Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses
Abstract Background A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal gene transfers that are frequent in prokaryotes. In consequence, gene clu...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-10-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-023-03089-3 |
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| author | Saioa Manzano-Morales Yang Liu Sara González-Bodí Jaime Huerta-Cepas Jaime Iranzo |
| author_facet | Saioa Manzano-Morales Yang Liu Sara González-Bodí Jaime Huerta-Cepas Jaime Iranzo |
| author_sort | Saioa Manzano-Morales |
| collection | DOAJ |
| description | Abstract Background A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal gene transfers that are frequent in prokaryotes. In consequence, gene clustering methods must deal with a trade-off between identifying vertically transmitted representatives of multicopy gene families, which are recognizable by synteny conservation, and retrieving complete sets of species-level orthologs. We studied the implications of adopting homology, orthology, or synteny conservation as formal criteria for gene clustering by performing comparative analyses of 125 prokaryotic pangenomes. Results Clustering criteria affect pangenome functional characterization, core genome inference, and reconstruction of ancestral gene content to different extents. Species-wise estimates of pangenome and core genome sizes change by the same factor when using different clustering criteria, allowing robust cross-species comparisons regardless of the clustering criterion. However, cross-species comparisons of genome plasticity and functional profiles are substantially affected by inconsistencies among clustering criteria. Such inconsistencies are driven not only by mobile genetic elements, but also by genes involved in defense, secondary metabolism, and other accessory functions. In some pangenome features, the variability attributed to methodological inconsistencies can even exceed the effect sizes of ecological and phylogenetic variables. Conclusions Choosing an appropriate criterion for gene clustering is critical to conduct unbiased pangenome analyses. We provide practical guidelines to choose the right method depending on the research goals and the quality of genome assemblies, and a benchmarking dataset to assess the robustness and reproducibility of future comparative studies. |
| first_indexed | 2024-03-11T12:41:05Z |
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| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-03-11T12:41:05Z |
| publishDate | 2023-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-cae4b6a6b6944cbbacbe4470c052a65c2023-11-05T12:19:42ZengBMCGenome Biology1474-760X2023-10-0124112710.1186/s13059-023-03089-3Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analysesSaioa Manzano-Morales0Yang Liu1Sara González-Bodí2Jaime Huerta-Cepas3Jaime Iranzo4Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC)Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC)Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC)Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC)Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC)Abstract Background A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal gene transfers that are frequent in prokaryotes. In consequence, gene clustering methods must deal with a trade-off between identifying vertically transmitted representatives of multicopy gene families, which are recognizable by synteny conservation, and retrieving complete sets of species-level orthologs. We studied the implications of adopting homology, orthology, or synteny conservation as formal criteria for gene clustering by performing comparative analyses of 125 prokaryotic pangenomes. Results Clustering criteria affect pangenome functional characterization, core genome inference, and reconstruction of ancestral gene content to different extents. Species-wise estimates of pangenome and core genome sizes change by the same factor when using different clustering criteria, allowing robust cross-species comparisons regardless of the clustering criterion. However, cross-species comparisons of genome plasticity and functional profiles are substantially affected by inconsistencies among clustering criteria. Such inconsistencies are driven not only by mobile genetic elements, but also by genes involved in defense, secondary metabolism, and other accessory functions. In some pangenome features, the variability attributed to methodological inconsistencies can even exceed the effect sizes of ecological and phylogenetic variables. Conclusions Choosing an appropriate criterion for gene clustering is critical to conduct unbiased pangenome analyses. We provide practical guidelines to choose the right method depending on the research goals and the quality of genome assemblies, and a benchmarking dataset to assess the robustness and reproducibility of future comparative studies.https://doi.org/10.1186/s13059-023-03089-3PangenomeOrthologyComparative genomicsHomologyCore geneAccessory genome |
| spellingShingle | Saioa Manzano-Morales Yang Liu Sara González-Bodí Jaime Huerta-Cepas Jaime Iranzo Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses Genome Biology Pangenome Orthology Comparative genomics Homology Core gene Accessory genome |
| title | Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses |
| title_full | Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses |
| title_fullStr | Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses |
| title_full_unstemmed | Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses |
| title_short | Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses |
| title_sort | comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses |
| topic | Pangenome Orthology Comparative genomics Homology Core gene Accessory genome |
| url | https://doi.org/10.1186/s13059-023-03089-3 |
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