Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq

Abstract

Bumblebees (Hymenoptera: Apidae) are important pollinating insects that play pivotal roles in crop production and natural ecosystem services. Although protein-coding genes in bumblebees have been extensively annotated, regulatory sequences of the genome, such as promoters and enhancers, have been poorly annotated. To achieve a comprehensive profile of accessible chromatin regions and provide clues for all possible regulatory elements in the bumblebee genome, we performed ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) on Bombus terrestris samples derived from four developmental stages: egg, larva, pupa, and adult, respectively. The ATAC-seq reads were mapped to the B. terrestris reference genome, and its accessible chromatin regions were identified and characterized using bioinformatic methods. We identified 36,390 chromatin accessible regions in total, including both shared and stage-specific chromatin accessible signals. Our study will provide an important resource, not only for uncovering regulatory elements in the bumblebee genome, but also for expanding our understanding of bumblebee biology throughout development.

Investigation of sex expression profiles and the cantharidin biosynthesis genes in two blister beetles

“…Subsequently, the clean reads were mapped to the reference gene [26] by Bowtie2 [29] program. In accordance with the recommendations of RSEM software (https://deweylab.github.io/RSEM/rsem-calculateexpression.html) and Zhao, X., et al [30], the bowtie parameters have been set to '-q-phred64 -sensitive-dpad 0-gbar 99999999-mp 1,1-np 1-score-min L,0,-0.1 -I 1 -X 1000-nomixed-no-discordant -p 8 -k 200'.…”

Large-scale genome analyses provide insights into Hymenoptera evolution

“…In addition, we also conducted whole genome alignment analysis (Cactus alignment) to investigate the evolutionary constraints and acceleration at the whole genome level (see Methods). We chose the bumblebee Bombus terrestris (Apidae) as a reference because the availability of ATAC-Seq data is helpful to infer potential regulatory elements 20 . In the 27-way alignment, 59.5% (233.69/392.96 Mb) of the B. terrestris genome was aligned to at least one species, and 21.5% and 8.5% of the genome were identified as constrained and accelerated regions, respectively, by calculating the phyloP score (Supplementary Figure 11A).…”

“…We excluded conserved elements less than 20 bp in length. To further investigate the chromatin accessibility of conserved no-coding elements, we downloaded raw ATAC-seq data for the egg, larva, pupa, and adult stages of B. terrestris 20 from NCBI (accessions in Supplementary Table 51). Trimmomatic 0.33 103 was used to filter raw reads, removing low-quality reads and adaptor sequences.…”

Gene regulatory dynamics during the development of a paleopteran insect, the mayflyCloeon dipterum

“…Therefore, much more detailed and comprehensive characterisations of CREs have been possible and several FAIRE-seq and ATAC-seq datasets have been generated during the last decade to address distinct questions related to insect development and evolution. Nonetheless, these works have been mostly done using few established model species, such as the fruitfly Drosophila melanogaster (Diptera), the red flour beetle Tribolium castaneum (Coleoptera), some butterfly and moth species (Lepidoptera) or certain species of ants and bees (Hymenoptera) (Lowe et al 2022; Wang et al 2020; Zhao et al 2020), all of which belong to a single monophyletic group of insects, the Holometabola (Fig. 1A)(Schmidt-Ott and Lynch 2016).…”