SNPs markers for the heavily overfished tambaqui Colossoma macropomum, a Neotropical fish, using next-generation sequencing-based de novo genotyping

Martínez, José Gregório; Machado, Valéria Nogueira; Caballero-Gaitán, Susana Josefina; Santos, Maria da Conceição Freitas; Alencar, Rodrigo Maciel; Escobar, L Maria Doris; Hrbek, Tomas; Farias, Izeni Pires

doi:10.1007/s12686-016-0610-3

Cited by 7 publications

(6 citation statements)

References 14 publications

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“…Studying 30 C . macropomum specimens, Martinez et al [16] analyzed nuclear Single Nucleotide Polymorphisms (SNPs) using Next Generation Sequencing-based genotyping. Using the genotyping by sequencing method, Nunes et al [17] identified a large number of SNPs in C .…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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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.

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Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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“…This species has been broadly farmed in different Amazon boundary countries and has been introduced to other Latin American countries2, as it is well-suited to aquaculture farming, accepts artificial feed, grows rapidly, and is accepted by consumer markets3. However, genetic studies of tambaqui are limited to genetic diversity surveys456, transcriptome analysis under specific conditions7, some SNPs markers8, and mitochondrial genome sequencing9.…”

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Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing

Nunes

Liu

Pértille

et al. 2017

Sci Rep

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Colossoma macropomum, or tambaqui, is the largest native Characiform species found in the Amazon and Orinoco river basins, yet few resources for genetic studies and the genetic improvement of tambaqui exist. In this study, we identified a large number of single-nucleotide polymorphisms (SNPs) for tambaqui and constructed a high-resolution genetic linkage map from a full-sib family of 124 individuals and their parents using the genotyping by sequencing method. In all, 68,584 SNPs were initially identified using minimum minor allele frequency (MAF) of 5%. Filtering parameters were used to select high-quality markers for linkage analysis. We selected 7,734 SNPs for linkage mapping, resulting in 27 linkage groups with a minimum logarithm of odds (LOD) of 8 and maximum recombination fraction of 0.35. The final genetic map contains 7,192 successfully mapped markers that span a total of 2,811 cM, with an average marker interval of 0.39 cM. Comparative genomic analysis between tambaqui and zebrafish revealed variable levels of genomic conservation across the 27 linkage groups which allowed for functional SNP annotations. The large-scale SNP discovery obtained here, allowed us to build a high-density linkage map in tambaqui, which will be useful to enhance genetic studies that can be applied in breeding programs.

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“…Estas nuevas plataformas como Roche 454, SOLID, Illumina, Ion torrent, PacBio SMRT, HeliScope, pueden generar de miles a millones de secuencias (Mardis, 2013;Mutz et al, 2013;Shokralla et al, 2012). Como ejemplo para Loreto es el caso de Lepidothrix coronata (Aves: Pipridae), así mismo, se ha adaptado la tecnología de NGS para estudiar la dinámica reproductiva de Siluriformes, a través de la identificación molecular masiva de sus larvas mediante Metabarcoding (Maggia et al, 2016), estos dos ejemplos forman parte de otras especies Amazónicas que poseen datos genómicos (p.ej., De Carvalho et al, 2017;Martínez et al, 2017).…”

Section: Perspectivas De Estudios Genéticos De Vertebrados En Loretounclassified

Situación Actual De La Base De Datos Genéticos De Vertebrados De La Región Loreto, Perú

2019

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La región Loreto presenta la mayor extensión geográfica del Perú y posee una megadiversidad de especies de flora y fauna que da soporte al desarrollo de actividades socioeconómicas y culturales. En este estudio actualizamos el conocimiento de la base de datos genéticos de vertebrados existentes en Loreto. Utilizamos el buscador de secuencias genéticas implementado en el paquete rentrez del programa R, organizamos y comparamos la cantidad de secuencias en diferentes niveles taxonómicos de cada orden de vertebrados, genes más empleados y verificamos la existencia de secuencias genéticas para especies de interés comercial. Los resultados indican la existencia de 1 960 secuencias genéticas depositadas en GenBank, de los cuales 38,52% pertenecen a la Clase Peces; 29,33% son anfibios; 21,98% aves; 8,92% mamíferos y 1,22% reptiles. Estimamos que solo el 19,44% de especies de vertebrados en Loreto poseen datos genéticos. Los genes más usados variaron en abundancia dependiendo del grupo de vertebrados. La mayoría de las especies de interés comercial no presentaron datos genéticos. Conocer el panorama de la base de datos genéticos de la región Loreto es indispensable para su integración con estudios ecológicos-evolutivos y la elaboración de planes de manejo y desarrollo sustentable.

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SNPs markers for the heavily overfished tambaqui Colossoma macropomum, a Neotropical fish, using next-generation sequencing-based de novo genotyping

Cited by 7 publications

References 14 publications

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

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

Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing

Situación Actual De La Base De Datos Genéticos De Vertebrados De La Región Loreto, Perú

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