A hybrid<i>de novo</i>genome assembly of the honeybee,<i>Apis mellifera</i>, with chromosome-length scaffolds

Wållberg, Andreas; Bunikis, Ignas; Pettersson, Olga Vinnere; Mosbech, Mai-Britt; Childers, Anna K.; Evans, Jay D.; Mikheyev, Alexander S.; Robertson, Hugh M.; Robinson, Gene E.; Webster, Matthew T.

doi:10.1101/361469

Cited by 33 publications

(55 citation statements)

References 72 publications

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“…We reprocessed original raw data for each dataset. Raw reads were mapped to the most recent A. mellifera genome assembly, build HAv3.1 77 , and the Deformed wing virus reference genome (GenBank accession number AJ489744 19 ) using the STAR (v2.5.3) aligner with default settings 78 . Numbers of reads were counted using the featureCounts 79 command in the Subread package (v1.5.2) 80 .…”

Section: Methodsmentioning

confidence: 99%

Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturation

Traniello

Bukhari

Kevill

et al. 2020

Sci Rep

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crop pollination by the western honey bee Apis mellifera is vital to agriculture but threatened by alarmingly high levels of colony mortality, especially in Europe and North America. Colony loss is due, in part, to the high viral loads of Deformed wing virus (DWV), transmitted by the ectoparasitic mite Varroa destructor, especially throughout the overwintering period of a honey bee colony. Covert DWV infection is commonplace and has been causally linked to precocious foraging, which itself has been linked to colony loss. taking advantage of four brain transcriptome studies that unexpectedly revealed evidence of covert DWV-A infection, we set out to explore whether this effect is due to DWV-A mimicking naturally occurring changes in brain gene expression that are associated with behavioral maturation. Consistent with this hypothesis, we found that brain gene expression profiles of DWV-A infected bees resembled those of foragers, even in individuals that were much younger than typical foragers. In addition, brain transcriptional regulatory network analysis revealed a positive association between DWV-A infection and transcription factors previously associated with honey bee foraging behavior. Surprisingly, single-cell RNA-Sequencing implicated glia, not neurons, in this effect; there are relatively few glial cells in the insect brain and they are rarely associated with behavioral plasticity. Covert DWV-A infection also has been linked to impaired learning, which together with precocious foraging can lead to increased occurrence of infected bees from one colony mistakenly entering another colony, especially under crowded modern apiary conditions. These findings provide new insights into the mechanisms by which DWV-A affects honey bee health and colony survival. Western honey bees (Apis mellifera) provide an essential pollination service for modern agriculture, with a value estimated at $15 billion per year in the United States 1,2. Extensive reliance on pollination by honey bees has led to great concerns over the massive losses of managed colonies that have occurred since 2006 3-5. These losses are widely thought to be caused by parasites, pathogens, pesticides and poor nutrition, and the main parasite is the ectoparasitic mite Varroa destructor 6-10. Varroa mites are the primary vectors of Deformed wing virus (DWV) 11,12 , a single-stranded, positive-sense RNA virus (family Iflaviridae) that specifically impacts arthropods 13-16. DWV is globally distributed, driving an economic and ecological crisis in honey bee populations 17. DWV was first discovered in symptomatic deformed winged honey bees from Japan in the early 1980s 18 , and the first full genome was sequenced in 2006 19 , hereafter referred to as type A or DWV-A 20. Martin et al. showed through screening the Hawaiian honey bee population that diverse DWV variants persisted prior to the arrival of Varroa 21 ; however, the establishment of Varroa selected for a single variant, DWV-A. DWV-A is currently the most prevalent variant in the North America 22 , thoug...

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Section: Methodsmentioning

confidence: 99%

Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturation

Traniello

Bukhari

Kevill

et al. 2020

Sci Rep

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“…The genus Apis mainly consists of four species, and the following whole genome data are currently available (three Apis species and three Apis cerana subspecies): A. mellifera (Am) (Wallberg et al, 2019), A. cerana japonica (Ack) (Yokoi et al, 2018), A. cerana cerana korea strain (Ack) (Park et al, 2015), A. cerana cerana china strain (Acc) (Diao et al, 2018), A. dorsata (Ad) (Oppenheim et al, 2020), and A. florea (Af) (Table 1). Apis genomes contain small numbers of TE, which mainly consist of class II TE, particularly MLEs (Weinstock et al, 2006; Yokoi et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Landscapes of transposable elements inApisspecies by meta-analysis

Yokoi

Kimura

Bono

2020

Preprint

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The transposable element (TE) mariner is a class II TE that moves within a host genome in a “copy and paste style” manner. Mariner and mariner-like elements (MLEs) are distributed in various species and their sequences are highly diverse; therefore, difficulties have been associated with the classification of these elements. A few TE in the genomes of Apis species mainly consist of mariner and MLE. Detailed classifications are needed to obtain a clearer understanding of Apis MLEs, particularly their movement and horizontal transfer. In the present study, MLEs were detected in the genomes of six Apis species using RepeatMasker. The MLEs were classified into 31 Dromar classes. In this classification, the MLEs in the Apis mellifera genome were classified into the 18 Dromar classes consisting of all five subfamilies, and the MLEs in other Apis species were classified into the Dromar classes from only mauritiana and mellifera subfamilies, suggesting the potential utilization of this classification in the analysis of TEs. A phylogenetic analysis was performed on each Dromar class, and the results obtained suggested that some A. mellifera MLEs invaded via horizontal transfer.

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“…A high-quality genome as a foundation to understand arthropod biology can be a powerful tool to combat invasions and disease-carrying vectors, aid in conservation, and many other fields (for examples, see [5][6][7][8]). To this end, large-scale initiatives are underway to comprehensively catalog the genomes of many arthropod species, including the i5K initiative aiming to sequence and analyze the genomes of 5,000 arthropod species [9][10][11] associated with the Darwin Tree of Life Project (https://www.sanger.ac.uk/news/view/genetic-code-66000-uk-species-besequenced), and the Earth BioGenome Project [12].…”

Section: Introductionmentioning

confidence: 99%

“…Moreover, genomic regions with high heterozygosity tend to be assembled into more fragmented contigs [20], so computational methods specifically developed for heterozygous samples are needed [21][22][23]. Recently, high-quality long-read assemblies have been published for a single diploid mosquito (Anopheles coluzzii) [24] and a single haploid honeybee (Apis mellifera) [7]. Despite both species having relatively small genomes (<300 Mb), multiple PacBio SMRT Cells were needed for sufficient sequencing coverage (N=3 for mosquito, N=29 for bee).…”

Section: Introductionmentioning

confidence: 99%

A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System

Kingan

Urban

Lambert

et al. 2019

Preprint

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A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies, however, long-read methods have historically had greater input DNA requirements and higher costs than next generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female Spotted Lanternfly (Lycorma delicatula) using a single PacBio SMRT Cell. The Spotted Lanternfly is an invasive species recently discovered in the northeastern United States, threatening to damage economically important crop plants in the region. The DNA from one individual was used to make one standard, size-selected library with an average DNA fragment size of ~20 kb. The library was run on one Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from

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A hybridde novogenome assembly of the honeybee,Apis mellifera, with chromosome-length scaffolds

Cited by 33 publications

References 72 publications

Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturation

Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturation

Landscapes of transposable elements inApisspecies by meta-analysis

A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System

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