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The Nuclear and Mitochondrial Genomes of the Facultatively Eusocial Orchid Bee Euglossa dilemma

View ORCID ProfilePhilipp Brand, Nicholas Saleh, Hailin Pan, Cai Li, Karen M. Kapheim and Santiago R. Ramírez
G3: Genes, Genomes, Genetics September 1, 2017 vol. 7 no. 9 2891-2898; https://doi.org/10.1534/g3.117.043687
Philipp Brand
Department for Evolution and Ecology, Center for Population Biology, and University of California, Davis, California 95616Graduate Group in Population Biology, University of California, Davis, California 95616
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  • ORCID record for Philipp Brand
  • For correspondence: pbrand@ucdavis.edu
Nicholas Saleh
Department for Evolution and Ecology, Center for Population Biology, and University of California, Davis, California 95616Graduate Group in Population Biology, University of California, Davis, California 95616
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Hailin Pan
China National Genebank, Beijing Genomics Institute, Shenzhen 518083, China
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Cai Li
China National Genebank, Beijing Genomics Institute, Shenzhen 518083, China
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Karen M. Kapheim
Department of Biology, Utah State University, Logan, Utah 84322
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Santiago R. Ramírez
Department for Evolution and Ecology, Center for Population Biology, and University of California, Davis, California 95616
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  • Figure 1
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    Figure 1

    Genomic features. (A) Phylogeny of the four corbiculate bee tribes with orchid bees as sistergroup to honey bees, stingless bees, and bumblebees (Romiguer et al. 2016). (B) K-mer distribution spectrum (k = 25) of genomic sequence reads. The positively skewed spectrum reveals a high abundance of a few k-mers, leading to an estimate of 87.7% repetitiveness of the E. dilemma genome. Red shows the k-mer spectrum before, and blue after error correction. (C) Genomic element density including genic and nongenic features as a fraction of the overall genome assembly length excluding stretches of N. 49.15% of the assembly could not be annotated with the selected methods. (D) Synteny between the E. dilemma and the honey bee (Apis mellifera) genome. In an analysis including E. dilemma scaffolds of ≥100 kb length, 83% showed ≥95% synteny to a single honey bee scaffold. Photographs in (A) are reproduced from Wikimedia under the CC BY-SA 3.0 license.

  • Figure 2
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    Figure 2

    Mitochondrial genome reconstruction. The structure of the honey bee mitochondrial genome and information of the homologous reconstructed parts of the E. dilemma mitochondrial genome. Nonreconstructed parts of incompletely reconstructed genes are hatched.

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  • Table 1 E. dilemma genome assembly statistics in comparison to previously published bee genomes
    SpeciesN50N25Longest ScaffoldScaffoldsAssembly LengthGC (%)Predicted GenesRef.
    Euglossa dilemma143,5901,417,00610,108,12022,698588,199,72039.9415,9041
    Eufriesea mexicana2427443,2314,677,3003,522,5431,031,837,97041.3812,0222
    Apis mellifera997,1921,922,1924,736,2995644234,070,65732.7015,3143
    Melipona quadrifasciata68,0851,896,32212,087,08738,604507,114,16138.8814,2572
    Bombus impatiens1,399,4932,389,5135,466,0905559249,185,05637.7515,8964
    Lasioglossum albipes616,4261,130,4133,533,89541,433341,616,64141.5013,4485
    • N50 and N25 indicate the length of the shortest scaffold of those including 50 and 25% of the base pairs in a genome assembly. References (Ref.): 1: this study, 2: Kapheim et al. (2015), 3: Elsik et al. (2014), 4: Sadd et al. (2015), 5: Kocher et al. (2012).

  • Table 2 Transposable element repeat class analysis
    Repeat Element FamilyNumber Unique ElementsTotal Number Elements in AssemblyCumulative Length (bp)Percent of Genome Assemblya
    Class I – retrotransposons3612,9898,843,5602.1
    Class II – DNA transposons10661,52416,133,7273.8
    Total classified transposons14274,51324,977,2875.9
    Unclassified424522,856138,407,54632.6
    Total repeat families566597,369163,384,83338.5
    • ↵a The percentage was calculated excluding all stretches of N in the scaffolds.

Additional Files

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  • Supplemental Material for Brand et al., 2017

    Supplemental Material

    • Table S1 -

      E. dilemma gene annotations with homology to the honey bee. (.txt)

    • Table S2 -

      Detailed transposable element repeat class analysis. (.xlsx)

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Volume 7 Issue 9, September 2017

G3: Genes|Genomes|Genetics: 7 (9)

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The Nuclear and Mitochondrial Genomes of the Facultatively Eusocial Orchid Bee Euglossa dilemma

View ORCID ProfilePhilipp Brand, Nicholas Saleh, Hailin Pan, Cai Li, Karen M. Kapheim and Santiago R. Ramírez
G3: Genes, Genomes, Genetics September 1, 2017 vol. 7 no. 9 2891-2898; https://doi.org/10.1534/g3.117.043687
Philipp Brand
Department for Evolution and Ecology, Center for Population Biology, and University of California, Davis, California 95616Graduate Group in Population Biology, University of California, Davis, California 95616
  • Find this author on Google Scholar
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  • Search for this author on this site
  • ORCID record for Philipp Brand
  • For correspondence: pbrand@ucdavis.edu
Nicholas Saleh
Department for Evolution and Ecology, Center for Population Biology, and University of California, Davis, California 95616Graduate Group in Population Biology, University of California, Davis, California 95616
  • Find this author on Google Scholar
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Hailin Pan
China National Genebank, Beijing Genomics Institute, Shenzhen 518083, China
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Cai Li
China National Genebank, Beijing Genomics Institute, Shenzhen 518083, China
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Karen M. Kapheim
Department of Biology, Utah State University, Logan, Utah 84322
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Santiago R. Ramírez
Department for Evolution and Ecology, Center for Population Biology, and University of California, Davis, California 95616
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Citation

The Nuclear and Mitochondrial Genomes of the Facultatively Eusocial Orchid Bee Euglossa dilemma

View ORCID ProfilePhilipp Brand, Nicholas Saleh, Hailin Pan, Cai Li, Karen M. Kapheim and Santiago R. Ramírez
G3: Genes, Genomes, Genetics September 1, 2017 vol. 7 no. 9 2891-2898; https://doi.org/10.1534/g3.117.043687
Philipp Brand
Department for Evolution and Ecology, Center for Population Biology, and University of California, Davis, California 95616Graduate Group in Population Biology, University of California, Davis, California 95616
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Philipp Brand
  • For correspondence: pbrand@ucdavis.edu
Nicholas Saleh
Department for Evolution and Ecology, Center for Population Biology, and University of California, Davis, California 95616Graduate Group in Population Biology, University of California, Davis, California 95616
  • Find this author on Google Scholar
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  • Search for this author on this site
Hailin Pan
China National Genebank, Beijing Genomics Institute, Shenzhen 518083, China
  • Find this author on Google Scholar
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  • Search for this author on this site
Cai Li
China National Genebank, Beijing Genomics Institute, Shenzhen 518083, China
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Karen M. Kapheim
Department of Biology, Utah State University, Logan, Utah 84322
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Santiago R. Ramírez
Department for Evolution and Ecology, Center for Population Biology, and University of California, Davis, California 95616
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