Hymenoptera Genome Database: Using HymenopteraMine to Enhance Genomic Studies of Hymenopteran Insects

Elsik, Christine G.; Tayal, Aditi; Unni, Deepak; Burns, Gregory W.; Hagen, Darren E.

doi:10.1007/978-1-4939-7737-6_17

Cited by 12 publications

(12 citation statements)

References 42 publications

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“…We then used the bio3d package in R to compare the sequences, removing duplicates to curate a final data set ( Grant et al 2021 ), We searched either the National Center for Biotechnology Information (NCBI) or the Hymenoptera Genome Database to provide accession numbers for the included P450s. ( Elsik et al 2018 ; NCBI Resource Coordinators 2018 ). For genes not currently included in an annotation but previously manually annotated, we included the scaffold accession number where the sequence can be found ( supplementary data 1, Supplementary Material online).…”

Section: Methodsmentioning

confidence: 99%

The Birth-and-Death Evolution of Cytochrome P450 Genes in Bees

Darragh

Nelson

Ramírez

2021

Genome Biology and Evolution

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The birth-and-death model of multigene family evolution describes how gene families evolve and diversify through duplication and deletion. The cytochrome P450s are one of the most diverse and well-studied multigene families, involved in both physiological and xenobiotic functions. Extensive studies of insect P450 genes have demonstrated their role in insecticide resistance. Bees are thought to experience toxin exposure through their diet of nectar and pollen, as well as the resin-collecting behavior exhibited by some species. Here, we describe the repertoire of P450 genes in the orchid bee Euglossa dilemma. Male orchid bees form perfume bouquets used in courtship displays by collecting volatile compounds, resulting in exposure to compounds known to be toxic. In addition, we conducted phylogenetic and selection analyses across ten bee species encompassing three bee families. We find that social behavior and resin collection are not correlated with the repertoire of P450 present in a bee species. However, our analyses revealed that P450 clades can be classified as stable and unstable, and that genes involved in xenobiotic metabolism are more likely to belong to unstable clades. Furthermore, we find that unstable clades are under more dynamic evolutionary pressures, and exhibit signals of adaptive evolution. This work highlights the complexity of multigene family evolution, revealing that multiple factors contribute to the diversification, stability and dynamics of this gene family. Furthermore, we provide a resource for future detailed studies investigating the function of different P450s in economically important bee species.

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Section: Methodsmentioning

confidence: 99%

The Birth-and-Death Evolution of Cytochrome P450 Genes in Bees

Darragh

Nelson

Ramírez

2021

Genome Biology and Evolution

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“…With the introduction of active inference into this space, it could be possible to bridge from these engineering fields, to more abstract areas such as information processing in networks, cybernetics, and collective graphical models (Sheldon and Dietterich, 2011 ; Baluška and Levin, 2016 ; Fekete, 2019 ). The Hymenopteran eusocial insects (ants, some bees and wasps) are highly biodiverse, have an increasing number of species with sequenced genomes, and have databases of ecological and trait data (e.g., Parr et al, 2017 ; Elsik et al, 2018 ; Friedman et al, 2020a ). Additionally the Hymenoptera present with several independent originations of fully eusocial living, as well as numerous elaborations (such as agriculture, polymorphic workers, symbioses, etc.).…”

Section: Concluding Remarkmentioning

confidence: 99%

Active Inferants: An Active Inference Framework for Ant Colony Behavior

Friedman

Tschantz

Ramstead

et al. 2021

Front. Behav. Neurosci.

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In this paper, we introduce an active inference model of ant colony foraging behavior, and implement the model in a series of in silico experiments. Active inference is a multiscale approach to behavioral modeling that is being applied across settings in theoretical biology and ethology. The ant colony is a classic case system in the function of distributed systems in terms of stigmergic decision-making and information sharing. Here we specify and simulate a Markov decision process (MDP) model for ant colony foraging. We investigate a well-known paradigm from laboratory ant colony behavioral experiments, the alternating T-maze paradigm, to illustrate the ability of the model to recover basic colony phenomena such as trail formation after food location discovery. We conclude by outlining how the active inference ant colony foraging behavioral model can be extended and situated within a nested multiscale framework and systems approaches to biology more generally.

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“…We then used the bio3d package in R to compare the sequences, removing duplicates to curate a final dataset (Grant et al 2021), We searched either the National Center for Biotechnology Information (NCBI) or the Hymenoptera Genome Database to provide accession numbers for the included P450s. (Elsik et al 2018; NCBI Resource Coordinators 2018). For genes not currently included in an annotation but previously manually annotated,…”

Section: Gene Family Annotationmentioning

confidence: 99%

“…We then annotated the P450 gene family in the Euglossa dilemma genome (Brand et al 2017) using all previously annotated Apis mellifera protein sequences as a reference (Elsik et al 2018). Firstly, we identified scaffolds in the Eg.…”

Section: Gene Family Annotationmentioning

confidence: 99%

The birth-and-death evolution of cytochrome P450 genes in bees

Darragh

Nelson

Ramírez

2021

Preprint

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The birth-and-death model of multigene family evolution describes how families can expand by duplication and contract by gene deletion and formation of pseudogenes. The phylogenetic stability of a gene is thought to be related to the degree of functional importance. However, it is unclear how much evolution of a gene in a gene family is driven by adaptive versus neutral processes. The cytochrome P450s are one of the most diverse and well-studied multigene families, involved in both physiological and xenobiotic functions. Bees have a high toxin exposure due to their diet of nectar and pollen, as well as the resin-collecting behavior exhibited by some bees. Here, we describe the P450s of the orchid bee Euglossa dilemma. Orchid bees are a neotropical clade in which males form perfume bouquets used in courtship displays by collecting a diverse set of volatile compounds, resulting in high chemical compound exposure. We conducted phylogenetic and selection analyses across ten bee species encompassing three bee families. We do not find a relationship between the ecology of a bee species and its P450 repertoire. Our analyses reveal that P450 clades can be classified into stable and unstable clades, and that genes involved in xenobiotic metabolism are more likely to belong to unstable clades. Furthermore, we find that unstable clades are under more dynamic evolutionary pressures, with signals of adaptive evolution detected, suggesting that both gene duplication and positive selection driving sequence divergence have played a role in the diversification of bee P450s. Our works highlights the complexity of multigene family evolution which does not always follow generalized predictions.

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Hymenoptera Genome Database: Using HymenopteraMine to Enhance Genomic Studies of Hymenopteran Insects

Cited by 12 publications

References 42 publications

The Birth-and-Death Evolution of Cytochrome P450 Genes in Bees

The Birth-and-Death Evolution of Cytochrome P450 Genes in Bees

Active Inferants: An Active Inference Framework for Ant Colony Behavior

The birth-and-death evolution of cytochrome P450 genes in bees

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