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Article ; Online: Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses.

Walsh, Amy T / Triant, Deborah A / Le Tourneau, Justin J / Shamimuzzaman, Md / Elsik, Christine G

2021 Volume 50, Issue D1, Page(s) D1032–D1039

Abstract: We report an update of the Hymenoptera Genome Database (HGD; http://HymenopteraGenome.org), a genomic database of hymenopteran insect species. The number of species represented in HGD has nearly tripled, with fifty-eight hymenopteran species, including ... ...

Abstract	We report an update of the Hymenoptera Genome Database (HGD; http://HymenopteraGenome.org), a genomic database of hymenopteran insect species. The number of species represented in HGD has nearly tripled, with fifty-eight hymenopteran species, including twenty bees, twenty-three ants, eleven wasps and four sawflies. With a reorganized website, HGD continues to provide the HymenopteraMine genomic data mining warehouse and JBrowse/Apollo genome browsers integrated with BLAST. We have computed Gene Ontology (GO) annotations for all species, greatly enhancing the GO annotation data gathered from UniProt with more than a ten-fold increase in the number of GO-annotated genes. We have also generated orthology datasets that encompass all HGD species and provide orthologue clusters for fourteen taxonomic groups. The new GO annotation and orthology data are available for searching in HymenopteraMine, and as bulk file downloads.
MeSH term(s)	Animals ; Computational Biology ; Databases, Genetic ; Genome, Insect/genetics ; Genomics/classification ; Hymenoptera/classification ; Hymenoptera/genetics ; Molecular Sequence Annotation ; Software
Language	English
Publishing date	2021-11-07
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab1018
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Article ; Online: Multi-tiered analyses of honey bees that resist or succumb to parasitic mites and viruses.

Weaver, Daniel B / Cantarel, Brandi L / Elsik, Christine G / Boncristiani, Dawn L / Evans, Jay D

BMC genomics

2021 Volume 22, Issue 1, Page(s) 720

Abstract: Background: Varroa destructor mites, and the numerous viruses they vector to their honey bee hosts, are among the most serious threats to honey bee populations, causing mortality and morbidity to both the individual honey bee and colony, the negative ... ...

Abstract	Background: Varroa destructor mites, and the numerous viruses they vector to their honey bee hosts, are among the most serious threats to honey bee populations, causing mortality and morbidity to both the individual honey bee and colony, the negative effects of which convey to the pollination services provided by honey bees worldwide. Here we use a combination of targeted assays and deep RNA sequencing to determine host and microbial changes in resistant and susceptible honey bee lineages. We focus on three study sets. The first involves field sampling of sympatric western bees, some derived from resistant stock and some from stock susceptible to mites. The second experiment contrasts three colonies more deeply, two from susceptible stock from the southeastern U.S. and one from mite-resistant bee stock from Eastern Texas. Finally, to decouple the effects of mites from those of the viruses they vector, we experimentally expose honey bees to DWV in the laboratory, measuring viral growth and host responses. Results: We find strong differences between resistant and susceptible bees in terms of both viral loads and bee gene expression. Interestingly, lineages of bees with naturally low levels of the mite-vectored Deformed wing virus, also carried lower levels of viruses not vectored by mites. By mapping gene expression results against current ontologies and other studies, we describe the impacts of mite parasitism, as well as viruses on bee health against two genetic backgrounds. We identify numerous genes and processes seen in other studies of stress and disease in honey bee colonies, alongside novel genes and new patterns of expression. Conclusions: We provide evidence that honey bees surviving in the face of parasitic mites do so through their abilities to resist the presence of devastating viruses vectored by these mites. In all cases, the most divergence between stocks was seen when bees were exposed to live mites or viruses, suggesting that gene activation, rather than constitutive expression, is key for these interactions. By revealing responses to viral infection and mite parasitism in different lineages, our data identify candidate proteins for the evolution of mite tolerance and virus resistance.
MeSH term(s)	Animals ; Bees ; RNA Viruses/genetics ; Varroidae ; Viral Load ; Virus Diseases
Language	English
Publishing date	2021-10-06
Publishing country	England
Document type	Journal Article
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-021-08032-z
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Article ; Online: The pea aphid genome sequence brings theories of insect defense into question.

Elsik, Christine G

Genome biology

2010 Volume 11, Issue 2, Page(s) 106

Abstract: The genome sequence of the pea aphid is the first for a basal hemimetabolous insect and provides insights into developmental plasticity, symbiosis and insect immunity. ...

Abstract	The genome sequence of the pea aphid is the first for a basal hemimetabolous insect and provides insights into developmental plasticity, symbiosis and insect immunity.
MeSH term(s)	Animals ; Aphids/genetics ; Aphids/immunology ; Aphids/microbiology ; Buchnera/physiology ; Genome, Insect ; Immunity/genetics ; Symbiosis/genetics
Language	English
Publishing date	2010
Publishing country	England
Document type	Comment ; Journal Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/gb-2010-11-2-106
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Article: Nuclear translocation of vitellogenin in the honey bee (

Salmela, Heli / Harwood, Gyan P / Münch, Daniel / Elsik, Christine G / Herrero-Galán, Elías / Vartiainen, Maria K / Amdam, Gro V

Apidologie

2022 Volume 53, Issue 1, Page(s) 13

Abstract: Vitellogenin (Vg) is a conserved protein used by nearly all oviparous animals to produce eggs. It is also pleiotropic and performs functions in oxidative stress resistance, immunity, and, in honey bees, behavioral development of the worker caste. It has ... ...

Abstract	Vitellogenin (Vg) is a conserved protein used by nearly all oviparous animals to produce eggs. It is also pleiotropic and performs functions in oxidative stress resistance, immunity, and, in honey bees, behavioral development of the worker caste. It has remained enigmatic how Vg affects multiple traits. Here, we asked whether Vg enters the nucleus and acts via DNA-binding. We used cell fractionation, immunohistology, and cell culture to show that a structural subunit of honey bee Vg translocates into cell nuclei. We then demonstrated Vg-DNA binding theoretically and empirically with prediction software and chromatin immunoprecipitation with sequencing (ChIP-seq), finding binding sites at genes influencing immunity and behavior. Finally, we investigated the immunological and enzymatic conditions affecting Vg cleavage and nuclear translocation and constructed a 3D structural model. Our data are the first to show Vg in the nucleus and suggest a new fundamental regulatory role for this ubiquitous protein. Supplementary information: The online version contains supplementary material available at 10.1007/s13592-022-00914-9.
Language	English
Publishing date	2022-03-15
Publishing country	France
Document type	Journal Article
ZDB-ID	280429-3
ISSN	1297-9678 ; 0044-8435 ; 0365-5407
ISSN (online)	1297-9678
ISSN	0044-8435 ; 0365-5407
DOI	10.1007/s13592-022-00914-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Nuclear translocation of vitellogenin in the honey bee (Apis mellifera)

Salmela, Heli / Harwood, Gyan P. / Münch, Daniel / Elsik, Christine G. / Herrero-Galán, Elías / Vartiainen, Maria K. / Amdam, Gro V.

Apidologie. 2022 Mar., v. 53, no. 1

2022

Abstract	Vitellogenin (Vg) is a conserved protein used by nearly all oviparous animals to produce eggs. It is also pleiotropic and performs functions in oxidative stress resistance, immunity, and, in honey bees, behavioral development of the worker caste. It has remained enigmatic how Vg affects multiple traits. Here, we asked whether Vg enters the nucleus and acts via DNA-binding. We used cell fractionation, immunohistology, and cell culture to show that a structural subunit of honey bee Vg translocates into cell nuclei. We then demonstrated Vg-DNA binding theoretically and empirically with prediction software and chromatin immunoprecipitation with sequencing (ChIP-seq), finding binding sites at genes influencing immunity and behavior. Finally, we investigated the immunological and enzymatic conditions affecting Vg cleavage and nuclear translocation and constructed a 3D structural model. Our data are the first to show Vg in the nucleus and suggest a new fundamental regulatory role for this ubiquitous protein.
Keywords	Apis mellifera ; cell culture ; cell fractionation ; chromatin immunoprecipitation ; computer software ; honey ; immunity ; models ; ovipary ; oxidative stress ; prediction ; stress tolerance ; vitellogenin
Language	English
Dates of publication	2022-03
Size	p. 13.
Publishing place	Springer Paris
Document type	Article
ZDB-ID	280429-3
ISSN	1297-9678 ; 0044-8435 ; 0365-5407
ISSN (online)	1297-9678
ISSN	0044-8435 ; 0365-5407
DOI	10.1007/s13592-022-00914-9
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Toward a data infrastructure for the Plant Cell Atlas

Fahlgren, Noah / Kapoor, Muskan / Yordanova, Galabina / Papatheodorou, Irene / Waese, Jamie / Cole, Benjamin / Harrison, Peter / Ware, Doreen / Tickle, Timothy / Paten, Benedict / Burdett, A. F. M. / Elsik, Christine G. / Tuggle, Christopher K. / Provart, Nicholas J.

Plant Physiology. 2023 Jan. 01, v. 191, no. 1 p.35-46

2023

Abstract: We review how a data infrastructure for the Plant Cell Atlas might be built using existing infrastructure and platforms. The Human Cell Atlas has developed an extensive infrastructure for human and mouse single cell data, while the European ... ...

Abstract	We review how a data infrastructure for the Plant Cell Atlas might be built using existing infrastructure and platforms. The Human Cell Atlas has developed an extensive infrastructure for human and mouse single cell data, while the European Bioinformatics Institute has developed a Single Cell Expression Atlas, that currently houses several plant data sets. We discuss issues related to appropriate ontologies for describing a plant single cell experiment. We imagine how such an infrastructure will enable biologists and data scientists to glean new insights into plant biology in the coming decades, as long as such data are made accessible to the community in an open manner.
Keywords	bioinformatics ; humans ; infrastructure ; plant physiology
Language	English
Dates of publication	2023-0101
Size	p. 35-46.
Publishing place	Oxford University Press (OUP)
Document type	Article ; Online
Note	Resource is Open Access
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1093/plphys/kiac468
Database	NAL-Catalogue (AGRICOLA)

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Article: The pea aphid genome sequence brings theories of insect defense into question

Elsik, Christine G

Genome biology. 2010 Feb., v. 11, no. 2

2010

Abstract: The genome sequence of the pea aphid is the first for a basal hemimetabolous insect and provides insights into developmental plasticity, symbiosis and insect immunity. ...

Abstract	The genome sequence of the pea aphid is the first for a basal hemimetabolous insect and provides insights into developmental plasticity, symbiosis and insect immunity.
Keywords	Acyrthosiphon pisum ; insect immunity ; insects ; nucleotide sequences ; symbiosis
Language	English
Dates of publication	2010-02
Size	p. 2400.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/gb-2010-11-2-106
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Differential gene expression in response to eCry3.1Ab ingestion in an unselected and eCry3.1Ab-selected western corn rootworm (Diabrotica virgifera virgifera LeConte) population.

Zhao, Zixiao / Meihls, Lisa N / Hibbard, Bruce E / Ji, Tieming / Elsik, Christine G / Shelby, Kent S

Scientific reports

2019 Volume 9, Issue 1, Page(s) 4896

Abstract: Diabrotica virgifera virgifera LeConte, the western corn rootworm (WCR) is one of the most destructive pests in the U.S. Corn Belt. Transgenic maize lines expressing various Cry toxins from Bacillus thuringiensis have been adopted as a management ... ...

Abstract	Diabrotica virgifera virgifera LeConte, the western corn rootworm (WCR) is one of the most destructive pests in the U.S. Corn Belt. Transgenic maize lines expressing various Cry toxins from Bacillus thuringiensis have been adopted as a management strategy. However, resistance to many Bt toxins has occurred. To investigate the mechanisms of Bt resistance we carried out RNA-seq using Illumina sequencing technology on resistant, eCry3.1Ab-selected and susceptible, unselected, whole WCR neonates which fed on seedling maize with and without eCry3.1Ab for 12 and 24 hours. In a parallel experiment RNA-seq experiments were conducted when only the midgut of neonate WCR was evaluated from the same treatments. After de novo transcriptome assembly we identified differentially expressed genes (DEGs). Results from the assemblies and annotation indicate that WCR neonates from the eCry3.1Ab-selected resistant colony expressed a small number of up and down-regulated genes following Bt intoxication. In contrast, unselected susceptible WCR neonates expressed a large number of up and down-regulated transcripts in response to intoxication. Annotation and pathway analysis of DEGs between susceptible and resistant whole WCR and their midgut tissue revealed genes associated with cell membrane, immune response, detoxification, and potential Bt receptors which are likely related to eCry3.1Ab resistance. This research provides a framework to study the toxicology of Bt toxins and mechanism of resistance in WCR, an economically important coleopteran pest species.
MeSH term(s)	Animals ; Bacillus thuringiensis/genetics ; Bacillus thuringiensis Toxins ; Bacterial Proteins/genetics ; Coleoptera/genetics ; Endotoxins/genetics ; Hemolysin Proteins/genetics ; Insecticide Resistance/genetics ; Larva/genetics ; Pest Control, Biological ; Plants, Genetically Modified ; Zea mays/genetics
Chemical Substances	Bacillus thuringiensis Toxins ; Bacterial Proteins ; Endotoxins ; Hemolysin Proteins ; insecticidal crystal protein, Bacillus Thuringiensis
Language	English
Publishing date	2019-03-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-41067-7
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Article ; Online: AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes.

Triant, Deborah A / Walsh, Amy T / Hartley, Gabrielle A / Petry, Bruna / Stegemiller, Morgan R / Nelson, Benjamin M / McKendrick, Makenna M / Fuller, Emily P / Cockett, Noelle E / Koltes, James E / McKay, Stephanie D / Green, Jonathan A / Murdoch, Brenda M / Hagen, Darren E / Elsik, Christine G

Mammalian genome : official journal of the International Mammalian Genome Society

2023 Volume 34, Issue 3, Page(s) 418–436

Abstract: Current genome sequencing technologies have made it possible to generate highly contiguous genome assemblies for non-model animal species. Despite advances in genome assembly methods, there is still room for improvement in the delineation of specific ... ...

Abstract	Current genome sequencing technologies have made it possible to generate highly contiguous genome assemblies for non-model animal species. Despite advances in genome assembly methods, there is still room for improvement in the delineation of specific gene features in the genomes. Here we present genome visualization and annotation tools to support seven livestock species (bovine, chicken, goat, horse, pig, sheep, and water buffalo), available in a new resource called AgAnimalGenomes. In addition to supporting the manual refinement of gene models, these browsers provide visualization tracks for hundreds of RNAseq experiments, as well as data generated by the Functional Annotation of Animal Genomes (FAANG) Consortium. For species with predicted gene sets from both Ensembl and RefSeq, the browsers provide special tracks showing the thousands of protein-coding genes that disagree across the two gene sources, serving as a valuable resource to alert researchers to gene model issues that may affect data interpretation. We describe the data and search methods available in the new genome browsers and how to use the provided tools to edit and create new gene models.
MeSH term(s)	Animals ; Cattle ; Swine ; Horses/genetics ; Sheep/genetics ; Animals, Domestic/genetics ; Molecular Sequence Annotation ; Databases, Genetic ; Genome/genetics ; Chromosome Mapping ; Goats/genetics
Language	English
Publishing date	2023-07-17
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1058547-3
ISSN	1432-1777 ; 0938-8990
ISSN (online)	1432-1777
ISSN	0938-8990
DOI	10.1007/s00335-023-10008-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 3489: Show issues

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Article ; Online: Toward a data infrastructure for the Plant Cell Atlas.

Fahlgren, Noah / Kapoor, Muskan / Yordanova, Galabina / Papatheodorou, Irene / Waese, Jamie / Cole, Benjamin / Harrison, Peter / Ware, Doreen / Tickle, Timothy / Paten, Benedict / Burdett, Tony / Elsik, Christine G / Tuggle, Christopher K / Provart, Nicholas J

Plant physiology

2022 Volume 191, Issue 1, Page(s) 35–46

Abstract	We review how a data infrastructure for the Plant Cell Atlas might be built using existing infrastructure and platforms. The Human Cell Atlas has developed an extensive infrastructure for human and mouse single cell data, while the European Bioinformatics Institute has developed a Single Cell Expression Atlas, that currently houses several plant data sets. We discuss issues related to appropriate ontologies for describing a plant single cell experiment. We imagine how such an infrastructure will enable biologists and data scientists to glean new insights into plant biology in the coming decades, as long as such data are made accessible to the community in an open manner.
MeSH term(s)	Animals ; Humans ; Mice ; Plant Cells ; Computational Biology ; Plants/genetics
Language	English
Publishing date	2022-10-11
Publishing country	United States
Document type	Review ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1093/plphys/kiac468
Database	MEDical Literature Analysis and Retrieval System OnLINE

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