Mitogenomic Phylogeny of freshwater mussels (Bivalvia: Unionida)

• Main Author: Teixeira, João Eduardo Afonso Teiga
• Publication Date: 2021
• Format: Master thesis
• Language: eng
• Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
• Download full: http://hdl.handle.net/10348/10575
• topic: Bioinformatics; Next-generation Sequencing

Freshwater mussels (Bivalvia: Unionida) play key ecological roles and provide important services to humans. However, they are among the most threatened faunal groups in the world. Most freshwater mussel species present two divergent mitochondrial DNA molecules (F-type or M-type) in males as a result of Doubly Uniparental Inheritance. The number of available freshwater mussel mitogenomes is low, particularly for M-type genomes. A further shortcoming is that published mitogenomes are restricted to only a few families within this order, with no mitogenomes being available for the others. In the present dissertation, 149 samples of freshwater mussels were newly sequenced by NextGeneration Sequencing (NGS) using MiSeq Illumina runs. Quality control of the obtained reads, assembly, and annotation was carried out using multiple bioinformatics tools. Comparative mitogenomic analyses were then performed using all obtained (F-type) mitogenomes with different evaluation metrics, e.g., mitogenome length, GC content, start and stop codon frequency, AT/GC skews, and Ka/Ks ratio on protein-coding genes. The results were compared with previous analyses on molluscan mitogenomes revealing interesting patterns that can be explored in future studies. A case study was carried out in a subset of the 149 mitogenomes, focusing on the subfamily Ambleminae, for which two out of five tribes lacked published complete mitogenomes. Phylogenetic analyses were carried out on these mitogenomes using standard methods, e.g., Maximum Likelihood and Bayesian Inference. The phylogeny on the newly analysed mitogenomes, i.e., Pleurobema oviforme, Amblema plicata, and Popenaias popeii, confirm the most recent tribal classification within Ambleminae. Results also suggest that all Ambelminae share the same gene arrangement (UF1).