Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine

Elsik, Christine G.; Tayal, Aditi; Diesh, Colin; Unni, Deepak; Emery, Marianne L.; Nguyen, Hung N.; Hagen, Darren E.

doi:10.1093/nar/gkv1208

Cited by 118 publications

(112 citation statements)

References 55 publications

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“…Then, we mapped these proteins to the benchmark sequences of A. mellifera proteome (version 3.2) downloaded from Bee Base (www.beebase.org) 36 by BLAST search. Finally, we obtained 906,294 non-redundant PPIs in 8,336 proteins of A. mellifera .…”

Section: Methodsmentioning

confidence: 99%

Phosphoproteome Analysis Reveals Phosphorylation Underpinnings in the Brains of Nurse and Forager Honeybees (Apis mellifera)

Bezabih

Cheng

Han

et al. 2017

Sci Rep

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The honeybee brain is a central organ in regulating wide ranges of honeybee biology, including life transition from nurse to forager bees. Knowledge is still lacking on how protein phosphorylation governs the neural activity to drive the age-specific labor division. The cerebral phosphoproteome of nurse and forager honeybees was characterized using Ti4+-IMAC phosphopeptide enrichment mass-spectrometry-based proteomics and protein kinases (PKs) were predicted. There were 3,077 phosphosites residing on 3,234 phosphopeptides from 1004 phosphoproteins in the nurse bees. For foragers the numbers were 3,056, 3,110, and 958, respectively. Notably, among the total 231 PKs in honeybee proteome, 179 novel PKs were predicted in the honeybee brain, of which 88 were experimentally identified. Proteins involved in wide scenarios of pathways were phosphorylated depending on age: glycolysis/gluconeogenesis, AGE/RAGE and phosphorylation in nurse bees and metal ion transport, ATP metabolic process and phototransduction in forager bees. These observations suggest that phosphorylation is vital to the tuning of protein activity to regulate cerebral function according to the biological duties as nursing and foraging bees. The data provides valuable information on phosphorylation signaling in the honeybee brain and potentially useful resource to understand the signaling mechanism in honeybee neurobiology and in other social insects as well.

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Section: Methodsmentioning

confidence: 99%

Phosphoproteome Analysis Reveals Phosphorylation Underpinnings in the Brains of Nurse and Forager Honeybees (Apis mellifera)

Bezabih

Cheng

Han

et al. 2017

Sci Rep

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“…Because we were unable to detect AstA5 in the mass spectrometric analysis, we conducted a sequence comparison of this peptide in ant species with genome data available. We blasted the respective C. floridanus peptide sequence against the scaffold assembly of Acromyrmex echinatior (Nygaard et al, ), Atta cephalotes (Suen et al, ), Harpegnathos saltator (Bonasio et al, ), Lasius niger, Linepithema humile (Smith et al, ), Pogonomyrmex barbatus (Smith et al, ), and Solenopsis invicta (Wurm et al, ) in the database of the National Center for Biotechnology Information (http://blast.ncbi.nlm.nih.gov/Blast.cgi) for Lasius niger or the Hymenopteran Genome database (http://hymenopteragenome.org [Elsik et al, ]) for all other ant species, using tblastn and the BLOSUM62 and PAM30 matrix. The sequences were aligned using the default MUSCLE algorithm in Jalview 2.9.0b2 (Waterhouse et al, ).…”

Section: Methodsmentioning

confidence: 99%

Neuropeptides in the desert ant Cataglyphis fortis: Mass spectrometric analysis, localization, and age‐related changes

Schmitt

Vanselow

Schlösser

et al. 2016

J of Comparative Neurology

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Cataglyphis desert ants exhibit an age-related polyethism, with ants performing tasks in the dark nest for the first ∼4 weeks of their adult life before they switch to visually based long-distance navigation to forage. Although behavioral and sensory aspects of this transition have been studied, the internal factors triggering the behavioral changes are largely unknown. We suggest the neuropeptide families allatostatin A (AstA), allatotropin (AT), short neuropeptide F (sNPF), and tachykinin (TK) as potential candidates. Based on a neuropeptidomic analysis in Camponotus floridanus, nano-LC-ESI MS/MS was used to identify these neuropeptides biochemically in Cataglyphis fortis. Furthermore, we show that all identified peptide families are present in the central brain and ventral ganglia of C. fortis whereas in the retrocerebral complex only sNPF could be detected. Immunofluorescence staining against AstA, AT, and TK in the brain revealed arborizations of AstA- and TK-positive neurons in primary sensory processing centers and higher order integration centers, whereas AT immunoreactivity was restricted to the central complex, the antennal mechanosensory and motor center, and the protocerebrum. For artificially dark-kept ants, we found that TK distribution changed markedly in the central complex from days 1 and 7 to day 14 after eclosion. Based on functional studies in Drosophila, this age-related variation of TK is suggestive of a modulatory role in locomotion behavior in C. fortis. We conclude that the general distribution and age-related changes in neuropeptides indicate a modulatory role in sensory input regions and higher order processing centers in the desert ant brain. J. Comp. Neurol. 525:901-918, 2017. © 2016 Wiley Periodicals, Inc.

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“…Protein-coding gene translations were retrieved for vertebrates and plants from Ensembl (13), for arthropods from AgripestBase, AphidBase (14), BeetleBase (15), DiamondBackMoth-DB (16), FlyBase (17), Hymenoptera Genome Database (18), NCBI (19), SilkDB (20), VectorBase (21), wFleaBase (22), as well as the i 5K pilot project (23) and several other genome consortia. Gene sets for the additional metazoan species were retrieved from the Joint Genome Institute (24).…”

Section: Coverage Of Organismsmentioning

confidence: 99%

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

et al. 2016

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OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from a single gene in their last common ancestor. In 2016 OrthoDB reached its 9th release, growing to over 22 million genes from over 5000 species, now adding plants, archaea and viruses. In this update we focused on usability of this fast-growing wealth of data: updating the user and programmatic interfaces to browse and query the data, and further enhancing the already extensive integration of available gene functional annotations. Collating functional annotations from over 100 resources, and enabled us to propose descriptive titles for 87% of ortholog groups. Additionally, OrthoDB continues to provide computed evolutionary annotations and to allow user queries by sequence homology. The OrthoDB resource now enables users to generate publication-quality comparative genomics charts, as well as to upload, analyze and interactively explore their own private data. OrthoDB is available from http://orthodb.org.

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Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine

Cited by 118 publications

References 55 publications

Phosphoproteome Analysis Reveals Phosphorylation Underpinnings in the Brains of Nurse and Forager Honeybees (Apis mellifera)

Phosphoproteome Analysis Reveals Phosphorylation Underpinnings in the Brains of Nurse and Forager Honeybees (Apis mellifera)

Neuropeptides in the desert ant Cataglyphis fortis: Mass spectrometric analysis, localization, and age‐related changes

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

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