Transcriptomic Divergence and Associated Markers Between Genomic Lineages of Silver Catfish (Rhamdia quelen)
ABSTRACT Rhamdia quelen is a catfish widely distributed throughout South America, characterized by a complex taxonomic history. This species is a valuable resource for both fisheries and aquaculture. Due to its cultural and economic importance, it has been prioritized for conservation in the Neotrop...
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Wiley
2025-03-01
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| Series: | Ecology and Evolution |
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| Online Access: | https://doi.org/10.1002/ece3.71021 |
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| author | Néstor Ríos Belén G. Pardo Carlos Fernández José Antonio Alvarez‐Dios Paulino Martínez Carmen Bouza Graciela García |
| author_facet | Néstor Ríos Belén G. Pardo Carlos Fernández José Antonio Alvarez‐Dios Paulino Martínez Carmen Bouza Graciela García |
| author_sort | Néstor Ríos |
| collection | DOAJ |
| description | ABSTRACT Rhamdia quelen is a catfish widely distributed throughout South America, characterized by a complex taxonomic history. This species is a valuable resource for both fisheries and aquaculture. Due to its cultural and economic importance, it has been prioritized for conservation in the Neotropical region. Population genomics studies supported two main lineages latitudinally distributed (North and South) in the Neotropical basins Río de la Plata and Laguna Merín based on current genetic isolation and signals of local adaptation. In this study, we characterized the R. quelen transcriptome in brain, head kidney, liver, skeletal muscle, testis, and ovary by RNAseq to target genes and associated markers involved in key adaptive traits. After filtering, a comprehensive catalog of 24,433 transcripts was annotated, providing insights into the immune function of head kidney and liver, the association of brain with the endocrine system, and the metabolic function of liver. Skeletal muscle and brain expressed genes associated with growth were also identified. Transcriptomic differences suggestive of adaptation to temperature and salinity were revealed between North and South genomic lineages. A total of 100,045 SNPs loci were identified within transcripts, most of them (78.8%) showing low genetic differentiation between lineages (FST ≤ 0.100). However, 2504 loci (2.5%) showed high differentiation (FST ≥ 0.800), some of them located within genes associated with putative adaptation of genomic lineages to environmental factors such as temperature and salinity. These SNPs represent useful gene markers for future functional and population genomic studies for sustainable management of wild populations and their application in breeding programs. |
| format | Article |
| id | doaj-art-ff2ebecb2c8649319626c24379e21d31 |
| institution | DOAJ |
| issn | 2045-7758 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj-art-ff2ebecb2c8649319626c24379e21d312025-08-20T03:14:22ZengWileyEcology and Evolution2045-77582025-03-01153n/an/a10.1002/ece3.71021Transcriptomic Divergence and Associated Markers Between Genomic Lineages of Silver Catfish (Rhamdia quelen)Néstor Ríos0Belén G. Pardo1Carlos Fernández2José Antonio Alvarez‐Dios3Paulino Martínez4Carmen Bouza5Graciela García6Sección Genética Evolutiva, Facultad de Ciencias UdelaR Montevideo UruguayDepartamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus Terra Universidade de Santiago de Compostela Lugo SpainDepartamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus Terra Universidade de Santiago de Compostela Lugo SpainDepartamento de Matemática Aplicada, Facultad de Matemáticas Universidade de Santiago de Compostela Santiago de Compostela SpainDepartamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus Terra Universidade de Santiago de Compostela Lugo SpainDepartamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus Terra Universidade de Santiago de Compostela Lugo SpainSección Genética Evolutiva, Facultad de Ciencias UdelaR Montevideo UruguayABSTRACT Rhamdia quelen is a catfish widely distributed throughout South America, characterized by a complex taxonomic history. This species is a valuable resource for both fisheries and aquaculture. Due to its cultural and economic importance, it has been prioritized for conservation in the Neotropical region. Population genomics studies supported two main lineages latitudinally distributed (North and South) in the Neotropical basins Río de la Plata and Laguna Merín based on current genetic isolation and signals of local adaptation. In this study, we characterized the R. quelen transcriptome in brain, head kidney, liver, skeletal muscle, testis, and ovary by RNAseq to target genes and associated markers involved in key adaptive traits. After filtering, a comprehensive catalog of 24,433 transcripts was annotated, providing insights into the immune function of head kidney and liver, the association of brain with the endocrine system, and the metabolic function of liver. Skeletal muscle and brain expressed genes associated with growth were also identified. Transcriptomic differences suggestive of adaptation to temperature and salinity were revealed between North and South genomic lineages. A total of 100,045 SNPs loci were identified within transcripts, most of them (78.8%) showing low genetic differentiation between lineages (FST ≤ 0.100). However, 2504 loci (2.5%) showed high differentiation (FST ≥ 0.800), some of them located within genes associated with putative adaptation of genomic lineages to environmental factors such as temperature and salinity. These SNPs represent useful gene markers for future functional and population genomic studies for sustainable management of wild populations and their application in breeding programs.https://doi.org/10.1002/ece3.71021genomic lineageslocal adaptationtranscriptomic divergence |
| spellingShingle | Néstor Ríos Belén G. Pardo Carlos Fernández José Antonio Alvarez‐Dios Paulino Martínez Carmen Bouza Graciela García Transcriptomic Divergence and Associated Markers Between Genomic Lineages of Silver Catfish (Rhamdia quelen) Ecology and Evolution genomic lineages local adaptation transcriptomic divergence |
| title | Transcriptomic Divergence and Associated Markers Between Genomic Lineages of Silver Catfish (Rhamdia quelen) |
| title_full | Transcriptomic Divergence and Associated Markers Between Genomic Lineages of Silver Catfish (Rhamdia quelen) |
| title_fullStr | Transcriptomic Divergence and Associated Markers Between Genomic Lineages of Silver Catfish (Rhamdia quelen) |
| title_full_unstemmed | Transcriptomic Divergence and Associated Markers Between Genomic Lineages of Silver Catfish (Rhamdia quelen) |
| title_short | Transcriptomic Divergence and Associated Markers Between Genomic Lineages of Silver Catfish (Rhamdia quelen) |
| title_sort | transcriptomic divergence and associated markers between genomic lineages of silver catfish rhamdia quelen |
| topic | genomic lineages local adaptation transcriptomic divergence |
| url | https://doi.org/10.1002/ece3.71021 |
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