Whole genome assembly of various bee species
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ABSTRACT:
PROVIDER: PRJNA163991 | ENA |
REPOSITORIES: ENA
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Project description:BACKGROUND: The honey bee is an important model system for increasing understanding of molecular and neural mechanisms underlying social behaviors relevant to the agricultural industry and basic science. The western honey bee, Apis mellifera, has served as a model species, and its genome sequence has been published. In contrast, the genome of the Asian honey bee, Apis cerana, has not yet been sequenced. A. cerana has been raised in Asian countries for thousands of years and has brought considerable economic benefits to the apicultural industry. A cerana has divergent biological traits compared to A. mellifera and it has played a key role in maintaining biodiversity in eastern and southern Asia. Here we report the first whole genome sequence of A. cerana. RESULTS: Using de novo assembly methods, we produced a 238 Mbp draft of the A. cerana genome and generated 10,651 genes. A.cerana-specific genes were analyzed to better understand the novel characteristics of this honey bee species. Seventy-two percent of the A. cerana-specific genes had more than one GO term, and 1,696 enzymes were categorized into 125 pathways. Genes involved in chemoreception and immunity were carefully identified and compared to those from other sequenced insect models. These included 10 gustatory receptors, 119 odorant receptors, 10 ionotropic receptors, and 160 immune-related genes. CONCLUSIONS: This first report of the whole genome sequence of A. cerana provides resources for comparative sociogenomics, especially in the field of social insect communication. These important tools will contribute to a better understanding of the complex behaviors and natural biology of the Asian honey bee and to anticipate its future evolutionary trajectory.
2015-01-01 | S-EPMC4326529 | BioStudies
Project description:The Asian honey bee (Apis dorsata) is distinct from its more widely distributed cousin Apis mellifera by a few key characteristics. Most prominently, A. dorsata, nest in the open by forming a colony clustered around the honeycomb, whereas A. mellifera nest in concealed cavities. Additionally, the worker and reproductive castes are all of the same size in A. dorsata. In order to investigate these differences, we performed whole genome sequencing of A. dorsata using a hybrid Oxford Nanopore and Illumina approach. The 223?Mb genome has an N50 of 35?kb with the largest scaffold of 302?kb. We have found that there are many genes in the dorsata genome that are distinct from other hymenoptera and also large amounts of transposable elements, and we suggest some candidate genes for A. dorsata's exceptional level of defensive aggression.
2020-01-01 | S-EPMC6953811 | BioStudies
Project description:Supergeneralists, defined as species that interact with multiple groups of species in ecological networks, can act as important connectors of otherwise disconnected species subsets. In Brazil, there are two supergeneralist bees: the honeybee Apis mellifera, a non-native species, and Trigona spinipes, a native stingless bee. We compared the role of both species and the effect of geographic and local factors on networks by addressing three questions: 1) Do both species have similar abundance and interaction patterns (degree and strength) in plant-bee networks? 2) Are both species equally influential to the network structure (nestedness, connectance, and plant and bee niche overlap)? 3) How are these species affected by geographic (altitude, temperature, precipitation) and local (natural vs. disturbed habitat) factors? We analyzed 21 plant-bee weighted interaction networks, encompassing most of the main biomes in Brazil. We found no significant difference between both species in abundance, in the number of plant species with which each bee species interacts (degree), and in the sum of their dependencies (strength). Structural equation models revealed the effect of A. mellifera and T. spinipes, respectively, on the interaction network pattern (nestedness) and in the similarity in bee's interactive partners (bee niche overlap). It is most likely that the recent invasion of A. mellifera resulted in its rapid settlement inside the core of species that retain the largest number of interactions, resulting in a strong influence on nestedness. However, the long-term interaction between native T. spinipes and other bees most likely has a more direct effect on their interactive behavior. Moreover, temperature negatively affected A. mellifera bees, whereas disturbed habitats positively affected T. spinipes. Conversely, precipitation showed no effect. Being positively (T. spinipes) or indifferently (A. mellifera) affected by disturbed habitats makes these species prone to pollinate plant species in these areas, which are potentially poor in pollinators.
2015-01-01 | S-EPMC4565550 | BioStudies
Project description:Background:Here we present a checklist of the bee species found on the C. Hart Merriam elevation gradient along the San Francisco Peaks in northern Arizona. Elevational gradients can serve as natural proxies for climate change, replacing time with space as they span multiple vegetation zones over a short geographic distance. Describing the distribution of bee species along this elevation gradient will help predict how bee communities might respond to changing climate. To address this, we initiated an inventory associated with ecological studies on pollinators that documented bees on the San Francisco Peaks. Sample sites spanned six life zones (vegetation zones) on the San Francisco Peaks from 2009 to 2019. We also include occurrence data from other studies, gathered by querying the Symbiota Collection of Arthropods Network (SCAN) portal covering the San Francisco Peaks region (hereafter referred to as "the Peaks"). New information:Our checklist reports 359 bee species and morphospecies spanning five families and 46 genera that have been collected in the Peaks region. Prior to our concerted sampling effort there were records for 155 bee species, yet there has not been a complete list of bee species inhabiting the Peaks published to date. Over a 10-year period, we documented an additional 204 bee species inhabiting the Peaks. Our study documents range expansions to northern Arizona for 15 species. The majority of these are range expansions from either southern Arizona, southern Utah, or the Rocky Mountain region of Colorado. Nine species are new records for Arizona, four of which are the southernmost record for that species. An additional 15 species are likely undescribed.
2020-01-01 | S-EPMC7145878 | BioStudies
Project description:Apis mellifera intermissa is the native honeybee subspecies of Algeria. A. m. intermissa occurs in Tunisia, Algeria and Morocco, between the Atlas and the Mediterranean and Atlantic coasts. This bee is very important due to its high ability to adapt to great variations in climatic conditions and due to its preferable cleaning behavior. Here we report the draft genome sequence of this honey bee, its Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JSUV00000000. The 240-Mb genome is being annotated and analyzed. Comparison with the genome of other Apis mellifera sub-species promises to yield insights into the evolution of adaptations to high temperature and resistance to Varroa parasite infestation.
1000-01-01 | S-EPMC4536049 | BioStudies
Project description:In face of a dramatic decline of wild bee species in many rural landscapes, potential conservation functions of urban areas gain importance. Yet effects of urbanization on pollinators, and in particular on wild bees, remain ambiguous and not comprehensively understood. This is especially true for amenity grassland and extensively managed wastelands within large-scale residential housing areas. Using Berlin as a study region, we aimed to investigate (a) if these greenspaces are accepted by wild bee assemblages as foraging habitats; (b) how assemblage structure of bees and individual bee species are affected by different habitat (e.g., management, flower density) and urban matrix variables (e.g., isolation, urbanization); and (c) to what extent grassland restoration can promote bees in urban environments. In summer 2012, we collected 62 bee species belonging to more than 20% of the taxa known for Berlin. Urbanization significantly affected species composition of bees; 18 species were affiliated to different levels of urbanization. Most bee species were not affected by any of the environmental variables tested, and urbanization had a negative effect only for one bee species. Further, we determined that restoration of diverse grasslands positively affected bee species richnesss in urban environments. We conclude that differently structured and managed greenspaces in large-scale housing areas can provide additional foraging habitats and refuges for pollinators. This supports approaches towards a biodiversity friendly management within urban regions and may be of particular importance given that anthropogenic pressure is increasing in many rural landscapes.
2016-01-01 | S-EPMC5131621 | BioStudies
Project description:Pollinator refuges such as wildflower strips are planted on farms with the goals of mitigating wild pollinator declines and promoting crop pollination services. It is unclear, however, whether or how these goals are impacted by managed honey bee (Apis mellifera L.) hives on farms. We examined how wildflower strips and honey bee hives and/or their interaction influence wild bee communities and the fruit count of two pollinator-dependent crops across 21 farms in the Mid-Atlantic U.S. Although wild bee species richness increased with bloom density within wildflower strips, populations did not differ significantly between farms with and without them whereas fruit counts in both crops increased on farms with wildflower strips during one of 2 years. By contrast, wild bee abundance decreased by 48%, species richness by 20%, and strawberry fruit count by 18% across all farm with honey bee hives regardless of wildflower strip presence, and winter squash fruit count was consistently lower on farms with wildflower strips with hives as well. This work demonstrates that honey bee hives could detrimentally affect fruit count and wild bee populations on farms, and that benefits conferred by wildflower strips might not offset these negative impacts. Keeping honey bee hives on farms with wildflower strips could reduce conservation and pollination services.
2021-01-01 | S-EPMC7865060 | BioStudies
Project description:Bumble bees are ecologically and economically important insect pollinators. Three abundant and widespread species in western North America, Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii, have been the focus of substantial research relating to diverse aspects of bumble bee ecology and evolutionary biology. We present de novo genome assemblies for each of the three species using hybrid assembly of Illumina and Oxford Nanopore Technologies sequences. All three assemblies are of high quality with large N50s (> 2.2 Mb), BUSCO scores indicating > 98% complete genes, and annotations producing 13,325 - 13,687 genes, comparing favorably with other bee genomes. Analysis of synteny against the most complete bumble bee genome, Bombus terrestris, reveals a high degree of collinearity. These genomes should provide a valuable resource for addressing questions relating to functional genomics and evolutionary biology in these species.
2020-01-01 | S-EPMC7407468 | BioStudies
Project description:The official standard for quality control of honey is currently based on physicochemical properties. However, this method is time-consuming, cost intensive, and does not lead to information on the originality of honey. This study aims to classify raw stingless bee honeys by bee species origins as a potential classifier using the NMR-LCMS-based metabolomics approach. Raw stingless bee honeys were analysed and classified by bee species origins using proton nuclear magnetic resonance (¹H-NMR) spectroscopy and an ultra-high performance liquid chromatography-quadrupole time of flight mass spectrometry (UHPLC-QTOF MS) in combination with chemometrics tools. The honey samples were able to be classified into three different groups based on the bee species origins of Heterotrigona itama, Geniotrigona thoracica, and Tetrigona apicalis. d-Fructofuranose (H. itama honey), ?-d-Glucose, d-Xylose, ?-d-Glucose (G. thoracica honey), and l-Lactic acid, Acetic acid, l-Alanine (T. apicalis honey) ident d-Fructofuranose identified via ¹H-NMR data and the diagnostic ions of UHPLC-QTOF MS were characterized as the discriminant metabolites or putative chemical markers. It could be suggested that the quality of honey in terms of originality and purity can be rapidly determined using the classification technique by bee species origins via the ¹H-NMR- and UHPLC-QTOF MS-based metabolomics approach.
1000-01-01 | S-EPMC6225217 | BioStudies
Project description:Pollinator reductions can leave communities less diverse and potentially at increased risk of infectious diseases. Species-rich plant and bee communities have high species turnover, making the study of disease dynamics challenging. To address how temporal dynamics shape parasite prevalence in plant and bee communities, we screened >5,000?bees and flowers over an entire growing season for five common bee microparasites (Nosema ceranae, Nosema bombi, Crithidia bombi, Crithidia expoeki and neogregarines). Over 110?bee species and 89?flower species were screened, revealing that 42% of bee species (12.2% individual bees) and 70% of flower species (8.7% individual flowers) had at least one parasite in or on them, respectively. Some common flowers (for example, Lychnis flos-cuculi) harboured multiple parasite species whilst others (for example, Lythrum salicaria) had few. Significant temporal variation of parasite prevalence in bees was linked to bee diversity, bee and flower abundance and community composition. Specifically, we found that bee communities had the highest prevalence late in the season, when social bees (Bombus spp. and Apis mellifera) were dominant and bee diversity was lowest. Conversely, prevalence on flowers was lowest late in the season when floral abundance was highest. Thus turnover in the bee community impacted community-wide prevalence, and turnover in the plant community impacted when parasite transmission was likely to occur at flowers. These results imply that efforts to improve bee health will benefit from the promotion of high floral numbers to reduce transmission risk, maintaining bee diversity to dilute parasites and monitoring the abundance of dominant competent hosts.
2020-01-01 | S-EPMC7529964 | BioStudies