A Chromosome-Scale Assembly of the Asian Honeybee Apis cerana Genome

Wang, Zilong; Zhu, Yaping; Yan, Qing; Wei, Yan; Zheng, Huajun; Zeng, Zhen

doi:10.3389/fgene.2020.00279

Cited by 22 publications

(31 citation statements)

References 30 publications

(37 reference statements)

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“…The assembled A. cerana genome contains 6.08% of repetitive sequences, and 0.7% of the genome are recognized as transposable elements (TEs). Mariner DNA transposons represent the most abundant TEs, consistent with previous reports for A. cerana in other countries [ 27 , 28 , 29 ].…”

Section: Resultssupporting

confidence: 90%

Genome Sequence of the Asian Honeybee in Pakistan Sheds Light on Its Phylogenetic Relationship with Other Honeybees

Tan

Naeem

Husnain³

et al. 2021

Insects

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In Pakistan, Apis cerana, the Asian honeybee, has been used for honey production and pollination services. However, its genomic makeup and phylogenetic relationship with those in other countries are still unknown. We collected A. cerana samples from the main cerana-keeping region in Pakistan and performed whole genome sequencing. A total of 28 Gb of Illumina shotgun reads were generated, which were used to assemble the genome. The obtained genome assembly had a total length of 214 Mb, with a GC content of 32.77%. The assembly had a scaffold N50 of 2.85 Mb and a BUSCO completeness score of 99%, suggesting a remarkably complete genome sequence for A. cerana in Pakistan. A MAKER pipeline was employed to annotate the genome sequence, and a total of 11,864 protein-coding genes were identified. Of them, 6750 genes were assigned at least one GO term, and 8813 genes were annotated with at least one protein domain. Genome-scale phylogeny analysis indicated an unexpectedly close relationship between A. cerana in Pakistan and those in China, suggesting a potential human introduction of the species between the two countries. Our results will facilitate the genetic improvement and conservation of A. cerana in Pakistan.

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Section: Resultssupporting

confidence: 90%

Genome Sequence of the Asian Honeybee in Pakistan Sheds Light on Its Phylogenetic Relationship with Other Honeybees

Tan

Naeem

Husnain³

et al. 2021

Insects

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“…We examined the copy numbers for all transposons included in this study and found that most families of transposons had only one or few copies, which suggests that most Tc1/mariner and pogo transposons do not display significant amplification in these lineages. This is consistent with previous findings that most Tc1/mariner is detected with low genomic coverage [ 68 , 71 ]. In addition, we found >10 intact copies of DD34D/ mariner in the genomes of Apis mellifera , Apis mellifera carnica , Apis mellifera caucasia , Apis mellifera mellifera, and Euglossa dilemma .…”

Section: Discussionsupporting

confidence: 94%

“…DNA transposons are the major repeat sequence, and mariner transposons are the most common element within this class [ 70 ]. A recent study reported that TEs in the genome of the Asian honeybee Apis cerana accounted for 9.15% and simple repeats accounted for most TEs [ 71 ]. The DNA transposons constitute 0.11% (247 kb) of the Apis cerana genome and 0.57% (1.34 Mb) of the Apis mellifera genome.…”

Section: Discussionmentioning

confidence: 99%

Diversity and Evolution of pogo and Tc1/mariner Transposons in the Apoidea Genomes

Liu

Zong

Diaby

et al. 2021

Biology

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Bees (Apoidea), the largest and most crucial radiation of pollinators, play a vital role in the ecosystem balance. Transposons are widely distributed in nature and are important drivers of species diversity. However, transposons are rarely reported in important pollinators such as bees. Here, we surveyed 37 bee genomesin Apoidea, annotated the pogo and Tc1/mariner transposons in the genome of each species, and performed a phylogenetic analysis and determined their overall distribution. The pogo and Tc1/mariner families showed high diversity and low abundance in the 37 species, and their proportion was significantly higher in solitary bees than in social bees. DD34D/mariner was found to be distributed in almost all species and was found in Apis mellifera, Apis mellifera carnica, Apis mellifera caucasia, and Apis mellifera mellifera, and Euglossa dilemma may still be active. Using horizontal transfer analysis, we found that DD29-30D/Tigger may have experienced horizontal transfer (HT) events. The current study displayed the evolution profiles (including diversity, activity, and abundance) of the pogo and Tc1/mariner transposons across 37 species of Apoidea. Our data revealed their contributions to the genomic variations across these species and facilitated in understanding of the genome evolution of this lineage.

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“…Therefore, we performed further analyses of Am genome data. While processing the present study, new and high-quality Acc genome data (Acc_new) were published (Wang et al 2020). To assess whether the results of RepeatMasker, particularly MLEs, were affected by the quality of input genome data, the detection of MLEs by RepeatMasker was conducted under the same conditions using Acc_new.…”

Section: Resultsmentioning

confidence: 99%

“…Differences in the MLE numbers detected between these Apis species were not due to the reference genome qualities of the six Apis species. For example, new Acc genome data were published during the processing of the present study (Wang et al 2020), and we attempted to detect MLEs using these data under the same conditions as those for other Apis genomes. Although the contig N50 values of new Acc genome data were more than 150-fold higher than that of the Acc genome used in the present study (Table 1), the numbers of MLEs detected were not markedly different between the two sets of genome data.…”

Section: Discussionmentioning

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 Chromosome-Scale Assembly of the Asian Honeybee Apis cerana Genome

Cited by 22 publications

References 30 publications

Genome Sequence of the Asian Honeybee in Pakistan Sheds Light on Its Phylogenetic Relationship with Other Honeybees

Genome Sequence of the Asian Honeybee in Pakistan Sheds Light on Its Phylogenetic Relationship with Other Honeybees

Diversity and Evolution of pogo and Tc1/mariner Transposons in the Apoidea Genomes

Landscapes of transposable elements inApisspecies by meta-analysis

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