De Novo Genome Assemblies for Three North American Bumble Bee Species: Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii

Abstract

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.

A genomic and morphometric analysis of alpine bumblebees: ongoing reductions in tongue length but no clear genetic component

“…Assembly statistics for BBAL_1.0 ( B. balteatus ) and BSYL_1.0 ( B. sylvicola ) are presented in table 1, which includes statistics for the assemblies of B. terrestris (BTER_1.0) and B. impatiens (BIMP_2.2) for comparison. Total assembly sizes of 250.1 and 252.1 Mbp for B. balteatus and B. sylvicola respectively are both above the average assembly size of Bombus genomes assembled to date of 247.9 Mbp (22 genomes, range 229.8 – 282.1 Mbp) (Heraghty et al, 2020; Sadd et al, 2015; Sun et al, 2020). Contig N50s of 8.60 and 3.02 for BBAL_1.0 and BSYL_1.0 respectively are the longest and third longest contig N50s of all published Bombus assemblies, demonstrating these to be highly contiguous assemblies.…”

“…These are highly comparable to the 11,874 genes in the B. terrestris gene set (v. 1.0), but lower than the 12,728 genes in the B. impatiens gene set (v. 2.1). Gene annotation of the Bombus assemblies presented in (Heraghty et al, 2020; Sun et al, 2020) also resulted in a greater number of genes annotated, ranging from 13,325 to 16,970 genes. BUSCO analyses of the annotated genes in our assemblies do suggest that we are missing some genes from our annotations (complete BUSCO genes in BBAL_01 and BSYL_01 respectively: 86.6% and 86.9%).…”

A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component

“…balteatus and B . sylvicola respectively are both above the average assembly size of Bombus genomes assembled to date of 247.9 Mbp (22 genomes, range 229.8–282.1 Mbp) (Heraghty et al, 2020; Sadd et al, 2015; Sun et al, 2020). Contig N50s of 8.60 and 3.02 for BBAL_1.0 and BSYL_1.0 respectively are the longest and third longest contig N50s of all published Bombus assemblies, demonstrating these to be highly contiguous assemblies.…”

“…impatiens gene set (v. 2.1). Gene annotation of the Bombus assemblies presented in (Heraghty et al, 2020; Sun et al, 2020) also resulted in a greater number of genes annotated, ranging from 13,325 to 16,970 genes. BUSCO analyses of the annotated genes in our assemblies do suggest that we are missing some genes from our annotations (complete BUSCO genes in BBAL_01 and BSYL_01, respectively: 86.6% and 86.9%).…”

Developmental Transcriptomics Reveals a Gene Network Driving Mimetic Color Variation in a Bumble Bee

“…The segment-specific manifestation of color and frequent color transitions across the phylogeny, along with an abundance of natural replicates in bumble bees makes this system well suited for addressing questions in evo-devo and testing fundamental evolutionary hypotheses driving phenotypic diversification ( Rapti et al 2014 ; Hines and Rahman 2019 ; Tian et al 2019 ). This system is primed for comparative genomic approaches to understanding this color diversity, as it has a well-established phylogenetic framework ( Cameron et al 2007 ), standardized methods of color pattern quantification ( Cameron et al 2007 ), multiple high-quality genome assemblies ( Sadd et al 2015 ; Heraghty et al 2020 ; Sun et al 2020 ), and detailed developmental staging protocols ( Tian and Hines 2018 ).…”