Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses

Walsh, Amy T.; Triant, Deborah A.; Tourneau, J. J. Le; Shamimuzzaman, Md.; Elsik, Christine G.

doi:10.1093/nar/gkab1018

Cited by 21 publications

(12 citation statements)

References 73 publications

(53 reference statements)

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“…To further explore this pattern, we analyzed currently publicly available, high quality bee genomes (n = 22) to examine patterns of presence or absence of the genes encoding PTTH, its receptor Torso, and another ligand for Torso named Trunk that is involved in embryonic patterning in some insects (Duncan et al, 2013). Here, with the exception of the Frieseomelitta varia genome, which we obtained from Genbank (accession number PRJNA528016), we accessed bee genomes from the Hymenoptera Genome Database (http://HymenopteraGenome.org; Walsh et al, 2021), a genomic database of fully sequenced and annotated hymenopteran insect species that allows for detailed examinations of the presence or absence of genes and pathways during social evolution. We excluded other publicly available bee genomes from our analysis due to the incomplete nature of some of these genomes; it is difficult to differentiate between true gene loss or assembly error.…”

Section: Hypothesis and Supporting Evidencementioning

confidence: 99%

Convergent Loss of Prothoracicotropic Hormone, A Canonical Regulator of Development, in Social Bee Evolution

et al. 2022

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The evolution of insect sociality has repeatedly involved changes in developmental events and their timing. Here, we propose the hypothesis that loss of a canonical regulator of moulting and metamorphosis, prothoracicotropic hormone (PTTH), and its receptor, Torso, is associated with the evolution of sociality in bees. Specifically, we posit that the increasing importance of social influences on early developmental timing in social bees has led to their decreased reliance on PTTH, which connects developmental timing with abiotic cues in solitary insects. At present, the evidence to support this hypothesis includes the absence of genes encoding PTTH and Torso from all fully-sequenced social bee genomes and its presence in all available genomes of solitary bees. Based on the bee phylogeny, the most parsimonious reconstruction of evolutionary events is that this hormone and its receptor have been lost multiple times, across independently social bee lineages. These gene losses shed light on possible molecular and cellular mechanisms that are associated with the evolution of social behavior in bees. We outline the available evidence for our hypothesis, and then contextualize it in light of what is known about developmental cues in social and solitary bees, and the multiple precedences of major developmental changes in social insects.

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Section: Hypothesis and Supporting Evidencementioning

confidence: 99%

Convergent Loss of Prothoracicotropic Hormone, A Canonical Regulator of Development, in Social Bee Evolution

et al. 2022

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“…The Ruminant Genome Database ( 72 ) paper reports significant expansion of its multi-omics content throughout. Insects are the focus of three returning database: InsectBase ( 73 ) reports dramatic increases in content as well as new features focusing on ncRNA–mRNA interactions and likely horizontal gene transfer; Hymenoptera Genome Database ( 74 ) covers a tripling of covered species and a focus on better Gene Ontology ( 75 ) assignments allowing, for example, better on-site GO enrichment analysis; and FlyAtlas 2 ( 76 ) enhances its (sub-) tissue-specific gene expression data and introduces a new co-expression tool. As usual, aspects of human genomics feature strongly.…”

Section: New and Updated Databasesmentioning

confidence: 99%

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Rigden

Fernández

2021

Nucleic Acids Research

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The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.

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“…Gene Ontology (GO) annotations for our gene families were taken from Hymenoptera Genome database [ 35 ]. The enrichment of functional categories was evaluated with the package topGO version 2.4 of Bioconductor [ 36 , 37 ].…”

Section: Methodsmentioning

confidence: 99%

Signatures of Positive Selection in the Genome of Apis mellifera carnica: A Subspecies of European Honeybees

Huang

Zhu

Fouks

et al. 2022

Life

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The technology of long reads substantially improved the contingency of the genome assembly, particularly resolving contiguity of the repetitive regions. By integrating the interactive fragment using Hi-C, and the HiFi technique, a solid genome of the honeybee Apis mellifera carnica was assembled at the chromosomal level. A distinctive pattern of genes involved in social evolution was found by comparing it with social and solitary bees. A positive selection was identified in genes involved with cold tolerance, which likely underlies the adaptation of this European honeybee subspecies in the north hemisphere. The availability of this new high-quality genome will foster further studies and advances on genome variation during subspeciation, honeybee breeding and comparative genomics.

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Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses

Cited by 21 publications

References 73 publications

Convergent Loss of Prothoracicotropic Hormone, A Canonical Regulator of Development, in Social Bee Evolution

Convergent Loss of Prothoracicotropic Hormone, A Canonical Regulator of Development, in Social Bee Evolution

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Signatures of Positive Selection in the Genome of Apis mellifera carnica: A Subspecies of European Honeybees

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