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BeeBase was an online bioinformatics database that hosted data related to Apis mellifera , the European honey bee along with some pathogens and other species. It was developed in collaboration with the Honey Bee Genome Sequencing Consortium. [1] In 2020 it was archived and replaced by the Hymenoptera Genome Database.
Biological data and services available on BeeBase included:
In Feb 2007, BeeBase consisted of a GBrowser-based genome viewer and a Cmap-based comparative map viewer, both modules of the Generic Model Organism Database (GMOD) project. The genome viewer included tracks for known honey bee genes, predicted gene sets (Ensembl, NCBI, EMBL-Heidelberg), STS markers (Solignac and Hunt linkage maps), honey bee expressed sequence tags (ESTs), homologs in fruit fly, mosquito and other insects and transposable elements. The honey bee comparative map viewer displayed linkage maps and the physical map (genome assembly), highlighting markers that are common among maps.
Additionally, a QTL viewer and a gene expression database were planned. The genome sequence was to serve as a reference to link these diverse data types.
Beebase organized the community annotation of the bee genome in collaboration with Baylor College of Medicine Human Genome Sequencing Center. [2]
The now archived site hosts the genome sequence for apis mellifera along with those of the following pathogens: [1]
Two additional species were under analysis: [1]
A honey bee is a eusocial flying insect within the genus Apis of the bee clade, all native to mainland Afro-Eurasia. After bees spread naturally throughout Africa and Eurasia, humans became responsible for the current cosmopolitan distribution of honey bees, introducing multiple subspecies into South America, North America, and Australia.
Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism and to annotate protein-coding genes and other important genome-encoded features. The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism. For a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome. For the human species, whose genome includes 22 pairs of autosomes and 2 sex chromosomes, a complete genome sequence will involve 46 separate chromosome sequences.
Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. In this branch of genomics, whole or large parts of genomes resulting from genome projects are compared to study basic biological similarities and differences as well as evolutionary relationships between organisms. The major principle of comparative genomics is that common features of two organisms will often be encoded within the DNA that is evolutionarily conserved between them. Therefore, comparative genomic approaches start with making some form of alignment of genome sequences and looking for orthologous sequences in the aligned genomes and checking to what extent those sequences are conserved. Based on these, genome and molecular evolution are inferred and this may in turn be put in the context of, for example, phenotypic evolution or population genetics.
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics.
The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust.
Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the retrieval of genomic information.
The Rat Genome Database (RGD) is a database of rat genomics, genetics, physiology and functional data, as well as data for comparative genomics between rat, human and mouse. RGD is responsible for attaching biological information to the rat genome via structured vocabulary, or ontology, annotations assigned to genes and quantitative trait loci (QTL), and for consolidating rat strain data and making it available to the research community. They are also developing a suite of tools for mining and analyzing genomic, physiologic and functional data for the rat, and comparative data for rat, mouse, human, and five other species.
The completion of the human genome sequencing in the early 2000s was a turning point in genomics research. Scientists have conducted series of research into the activities of genes and the genome as a whole. The human genome contains around 3 billion base pairs nucleotide, and the huge quantity of data created necessitates the development of an accessible tool to explore and interpret this information in order to investigate the genetic basis of disease, evolution, and biological processes. The field of genomics has continued to grow, with new sequencing technologies and computational tool making it easier to study the genome.
The Honey Bee Genome Sequencing Consortium is an international collaborative group of genomics scientists, scientific organisations and universities trying to decipher the genome sequences of the honey bee. It was formed in 2001 by American scientists. In the US, the project is funded by the National Human Genome Research Institute, the United States Department of Agriculture (USDA), the Texas Agricultural Experiment Station, the University of Illinois Sociogenomics Initiative, and various beekeepers association and the bee industry.
The Pathogen-Host Interactions database (PHI-base) is a biological database that contains manually curated information on genes experimentally proven to affect the outcome of pathogen-host interactions. The database has been maintained by researchers at Rothamsted Research and external collaborators since 2005. PHI-base has been part of the UK node of ELIXIR, the European life-science infrastructure for biological information, since 2016.
Deformed wing virus (DWV) is an RNA virus, one of 22 known viruses affecting honey bees. While most commonly infecting the honey bee, Apis mellifera, it has also been documented in other bee species, like Bombus terrestris, thus, indicating it may have a wider host specificity than previously anticipated. The virus was first isolated from a sample of symptomatic honeybees from Japan in the early 1980s and is currently distributed worldwide. It is found also in pollen baskets and commercially reared bumblebees. Its main vector in A. mellifera is the Varroa mite. It is named after what is usually the most obvious deformity it induces in the development of a honeybee pupa, which is shrunken and deformed wings, but other developmental deformities are often present.
The Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) was established by Richard A. Gibbs in 1996 when Baylor College of Medicine was chosen as one of six worldwide sites to complete the final phase of the international Human Genome Project. Gibbs is the current director of the BCM-HGSC.
MicrobesOnline is a publicly and freely accessible website that hosts multiple comparative genomic tools for comparing microbial species at the genomic, transcriptomic and functional levels. MicrobesOnline was developed by the Virtual Institute for Microbial Stress and Survival, which is based at the Lawrence Berkeley National Laboratory in Berkeley, California. The site was launched in 2005, with regular updates until 2011.
The western honey bee or European honey bee is the most common of the 7–12 species of honey bees worldwide. The genus name Apis is Latin for "bee", and mellifera is the Latin for "honey-bearing" or "honey carrying", referring to the species' production of honey.
The genetics of social behavior is an area of research that attempts to address the question of the role that genes play in modulating the neural circuits in the brain which influence social behavior. Model genetic species, such as D.melanogaster and Apis mellifera, have been rigorously studied and proven to be instrumental in developing the science of genetics. Many examples of genetic factors of social behavior have been derived from a bottom-up method of altering a gene and observing the change it produces in an organism. Sociogenomics is an integrated field that accounts for the complete cellular genetic complement of an organism from a top-down approach, accounting for all biotic influences that effect behavior on a cellular level.
Digital transcriptome subtraction (DTS) is a bioinformatics method to detect the presence of novel pathogen transcripts through computational removal of the host sequences. DTS is the direct in silico analogue of the wet-lab approach representational difference analysis (RDA), and is made possible by unbiased high-throughput sequencing and the availability of a high-quality, annotated reference genome of the host. The method specifically examines the etiological agent of infectious diseases and is best known for discovering Merkel cell polyomavirus, the suspect causative agent in Merkel-cell carcinoma.
Robert E. Page Jr. is one of the foremost honey bee geneticists in the world and a Foundation Chair of Life Sciences of Arizona State University. An author of more than 250 research papers and articles, his work on the self-organizing regulatory networks of honey bees has been outlined in his book, "The Spirit of the Hive: The Mechanisms of Social Evolution," published by Harvard University Press in 2013. Page currently holds the titles of Arizona State University Provost Emeritus and Regents Professor Emeritus. He is also chair and professor emeritus at the University of California-Davis and an external professor at the Santa Fe Institute.
Apicystis bombi is a species of parasitic alveolates in the phylum Apicomplexa. It infects bees, especially bumblebees. It is believed to have a cosmopolitan distribution in bumblebees and a sporadic occurrence in honey bees, and causes disease symptoms in nonresistant bee species.
SoyBase is a database created by the United States Department of Agriculture. It contains genetic information about soybeans. It includes genetic maps, information about Mendelian genetics and molecular data regarding genes and sequences. It was started in 1990 and is freely available to individuals and organizations worldwide.
Snodgrassella alvi is a species of Gram-negative bacteria within the Neisseriaceae and was previously the only known species of the genus Snodgrassella. It was isolated and scientifically described in 2012 by Waldan K. Kwong and Nancy A. Moran, who named the bacteria after the American entomologist Robert Evans Snodgrass.
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