Publicação
Mitogenomic Phylogeny of freshwater mussels (Bivalvia: Unionida)
| Resumo: | 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). |
|---|---|
| Autores principais: | Teixeira, João Eduardo Afonso Teiga |
| Assunto: | Bioinformatics Next-generation Sequencing |
| Ano: | 2021 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso restrito |
| Instituição associada: | Universidade de Trás-os-Montes e Alto Douro |
| Idioma: | inglês |
| Origem: | Repositório da UTAD |
| _version_ | 1863854931336757248 |
|---|---|
| author | Teixeira, João Eduardo Afonso Teiga |
| author_facet | Teixeira, João Eduardo Afonso Teiga |
| author_role | author |
| contributor.other.fl_str_mv | Pires, Eduardo Solteiro |
| contributor_name_str_mv | Andrade, Elsa Maria Branco Froufe Lima, Manuel Peixoto de Magalhães Lopes Pires, Eduardo Solteiro Repositório Institucional da UTAD |
| country_str | PT |
| creators_json_str | [{\"Person.name\":\"Teixeira, João Eduardo Afonso Teiga\"}] |
| datacite.contributors.contributor.contributorName.fl_str_mv | Andrade, Elsa Maria Branco Froufe Lima, Manuel Peixoto de Magalhães Lopes Pires, Eduardo Solteiro Repositório Institucional da UTAD |
| datacite.creators.creator.creatorName.fl_str_mv | Teixeira, João Eduardo Afonso Teiga |
| datacite.date.Accepted.fl_str_mv | 2021-01-22T00:00:00Z |
| datacite.date.available.fl_str_mv | 2021-07-15T13:38:00Z |
| datacite.date.embargoed.fl_str_mv | 2021-07-15T13:38:00Z |
| datacite.rights.fl_str_mv | http://purl.org/coar/access_right/c_16ec |
| datacite.subjects.subject.fl_str_mv | Bioinformatics Next-generation Sequencing |
| datacite.titles.title.fl_str_mv | Mitogenomic Phylogeny of freshwater mussels (Bivalvia: Unionida) |
| dc.contributor.none.fl_str_mv | Andrade, Elsa Maria Branco Froufe Lima, Manuel Peixoto de Magalhães Lopes Pires, Eduardo Solteiro Repositório Institucional da UTAD |
| dc.creator.none.fl_str_mv | Teixeira, João Eduardo Afonso Teiga |
| dc.date.Accepted.fl_str_mv | 2021-01-22T00:00:00Z |
| dc.date.available.fl_str_mv | 2021-07-15T13:38:00Z |
| dc.date.embargoed.fl_str_mv | 2021-07-15T13:38:00Z |
| dc.format.none.fl_str_mv | application/pdf application/pdf application/pdf |
| dc.identifier.none.fl_str_mv | http://hdl.handle.net/10348/10575 |
| dc.language.none.fl_str_mv | eng |
| dc.rights.none.fl_str_mv | http://purl.org/coar/access_right/c_16ec |
| dc.subject.none.fl_str_mv | Bioinformatics Next-generation Sequencing |
| dc.title.fl_str_mv | Mitogenomic Phylogeny of freshwater mussels (Bivalvia: Unionida) |
| dc.type.none.fl_str_mv | http://purl.org/coar/resource_type/c_bdcc |
| description | 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). |
| dirty | 0 |
| eu_rights_str_mv | restrictedAccess |
| format | masterThesis |
| fulltext.url.fl_str_mv | https://repositorio.utad.pt/bitstreams/82465a1c-ac0b-414b-8671-3c280367fbc8/download |
| id | utad_d5f0338ce9bd2efeae2f1c40c867da2b |
| identifier.url.fl_str_mv | http://hdl.handle.net/10348/10575 |
| instacron_str | utad |
| institution | Universidade de Trás-os-Montes e Alto Douro |
| instname_str | Universidade de Trás-os-Montes e Alto Douro |
| language | eng |
| network_acronym_str | utad |
| network_name_str | Repositório da UTAD |
| oai_identifier_str | oai:repositorio.utad.pt:10348/10575 |
| organization_str_mv | urn:organizationAcronym:utad |
| person_str_mv | Teixeira, João Eduardo Afonso Teiga Pires, Eduardo Solteiro Pires, Eduardo Solteiro https://www.ciencia-id.pt/7C13-4B09-5924 7C13-4B09-5924 http://orcid.org/0000-0003-3224-4926 0000-0003-3224-4926 |
| publishDate | 2021 |
| reponame_str | Repositório da UTAD |
| repository_id_str | urn:repositoryAcronym:utad |
| service_str_mv | urn:repositoryAcronym:utad |
| spelling | engpt_PTFreshwater 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).application/pdfapplication/pdfapplication/pdfpt_PTMitogenomic Phylogeny of freshwater mussels (Bivalvia: Unionida)Teixeira, João Eduardo Afonso TeigaAndrade, Elsa Maria Branco FroufeLima, Manuel Peixoto de Magalhães LopesOtherPersonalPires, Eduardo SolteiroEduardo José SolteiroPiresScopus Author IDhttps://www.scopus.com6507393290Scopus Author IDhttps://www.scopus.com35564675700Scopus Author IDhttps://www.scopus.com56785494500Ciência IDhttps://www.ciencia-id.pt7C13-4B09-5924ORCIDhttp://orcid.org0000-0003-3224-4926Researcher IDhttps://www.researcherid.comM-8833-2013HostingInstitutionOrganizationalRepositório Institucional da UTADe-mailmailto:jborges@utad.ptjborges@utad.pt2021-07-15T13:38:00Z2021-01-222021-01-22T00:00:00ZHandlehttp://hdl.handle.net/10348/10575http://purl.org/coar/access_right/c_16ecrestricted accessBioinformaticsNext-generation Sequencing114398 bytes3956939 bytes288115 bytesliteraturehttp://purl.org/coar/resource_type/c_bdccmaster thesishttp://purl.org/coar/access_right/c_16ecapplication/pdffulltexthttps://repositorio.utad.pt/bitstreams/82465a1c-ac0b-414b-8671-3c280367fbc8/downloadhttp://purl.org/coar/access_right/c_16ecapplication/pdffulltexthttps://repositorio.utad.pt/bitstreams/f1d03606-fad4-47f9-8f54-1990d242322d/downloadhttp://purl.org/coar/access_right/c_16ecapplication/pdffulltexthttps://repositorio.utad.pt/bitstreams/d0ec9207-5f12-4819-9dbb-7e207fe96118/download |
| spellingShingle | Mitogenomic Phylogeny of freshwater mussels (Bivalvia: Unionida) Teixeira, João Eduardo Afonso Teiga Bioinformatics Next-generation Sequencing |
| subject.fl_str_mv | Bioinformatics Next-generation Sequencing |
| title | Mitogenomic Phylogeny of freshwater mussels (Bivalvia: Unionida) |
| title_full | Mitogenomic Phylogeny of freshwater mussels (Bivalvia: Unionida) |
| title_fullStr | Mitogenomic Phylogeny of freshwater mussels (Bivalvia: Unionida) |
| title_full_unstemmed | Mitogenomic Phylogeny of freshwater mussels (Bivalvia: Unionida) |
| title_short | Mitogenomic Phylogeny of freshwater mussels (Bivalvia: Unionida) |
| title_sort | Mitogenomic Phylogeny of freshwater mussels (Bivalvia: Unionida) |
| topic | Bioinformatics Next-generation Sequencing |
| topic_facet | Bioinformatics Next-generation Sequencing |
| url | http://hdl.handle.net/10348/10575 |
| visible | 1 |