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Apis mellifera graph genome
<p><strong>AmelGraph 1.1.0</strong></p> <p>We aligned 5 different publicly available assemblies with the cactus pangenome workflow (v2.0.5):</p> <table> <tbody> <tr> <td> <p><strong>Use </strong></p> </td> <td> <p><strong>Species </strong></p> </td> <td> <p><strong>Genome ID </strong></p> </td> <td> <p><strong>Accession </strong></p> </td> <td> <p><strong>Graph ID </strong></p> </td> <td> <p><strong>Size (Mb) </strong></p> </td> </tr> <tr> <td> <p>Reference </p> </td> <td> <p><em>A. mellifera</em> (DH4) </p> </td> <td> <p>Amel_HAv3.1 </p> </td> <td> <p>GCF_003254395.2 </p> </td> <td> <p>DH4 </p> </td> <td> <p>225.2 </p> </td> </tr> <tr> <td> <p>Derivate </p> </td> <td> <p><em>A. m. mellifera </em></p> </td> <td> <p>INRA_AMelMel_1.0 </p> </td> <td> <p>GCA_003314205.1 </p> </td> <td> <p>mellifera </p> </td> <td> <p>227.0 </p> </td> </tr> <tr> <td> <p>Derivate </p> </td> <td> <p><em>A. m. carnica </em></p> </td> <td> <p>ASM1384124v2 </p> </td> <td> <p>GCA_013841245.2 </p> </td> <td> <p>carnica </p> </td> <td> <p>226.0 </p> </td> </tr> <tr> <td> <p>Derivate </p> </td> <td> <p><em>A. m. caucasica </em></p> </td> <td> <p>ASM1384120v1 </p> </td> <td> <p>GCA_013841205.1 </p> </td> <td> <p>caucasica </p> </td> <td> <p>224.8 </p> </td> </tr> <tr> <td> <p>Derivate </p> </td> <td> <p><em>A. m. ligustica </em></p> </td> <td> <p>ASM1932182v1 </p> </td> <td> <p>GCA_019321825.1 </p> </td> <td> <p>ligustica </p> </td> <td> <p>231.1 </p> </td> </tr> </tbody> </table> <p> </p> <p>We used the cactus<sup>1</sup> <a href="https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md">pangenome workflow</a><a href="https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md"> </a>to generate a 5-ways pangenome alignment, masking in blocks of 10Kb, and considering all the sequences in the different data. Due to incompatibilities with the pangenome workflow generation of the indexes, we regenerated the giraffe indexes from the output GFA/VCF file. We also downloaded annotations available for three genomes (DH4, <em>A. m. carnica</em> and <em>A. m. caucasica</em>), modifying the naming of the contigs to include the subspecies name (i.e. 'LG1' for <em>A. m. caucasica</em> modified to 'caucasica.LG1'). We then ran the vg autoindex function:</p> <pre><code>vg autoindex -w giraffe -o pangenome -t 8 -T ./TMP -x carnica.gff -x caucasica.gff -R XG -x DH4.gff</code></pre> <p>We compared this 'full' cactus graph to one built using only sequence on the linkage groups, and to one generated using the <a href="https://github.com/pangenome/pggb">PGGB workflow</a>. We evaluated the different graphs using <a href="https://github.com/pangenome/pgge">PGGE</a>. This full cactus graph returned the highst aligned identity, sequence matches, and unique alignments, while having the lowest number of multiple mapping and missing alignments.</p> <p> </p> <table> <tbody> <tr> <td> <p><strong>Parameter </strong></p> </td> <td> <p><strong>CACTUS (LG) </strong></p> </td> <td> <p><strong>CACTUS (FULL) </strong></p> </td> <td> <p><strong>PGGB (norm) </strong></p> </td> </tr> <tr> <td> <p>HAv3.1 size </p> </td> <td> <p>221,626,419 </p> </td> <td> <p>225,250,884 </p> </td> <td> <p>225,250,884 </p> </td> </tr> <tr> <td> <p>Graph length (bp) </p> </td> <td> <p>243,077,200 </p> </td> <td> <p>246,675,144 </p> </td> <td> <p>315,672,860 </p> </td> </tr> <tr> <td> <p>Extra sequence </p> </td> <td> <p>21,450,781 </p> </td> <td> <p>21,424,260 </p> </td> <td> <p>90,421,976 </p> </td> </tr> <tr> <td> <p># nodes </p> </td> <td> <p>17,120,383 </p> </td> <td> <p>11,664,080 </p> </td> <td> <p>17,952,597 </p> </td> </tr> <tr> <td> <p># edges </p> </td> <td> <p>21,385,634 </p> </td> <td> <p>15,990,593 </p> </td> <td> <p>21,702,958 </p> </td> </tr> </tbody> </table> <p> </p> <p><strong>References</strong></p> <p>1. Armstrong, J. <em>et al</em>. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. <em>Nature</em> <strong>587</strong>, (2020). </p> <p> </p>
Feeding with plant powders increases longevity and body weight of Western honeybee workers (Apis mellifera)
<p>Beekeepers routinely substitute honey from managed western honeybees, <em>Apis mellifera</em>, colonies with sugar water post-harvest, potentially leading to malnutrition. Although nutritional supplements have been created, a general consensus on proper colony nutrition for beekeeping has yet to be reached. Thus, finding easily obtainable fortified <em>A. mellifera</em> food alternatives is still of interest. Here, we test plant powder-enriched food supplements since <em>a priori</em> evidence suggests plant extracts can enhance dry body weight and longevity of workers. Freshly emerged workers were kept in hoarding cages (N=69 days) and fed either with 50 % (w/v) sucrose solution alone or additionally with one of 12 powders: <em>Laurus nobilis, Quercus </em>spp<em>., Curcuma longa, Hypericum </em>spp<em>., Spirulina platensis, Calendula officinalis, Chlorella vulgaris, Melissa officinalis, Moringa oleifera, Rosa canina, Trigonella foenum-graecum, </em>and<em> Urtica dioica </em>(N=2028 workers total). The dry body weight was significantly increased in <em>Quercus</em> spp., <em>Hypericum</em> spp., <em>Spirunlina platensis, Mellisa officinalis, Moringa oelifera</em>, and <em>Trigonella foenum-graecum</em> treatments. Further, the longevity was significantly increased in <em>Quercus </em>spp., <em>Curcuma longa, Calendulae officinalis, Chlorella vulgaris, Melissa officinalis, Rosa canina, Trigonella foenum-graecum, </em>and<em> Urtica diocia</em> treatments<em>.</em> Given that plant extracts can enhance <em>A. mellifera</em> health, plant powders possibly provide additional macro- (i.e. proteins, lipids, peptides) and micronutrients (minerals and vitamins) thereby enhancing nutrient availability. Further investigations into the mechanisms underlying these effects and field studies are recommended to validate these findings in real-hive scenarios.</p>
Identification data for discrimination between Apis mellifera pomonella from Kazakhstan and honey bees from other parts of the world
<p>The data in dw.xml file can be used for identification of <em>Apis mellifera pomonella</em> from Kazakhstan. This file should be open in IdentiFly software http://drawwing.org/identifly and used as classification data. The discrimination is based on 19 landmarks of a forewing. For more details see:</p> <p><br>Nawrocka A., Kandemir I., Fuchs S., Tofilski A. 2018. Computer software for identification of honey bee subspecies and evolutionary lineages. Apidologie 49: 172-184. https://doi.org/10.1007/s13592-017-0538-y</p> <p>Temirbayeva, K., Torekhanov A., Nuralieva U., Sheralieva Z., Tofilski A. 2023. In Search of Apis mellifera pomonella in Kazakhstan. Life 13:1860. https://doi.org/10.3390/life13091860</p>
The more the better: Fatty acids are predictive markers of honey bee, Apis mellifera, worker longevity
<p>Fatty acids (FA), stemming from nutrition, form triglycerides that are key components for insect energy reserves. In managed <em>Apis mellifera</em> colonies, supplementary feeding is common practice, yet micronutrients and microbiota (i.e. B-vitamins and probiotics) are often neglected. Given that B-vitamins are obligate cofactors for FA metabolism, and probiotics likely play key roles as well (i.e. <em>Lactobacillus</em> spp. synthesize B-vitamins), understanding how they contribute to FA acquisition remains unknown. Indeed, FAs are established predictors to <em>A. mellifera</em> longevity, and as such, are a logical point of interest in long-lived "winter" bees, where <em>A. mellifera</em> colony losses typically occur. Here, in a hoarding cage trial, freshly emerged adult winter workers were exposed to antibiotics (ABX) to decouple innate benefits associated to native gut microbiota, or left unexposed to ABX (N=72 cages, N=2088 experimental workers). Subsequently, all workers were fed different diets containing either probiotics, B-vitamins, with replicate treatments given <em>ad libitum</em> access to pollen (mimicking real-hive scenarios) or left blank (control). At the end of the trial, a subsample (n=356) had their total FA contents analyzed using <u>G</u>as <u>C</u>hromatography coupled to <u>F</u>lame <u>I</u>onization <u>D</u>etector (GC-FID). Irrespective of dietary treatment, every worker contained all 11 identified FAs, aligning our results with <em>a priori</em> evidence and highlighting their underlying key roles for bee physiology and health. We show for the first time that B-vitamins alone did not improve the overall abundance of individual FAs (g), yet significant differences were associated with presence/absence of bacteria and/or access to pollen, reconfirming likely ties of microbiota aiding in nutrient breakdown of complex polysaccharides found in pollen. Finally, of clear importance, there was a positive significant correlation between total lipid content and worker longevity (+2.4 median day lifespan increase / mg of FA), thereby confirming the relevance of FAs for honey bee worker longevity.</p>
Fig. 1 in Differences in volatile composition and sexual morphs in rambutan (Nephelium lappaceum L.) flowers and their effect in the Apis mellifera L. (Hymenoptera, Apidae) attraction
Fig. 1. Relation between compounds in rambutan hermaphrodite flowers from Herradero (Her RH) and Metapa orchard (Her RM), and male flowers (Male RH).
Figure 1 in The association between ClaI polymorphism and hygienic behavior in Apis mellifera
Figure 1. Left image; hygienic colony sample (100% cleaned cells-Carniolan hybrid) and Right image; unhygienic colony sample (71% cleaned cells-Anatolian hybrid).
Fig. 1 in Prevalence Nosema areas of Varroa destructor and first report of sp. in Apis mellifera drone congregation
Fig. 1. Study area. Argentina-Tucumán-Yerba Buena. Image on the left the map of Argentina. On the right, the site that contains the three Drone Congregation Areas (DCA 1 School, DCA 2 Module, DCA 3 Río Muerto), marked with yellow tags and the experimental Apiary in orange. Located in the year 2018-19 in the spring reproductive season.
Fig. 2 in Prevalence Nosema areas of Varroa destructor and first report of sp. in Apis mellifera drone congregation
Fig. 2. Porcentaje de infestación por Varroa destructor (varroa forética) en las ACZ analizadas durante los cuatro años de muestreo.
Figura 1 in Using ( food a sentinel colony of Apis mellifera Hymenoptera: Apidae) to assess pesticides and sources
Figura 1. Imagen de la izquierda: mapa de Argentina y zona de estudio indicada con el círculo amarillo. Imagen de la derecha: rango de hogar de las abejas melíferas pecoreadoras en nuestro apiario experimental en la Escuela de Agricultura y Sacarotecnia, Argentina.
Fig. 4 in Temporal variation in the behavior of Apis mellifera (Hymenoptera: Apidae) and Lycastrirhyncha nitens (Diptera: Syrphidae) on Pontederia sagittata (Commelinales: Pontederiaceae) inflorescences in relation to nectar availability
Fig. 4. Mean (± 95 % CI) standing crop of floral nectar on inflorescences of three floral morphs of Pontederia sagittata during daily periods of video-recording.
Fig. 3 in Temporal variation in the behavior of Apis mellifera (Hymenoptera: Apidae) and Lycastrirhyncha nitens (Diptera: Syrphidae) on Pontederia sagittata (Commelinales: Pontederiaceae) inflorescences in relation to nectar availability
Fig. 3. Mean (± 95 % CI) number and duration of the foraging events recorded by Apis mellifera (A, B) and Lycastrirhyncha nitens (C, D) on inflorescences of L (black circle), M (gray circle) and S (white circle) morphs of Pontederia sagittata during daily periods of video-recording.
Fig. 2 in Temporal variation in the behavior of Apis mellifera (Hymenoptera: Apidae) and Lycastrirhyncha nitens (Diptera: Syrphidae) on Pontederia sagittata (Commelinales: Pontederiaceae) inflorescences in relation to nectar availability
Fig. 2. Total activity time (± 95 % CI) of Apis mellifera and Lycastrirhyncha nites on inflorescences of L (black circle), M (gray circle) and S (white circle) morphs of Pontederia sagittata during daily periods of video-recording.
Fig. 1 in Temporal variation in the behavior of Apis mellifera (Hymenoptera: Apidae) and Lycastrirhyncha nitens (Diptera: Syrphidae) on Pontederia sagittata (Commelinales: Pontederiaceae) inflorescences in relation to nectar availability
Fig. 1. Position of styles and stamens and differences in pollen size in the three floral morphs of Pontederia sp. a) long-styled [L], b) mid-styled [M] and c) shortstyled [S] (Zomlefer 1994). Legitimate pollinations are indicated by arrows.
Figures 1-4 in Ultrastructural detection of lipids in the cephalic salivary glands of Apis mellifera and Scaptotrigona postica (Hymenoptera: Apidae) workers
Figures 1-4. Lipids, detected using imidazole-osmium, in cephalic salivary gland (CSG) cells of Apis mellifera workers. (1-2) Small droplets of lipid (arrows) dispersed in the cellular cytoplasm of a newly emerged worker (NE), mitochondria (m) of medium electron density and narrow alveolar lumens (l) containing scarce IO-positive secretion (s). (3-4) Gland cells from workers working in the brood comb area (CA). Note lipid droplets dispersed in the cytoplasm (arrows) (1C), heterogeneous granules (gr) (1D) and large amounts of lipid secretion (s) in the alveolar lumen (l). (c) Cuticle, (n) nuclei. Scale bars: 1, 2, 4 = 1 µm, 3 = 3 µm.
Figures 5-8 in Ultrastructural detection of lipids in the cephalic salivary glands of Apis mellifera and Scaptotrigona postica (Hymenoptera: Apidae) workers
Figures 5-8. Imidazole-osmium preparations for lipid detection in gland cells from Apis mellifera workers. (5-6) Gland cells from worker working in the brood comb area (CA) (5) and forager (FO) (6) showing lipid droplets dispersed in the apical region (arrow), infolds (i) of the apical membrane forming channels flanked by mitochondria (m). (6) Note the presence of lipid droplets in the apical channels (arrows). (7-8) Osmium-imidazole-positive dots spread in the cytoplasm (arrows) and vesicles (ve) of forager cellular glands. (c) Cuticle, (s) secretion. Scale bars: 5 = 3 µm, 6 = 2 µm, 7-8 = 1 µm.
Figure 1 in Comparison of two morphometric methods for discriminating honey bee (Apis mellifera L.) populations in Turkey
Figure 1. Sampling locations in Turkey (Thrace: 1–2; Aegean: 3; Central Anatolia/ Mediterranean: 4–11; Southeastern Anatolia: 12–13; Northeastern Anatolia: 14–15).
Fig. 1 in Effect of entomopathogens on Africanized Apis mellifera L. (Hymenoptera: Apidae)
Fig. 1. Survival curve (hours) of Africanized Apis mellifera workers. (A) Entomopathogens sprayed on A. mellifera, (B) entomopathogens on a smooth surface, (C) entomopathogens on soy leaves and (D) entomopathogens mixed with candy paste. Kaplan–Meier vs Weibull survival test adjusted for time (h). Temperature 27 ± 2 ◦ C, 12-h photophase and relative humidity of 60 ± 10%. Sterilized distilled water.
Fig. 1 in Behavioral repertoires and interactions between Apis mellifera (Hymenoptera: Apidae) and the native bee Lithurgus littoralis (Hymenoptera: Megachilidae) in flowers of Opuntia huajuapensis (Cactaceae) in the Tehuacán desert
Fig. 1. Behavior accumulation curves of bees in 150 flowers of Opuntia huajuapensis. A: Apis mellifera (1) and Lithurgus littoralis (2). B: L. littoralis females (3) and L. littoralis males (4). Dotted lines indicate the 95% confidence intervals.
Fig. 2 in Behavioral repertoires and interactions between Apis mellifera (Hymenoptera: Apidae) and the native bee Lithurgus littoralis (Hymenoptera: Megachilidae) in flowers of Opuntia huajuapensis (Cactaceae) in the Tehuacán desert
Fig. 2. Time spent (A) and mean feeding duration (B) in flowers of Opuntia huajuapensis by Apis mellifera females and Lithurgus littoralis females and males. No A. mellifera males were recorded at any time during the experiment. Vertical bars indicate 95% confidence intervals.
Collection of images and raw coordinates of honey bee (Apis mellifera) wings from the central highlands of Ecuador.
<p>Images and raw coordinates of honey bee (Apis mellifera) wings from the central highlands of Ecuador</p>
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