Publicação
Identify gene expression profiles in freshwater mussels under thermal stress
| Resumo: | Due to global climate change, the temperatures of streams and rivers are increasing, negatively affecting aquatic life, including bivalve species. Freshwater mussels are vital components of rivers, streams, and lake ecosystems, participating in essential ecological roles such as nutrient cycling, and increasing water quality. Furthermore, they serve as essential ecosystem engineers, providing habitat to other organisms and supporting intricate food webs. Besides their biological importance, freshwater mussels are poorly studied in terms of genomics. In the present work, the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793 (Bivalvia: Unionoida) was used as a model species to investigate the effects of climate change in freshwater mussels. The primary objective of this thesis was to determine the gene expression patterns in a model species of freshwater mussels under the effects of thermal stress exacerbated by climate change, with an overall goal of understanding the potential consequences for freshwater mussel populations. Two different ecological experiments were performed: chronic and acute. The chronic experiments where temperatures were gradually increased to simulate a scenario of progressive increasing temperatures. The acute experiments where temperatures were rapidly increased to replicate the effects of a briefer extreme climatic event. To achieve this main goal, a comprehensive bioinformatic pipeline focused on transcriptomics analysis was developed using the R Bioconductor package to generate the differential gene expression profiles of these individuals under thermal stress. The bioinformatic methodology of this work differs from the past studies, by developing an R code compilation of three methods, EdgeR, limma, and DESeq2 for differential gene expression analysis in these organisms. The output of the present work provides a comprehensive overview of gene expression profile responses of U. delphinus under climate change scenarios. Additionally, the results revealed a wide range of pathways and the corresponding genes that are impacted by thermal stress, with a particular emphasis on the up-regulation of the genes ATP6V1A, ATP6V0A1, ATP6V0A, and ATP6V1. In the chronic experiments, and high temperatures, mussels expressed these genes and, interestingly, all the pathways that these genes included appeared up-regulated. The discovered genes and pathways provide vital insights into these organisms’ adaptation tactics and identify prospective targets for monitoring and conservation efforts. |
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| Autores principais: | Silva, Beatriz Ferreira da |
| Assunto: | Freshwater mussels Transcriptomics Bioinformatics Gene expression Climate change Mexilhões de água doce Transcriptómica Bioinformática Expressão genética Alterações climática |
| Ano: | 2024 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Universidade do Minho |
| Idioma: | inglês |
| Origem: | RepositóriUM - Universidade do Minho |
| Resumo: | Due to global climate change, the temperatures of streams and rivers are increasing, negatively affecting aquatic life, including bivalve species. Freshwater mussels are vital components of rivers, streams, and lake ecosystems, participating in essential ecological roles such as nutrient cycling, and increasing water quality. Furthermore, they serve as essential ecosystem engineers, providing habitat to other organisms and supporting intricate food webs. Besides their biological importance, freshwater mussels are poorly studied in terms of genomics. In the present work, the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793 (Bivalvia: Unionoida) was used as a model species to investigate the effects of climate change in freshwater mussels. The primary objective of this thesis was to determine the gene expression patterns in a model species of freshwater mussels under the effects of thermal stress exacerbated by climate change, with an overall goal of understanding the potential consequences for freshwater mussel populations. Two different ecological experiments were performed: chronic and acute. The chronic experiments where temperatures were gradually increased to simulate a scenario of progressive increasing temperatures. The acute experiments where temperatures were rapidly increased to replicate the effects of a briefer extreme climatic event. To achieve this main goal, a comprehensive bioinformatic pipeline focused on transcriptomics analysis was developed using the R Bioconductor package to generate the differential gene expression profiles of these individuals under thermal stress. The bioinformatic methodology of this work differs from the past studies, by developing an R code compilation of three methods, EdgeR, limma, and DESeq2 for differential gene expression analysis in these organisms. The output of the present work provides a comprehensive overview of gene expression profile responses of U. delphinus under climate change scenarios. Additionally, the results revealed a wide range of pathways and the corresponding genes that are impacted by thermal stress, with a particular emphasis on the up-regulation of the genes ATP6V1A, ATP6V0A1, ATP6V0A, and ATP6V1. In the chronic experiments, and high temperatures, mussels expressed these genes and, interestingly, all the pathways that these genes included appeared up-regulated. The discovered genes and pathways provide vital insights into these organisms’ adaptation tactics and identify prospective targets for monitoring and conservation efforts. |
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