberto Teixeira Nunes, and Horacio Schneider

Subjects
0106 biological sciences, 0301 basic medicine, Male, Serum Proteins, Skin Neoplasms, ved/biology.organism_classification_rank.species, De novo transcriptome assembly, Cell Membranes, lcsh:Medicine, Gene Expression, 01 natural sciences, Biochemistry, Transcriptome, Medicine and Health Sciences, lcsh:Science, Skin Tumors, Sex Characteristics, Multidisciplinary, Bacia Amaz?nica (BR), Pigmentation, Liver Diseases, Gene Ontologies, Fishes, High-Throughput Nucleotide Sequencing, Genomics, Oncology, Liver, Female, Anatomy, Cellular Structures and Organelles, Transcriptome Analysis, Research Article, Transcriptoma / gen?tica, Caracteres Sexuais, Dermatology, Gastroenterology and Hepatology, Biology, 010603 evolutionary biology, Sequenciamento Completo do Genoma / m?todos, DNA sequencing, 03 medical and health sciences, Pirarucu, Arapaima, Peixes / anatomia & histologia, Genetics, Animals, Blast2GO, ved/biology, Gene Expression Profiling, lcsh:R, Biology and Life Sciences, Computational Biology, Cancers and Neoplasms, Proteins, Membrane Proteins, Molecular Sequence Annotation, Cell Biology, biology.organism_classification, Genome Analysis, Sexual dimorphism, Fatty Liver, 030104 developmental biology, Evolutionary biology, Pyrosequencing, lcsh:Q, Arapaima gigas
Abstract

The study was funded by the Center of Technological Innovation (CIT), Evandro Chagas Institute (IEC) and National Council of Scientific and Technological Development (CNPq) (Bionorte Project: 550939/2010-5) Universidade Federal do Par? - Campus de Bragan?a. Instituto de Estudos Costeiros. Laborat?rio de Gen?tica e Biologia Molecular. Bragan?a, PA, Brazil. Universidade Federal do Par? - Campus de Bragan?a. Instituto de Estudos Costeiros. Laborat?rio de Gen?tica e Biologia Molecular. Bragan?a, PA, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Universidade Federal do Par? - Campus de Bragan?a. Instituto de Estudos Costeiros. Laborat?rio de Gen?tica e Biologia Molecular. Bragan?a, PA, Brazil. Universidade Federal do Par? - Campus de Bragan?a. Instituto de Estudos Costeiros. Laborat?rio de Gen?tica e Biologia Molecular. Bragan?a, PA, Brazil. BACKGROUND: The Arapaima (Arapaima gigas) is one of the world's largest freshwater bony fish, and is found in the rivers of the Amazon basin. This species is a potential aquaculture resource, although reproductive management in captivity is limited in particular due to the lack of external sexual dimorphism. In this study, using the 454 Roche platform (pyrosequencing) techniques, we evaluated a major portion of the transcriptome of this important Amazonian species. RESULTS: Four libraries obtained from the liver and skin tissue of juvenile specimens (representing males and females separately) were sequenced, yielding 5,453,919 high-quality reads. The de novo transcriptome assembly resulted in 175,792 contigs, with 51,057 significant blast hits. A total of 38,586 transcripts were mapped by Gene Ontology using Blast2GO. We identified 20,219 genes in the total transcriptome (9,551 in the liver and 16,818 in the skin). The gene expression analyses indicated 105 genes in the liver and 204 in the skin with differentiated expression profiles, with 95 being over-expressed in the females and 214 in the males. The log2 Fold Change and heatmap based on Reads Per Kilobase per Million mapped reads (RPKM) revealed that the gene expression in the skin is highly differentiated between male and female arapaima, while the levels of expression in the liver are similar between the sexes. CONCLUSION: Transcriptome analysis based on pyrosequencing proved to be a reliable tool for the identification of genes with differentiated expression profiles between male and female arapaima. These results provide useful insights into the molecular pathways of sexual dimorphism in this important Amazonian species, and for comparative analyses with other teleosts

Published
2018

8. Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing

Author

Fátima Gomes, Márcio Roberto Teixeira Nunes, Sérgio Ricardo Nozawa, Iracilda Sampaio, João L.S.G. Vianez, Horacio Schneider, Jedson Ferreira Cardoso, Luciana Watanabe, and Layanna Freitas de Oliveira

Subjects
0301 basic medicine, Gene regulatory network, An?lise de Sequ?ncia de RNA, Computational biology, Biology, Biologia Computacional, DNA sequencing, 03 medical and health sciences, Sequenciamento de Nucleot?deos em Larga Escala, Caraciformes / gen?tica, Ecossistema Amaz?nico (BR), MicroRNAs / gen?tica, Peixes / anatomia & histologia, microRNA, Genetics, Animals, Gene, Caraciformes / metabolismo, Skin, Regulation of gene expression, Peixes, Amazon rainforest, business.industry, Sequence Analysis, RNA, Pele / metabolismo, Computational Biology, High-Throughput Nucleotide Sequencing, Ecossistema Amaz?nico, F?gado / metabolismo, Biotechnology, Transcriptoma, MicroRNAs, 030104 developmental biology, Functional annotation, Liver, Identification (biology), Characiformes, business, Transcriptome, Express?o G?nica
Abstract

Federal University of Par? - Campus of Bragan?a. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragan?a, PA, Brazil. Federal University of Par? - Campus of Bragan?a. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragan?a, PA, Brazil. Dow AgroSciences. Ribeir?o Preto, SP, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Centro de Inova??es Tecnol?gicas. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Centro de Inova??es Tecnol?gicas. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Centro de Inova??es Tecnol?gicas. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Centro de Inova??es Tecnol?gicas. Ananindeua, PA, Brasil. Federal University of Par? - Campus of Bragan?a. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragan?a, PA, Brazil. Federal University of Par? - Campus of Bragan?a. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragan?a, PA, Brazil. Colossoma macropomum is a resistant species native of Amazonas and Orinoco river basins. It is regarded as the second largest finfish of Solim?es and Amazon rivers, representing a major fishery resource in Amazonas and an important species in tropical aquaculture. MicroRNAs are non-coding endogenous riboregulators of nearly 22 nucleotides that play a key role in post-transcriptional gene regulation of several organisms. We analyzed samples of liver and skin from specimens of C. macropomum using next generation sequencing. The dataset was evaluated using computational programs to check the quality of sequences, identification of miRNAs, as well as to evaluate the expression levels of these microRNAs and interaction of target genes. We identified 279 conserved miRNAs, being 257 from liver and 272 from skin, with several miRNAs shared between tissues, with divergence in the number of reads. The strands miR-5p and miR-3p were observed in 72 miRNAs, some of them presenting a higher number of 3p reads. The functional annotation of the most expressed miRNAs resulted in 27 pathways for the liver and skin mainly related to the ?biological processes? domain. Based on the identified pathways, we visualized a large gene network, suggesting the regulation of selected miRNA over this interactive dataset. We were able to identify and characterize the expression levels of miRNAs in two tissues of great activity in C. macropomum, which stands out as the beginning of several studies that can be carried out to elucidate the influence of miRNAs in this species and their applicability as biotechnological tools.

Published
2017

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