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Professor MARY O'CONNELL's Outputs (23)

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation (2024)
Journal Article
Kosch, T. A., Torres-Sánchez, M., Liedtke, H. C., Summers, K., Yun, M. H., Crawford, A. J., Maddock, S. T., Ahammed, M. S., Araújo, V. L., Bertola, L. V., Bucciarelli, G. M., Carné, A., Carneiro, C. M., Chan, K. O., Chen, Y., Crottini, A., da Silva, J. M., Denton, R. D., Dittrich, C., Espregueira Themudo, G., …Wogan, G. O. (2024). The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation. BMC Genomics, 25(1), Article 1025. https://doi.org/10.1186/s12864-024-10899-7

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal cla... Read More about The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.

Understanding conceptus-maternal interactions: what tools do we need to develop? (2023)
Journal Article
Butt, Z., Tinning, H., O'Connell, M. J., Fenn, J., Alberio, R., & Forde, N. (2023). Understanding conceptus-maternal interactions: what tools do we need to develop?. Reproduction, Fertility and Development, 36(2), 81-92. https://doi.org/10.1071/RD23181

Communication between the maternal endometrium and developing embryo/conceptus is critical to support successful pregnancy to term. Studying the peri-implantation period of pregnancy is critical as this is when most pregnancy loss occurs in cattle. O... Read More about Understanding conceptus-maternal interactions: what tools do we need to develop?.

Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians (2023)
Journal Article
Ovchinnikov, V., Uliano-Silva, M., Wilkinson, M., Wood, J., Smith, M., Oliver, K., Sims, Y., Torrance, J., Suh, A., McCarthy, S. A., Durbin, R., & O’Connell, M. J. (2023). Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians. Molecular Biology and Evolution, 40(5), 1-11. https://doi.org/10.1093/molbev/msad102

We present genome sequences for the caecilians Geotrypetes seraphini (3.8 Gb) and Microcaecilia unicolor (4.7 Gb), representatives of a limbless, mostly soil-dwelling amphibian clade with reduced eyes, and unique putatively chemosensory tentacles. Mo... Read More about Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians.

A burst of genomic innovation at the origin of placental mammals mediated embryo implantation (2023)
Journal Article
Taylor, A. S., Tinning, H., Ovchinnikov, V., Edge, J., Smith, W., Pullinger, A. L., Sutton, R. A., Constantinides, B., Wang, D., Forbes, K., Forde, N., & O'Connell, M. J. (2023). A burst of genomic innovation at the origin of placental mammals mediated embryo implantation. Communications Biology, 6, Article 459. https://doi.org/10.1038/s42003-023-04809-y

The origin of embryo implantation in mammals ~148 million years ago was a dramatic shift in reproductive strategy, yet the molecular changes that established mammal implantation are largely unknown. Although progesterone receptor signalling predates... Read More about A burst of genomic innovation at the origin of placental mammals mediated embryo implantation.

Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny (2023)
Journal Article
McCarthy, C. G., Mulhair, P. O., Siu-Ting, K., Creevey, C. J., & O’Connell, M. J. (2023). Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny. Molecular Biology and Evolution, 40(1), Article msac276. https://doi.org/10.1093/molbev/msac276

There is conflicting evidence as to whether Porifera (sponges) or Ctenophora (comb jellies) comprise the root of the animal phylogeny. Support for either a Porifera-sister or Ctenophore-sister tree has been extensively examined in the context of mode... Read More about Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny.

Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life (2022)
Journal Article
Mulhair, P. O., McCarthy, C. G., Siu-Ting, K., Creevey, C. J., & O’Connell, M. J. (2022). Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life. Current Biology, 32(23), 5180-5188.e3. https://doi.org/10.1016/j.cub.2022.10.036

Conflicting studies place a group of bilaterian invertebrates containing xenoturbellids and acoelomorphs, the Xenacoelomorpha, as either the primary emerging bilaterian phylum or within Deuterostomia, sister to Ambulacraria. Although their placement... Read More about Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life.

Adaptive Evolution in TRIF Leads to Discordance between Human and Mouse Innate Immune Signaling (2021)
Journal Article
Hyland, E. M., Webb, A. E., Kennedy, K. F., Gerek Ince, Z. N., Loscher, C. E., & O'Connell, M. J. (2021). Adaptive Evolution in TRIF Leads to Discordance between Human and Mouse Innate Immune Signaling. Genome Biology and Evolution, 13(12), Article evab268. https://doi.org/10.1093/gbe/evab268

The TIR domain-containing adapter inducing IFN-β (TRIF) protein is an innate immune system protein that mediates the MyD88-independent toll-like receptor response pathway in mice and humans. Previously, we identified positive selection at seven disti... Read More about Adaptive Evolution in TRIF Leads to Discordance between Human and Mouse Innate Immune Signaling.

Cytoplasmic long noncoding rnas are differentially regulated and translated during human neuronal differentiation (2021)
Journal Article
DOUKA, K., BIRDS, I., WANG, D., KOSTELETOS, A., CLAYTON, S., BYFORD, A., VASCONCELOS, E. J., O'CONNELL, M. J., DEUCHARS, J., WHITEHOUSE, A., & ASPDEN, J. L. (2021). Cytoplasmic long noncoding rnas are differentially regulated and translated during human neuronal differentiation. RNA, 27(9), 1082-1101. https://doi.org/10.1261/rna.078782.121

The expression of long noncoding RNAs is highly enriched in the human nervous system. However, the function of neuronal lncRNAs in the cytoplasm and their potential translation remains poorly understood. Here we performed Poly-Ribo-Seq to understand... Read More about Cytoplasmic long noncoding rnas are differentially regulated and translated during human neuronal differentiation.

Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching (2021)
Journal Article
Hopes, T., Norris, K., Agapiou, M., McCarthy, C. G., Lewis, P. A., O'Connell, M. J., Fontana, J., & Aspden, J. L. (2022). Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching. Nucleic Acids Research, 50(4), 2240-2257. https://doi.org/10.1093/nar/gkab606

Ribosomes have long been thought of as homogeneous macromolecular machines, but recent evidence suggests they are heterogeneous and could be specialised to regulate translation. Here, we have characterised ribosomal protein heterogeneity across 4 tis... Read More about Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching.

Spectrum of pathogenic variants and founder effects in amelogenesis imperfecta associated with MMP20 (2021)
Journal Article
Nikolopoulos, G., Smith, C. E. L., Poulter, J. A., Murillo, G., Silva, S., Lamb, T., Berry, I. R., Brown, C. J., Day, P. F., Soldani, F., Al‐Bahlani, S., Harris, S. A., O'Connell, M. J., Inglehearn, C. F., & Mighell, A. J. (2021). Spectrum of pathogenic variants and founder effects in amelogenesis imperfecta associated with MMP20. Human Mutation, 42(5), 567-576. https://doi.org/10.1002/humu.24187

Amelogenesis imperfecta (AI) describes a heterogeneous group of developmental enamel defects that typically have Mendelian inheritance. Exome sequencing of 10 families with recessive hypomaturation AI revealed four novel and one known variants in the... Read More about Spectrum of pathogenic variants and founder effects in amelogenesis imperfecta associated with MMP20.

The role of CAPG in molecular communication between the embryo and the uterine endometrium: Is its function conserved in species with different implantation strategies? (2020)
Journal Article
Tinning, H., Taylor, A., Wang, D., Constantinides, B., Sutton, R., Oikonomou, G., Velazquez, M. A., Thompson, P., Treumann, A., O'Connell, M. J., & Forde, N. (2020). The role of CAPG in molecular communication between the embryo and the uterine endometrium: Is its function conserved in species with different implantation strategies?. FASEB Journal, 34(8), 11015-11029. https://doi.org/10.1096/fj.202000882rr

© 2020. The Authors. The FASEB Journal published by Wiley Periodicals LLC on behalf of Federation of American Societies for Experimental Biology During the preimplantation period of pregnancy in eutherian mammals, transcriptional and proteomic change... Read More about The role of CAPG in molecular communication between the embryo and the uterine endometrium: Is its function conserved in species with different implantation strategies?.

New missense variants in RELT causing hypomineralised amelogenesis imperfecta (2020)
Journal Article
Nikolopoulos, G., Smith, C. E., Brookes, S. J., El-Asrag, M. E., Brown, C. J., Patel, A., Murillo, G., O'Connell, M. J., Inglehearn, C. F., & Mighell, A. J. (2020). New missense variants in RELT causing hypomineralised amelogenesis imperfecta. Clinical Genetics, 97(5), 688-695. https://doi.org/10.1111/cge.13721

© 2020 The Authors. Clinical Genetics published by John Wiley & Sons Ltd. Amelogenesis imperfecta (AI) is a heterogeneous group of genetic diseases characterised by dental enamel malformation. Pathogenic variants in at least 33 genes cause syndromi... Read More about New missense variants in RELT causing hypomineralised amelogenesis imperfecta.

Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation (2019)
Journal Article
Walker, C., Siu-Ting, K., Taylor, A., O'Connell, M. J., & Bennett, T. (2019). Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation. BMC Biology, 17, 1-19. https://doi.org/10.1186/s12915-019-0689-6

Background
Strigolactones (SLs) are an important class of carotenoid-derived signalling molecule in plants, which function both as exogenous signals in the rhizosphere and as endogenous plant hormones. In flowering plants, SLs are synthesized by a c... Read More about Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation.

Gene Fusions derived by transcriptional readthrough are Driven by Segmental Duplication in Human (2019)
Journal Article
Mccartney, A., Hyland, E., Cormican, P., Moran, R., Webb, A., Lee, K., Hernandez, J., Prado-Martinez, J., Creevey, C., Aspden, J., McInerney, J., Marques-Bonet, T., & O'Connell, M. (2019). Gene Fusions derived by transcriptional readthrough are Driven by Segmental Duplication in Human. Genome Biology and Evolution, 11(9), 2678-2690. https://doi.org/10.1093/gbe/evz163

Gene fusion occurs when two or more individual genes with independent open reading frames becoming juxtaposed under the same open reading frame creating a new fused gene. A small number of gene fusions described in detail have been associated with no... Read More about Gene Fusions derived by transcriptional readthrough are Driven by Segmental Duplication in Human.

Return to the sea, get huge, beat cancer: an analysis of cetacean genomes including an assembly for the humpback whale (Megaptera novaeangliae) (2019)
Journal Article
Tollis, M., Robbins, J., Webb, A. E., Kuderna, L. F., Caulin, A. F., Garcia, J. D., Bèrubè, M., Pourmand, N., Marques-Bonet, T., O'Connell, M. J., Palsbøll, P. J., & Maley, C. C. (2019). Return to the sea, get huge, beat cancer: an analysis of cetacean genomes including an assembly for the humpback whale (Megaptera novaeangliae). Molecular Biology and Evolution, 36(8), 1746-1763. https://doi.org/10.1093/molbev/msz099

Cetaceans are a clade of highly specialized aquatic mammals that include the largest animals that have ever lived. The largest whales can have ~1000X more cells than a human, with long lifespans, leaving them theoretically susceptible to cancer. Howe... Read More about Return to the sea, get huge, beat cancer: an analysis of cetacean genomes including an assembly for the humpback whale (Megaptera novaeangliae).

Paternally expressed imprinted genes under positive Darwinian selection in Arabidopsis thaliana (2019)
Journal Article
Tuteja, R., McKeown, P. C., Ryan, P., Morgan, C. C., Donoghue, M. T., Downing, T., O'Connell, M. J., & Spillane, C. (2019). Paternally expressed imprinted genes under positive Darwinian selection in Arabidopsis thaliana. Molecular Biology and Evolution, 36(6), 1239–1253. https://doi.org/10.1093/molbev/msz063

Genomic imprinting is an epigenetic phenomenon where autosomal genes display uniparental expression depending on whether they are maternally or paternally inherited. Genomic imprinting can arise from parental conflicts over resource allocation to the... Read More about Paternally expressed imprinted genes under positive Darwinian selection in Arabidopsis thaliana.

Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics (2019)
Journal Article
Siu-Ting, K., Torres-Sánchez, M., San Mauro, D., Wilcockson, D., Wilkinson, M., Pisani, D., O’Connell, M. J., & Creevey, C. J. (2019). Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics. Molecular Biology and Evolution, 36(6), 1344-1356. https://doi.org/10.1093/molbev/msz067

Increasingly, large phylogenomic datasets include transcriptomic data from non-model organisms. This has allowed controversial and unexplored evolutionary relationships in the tree of life to be addressed but also increases the risk of inadvertent in... Read More about Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics.

Why prokaryotes have pangenomes (2017)
Journal Article
McInerney, J. O., McNally, A., & O'Connell, M. J. (2017). Why prokaryotes have pangenomes. Nature Microbiology, 2(4), Article 17040. https://doi.org/10.1038/nmicrobiol.2017.40

The existence of large amounts of within-species genome content variability is puzzling. Population genetics tells us that fitness effects of new variants—either deleterious, neutral or advantageous—combined with the long-term effective population si... Read More about Why prokaryotes have pangenomes.