Article Figures & Data
Figures
- 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
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.
Tables
- Table 1 E. dilemma genome assembly statistics in comparison to previously published bee genomes
Species N50 N25 Longest Scaffold Scaffolds Assembly Length GC (%) Predicted Genes Ref. Euglossa dilemma 143,590 1,417,006 10,108,120 22,698 588,199,720 39.94 15,904 1 Eufriesea mexicana 2427 443,231 4,677,300 3,522,543 1,031,837,970 41.38 12,022 2 Apis mellifera 997,192 1,922,192 4,736,299 5644 234,070,657 32.70 15,314 3 Melipona quadrifasciata 68,085 1,896,322 12,087,087 38,604 507,114,161 38.88 14,257 2 Bombus impatiens 1,399,493 2,389,513 5,466,090 5559 249,185,056 37.75 15,896 4 Lasioglossum albipes 616,426 1,130,413 3,533,895 41,433 341,616,641 41.50 13,448 5 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 Family Number Unique Elements Total Number Elements in Assembly Cumulative Length (bp) Percent of Genome Assemblya Class I – retrotransposons 36 12,989 8,843,560 2.1 Class II – DNA transposons 106 61,524 16,133,727 3.8 Total classified transposons 142 74,513 24,977,287 5.9 Unclassified 424 522,856 138,407,546 32.6 Total repeat families 566 597,369 163,384,833 38.5 ↵a The percentage was calculated excluding all stretches of N in the scaffolds.
