Comparative Genomics Reveals Recent Adaptive Evolution in Himalayan Giant Honeybee <i>Apis laboriosa</i>

Lin, Dan; Lan, Lan; Zheng, Tingting; Shi, Peng; Xu, Jianlong; Li, Jun

doi:10.1093/gbe/evab227

Cited by 8 publications

(9 citation statements)

References 32 publications

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“…S1, Supplementary Material online). By comparing our assembly to a recently published assembly of A. laboriosa from Western Yunnan (Shangri-La) ( Lin et al, 2021 ), we found that the two genomes share a high level of average nucleotide identity (ANI, 99.48%), and completeness BUSCO score (97.4% vs. 97.7%), confirming the high quality of two genomes. In this study, we used our assembly for the population-based analyses.…”

Section: Resultssupporting

confidence: 66%

“…In this study, we sequenced and assembled the genome of A. laboriosa for population-related genomic analyses. Based on this, A. laboriosa and A. dorsata seem to have diverged ∼2.61 Ma, mirroring the estimation by Lin et al (2021) . To date, there has been no convincing evidence to indicate what barriers might have separated proto- dorsata populations into distinct A. laboriosa and A. dorsata species.…”

Section: Discussionsupporting

confidence: 70%

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Population Structure, Demographic History, and Adaptation of Giant Honeybees in China Revealed by Population Genomic Data

Cao

Dai

Tan

et al. 2023

Genome Biology and Evolution

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There have been many population-based genomic studies on human-managed honeybees (Apis mellifera and Apis cerana), but there has been a notable lack of analysis with regard to wild honeybees, particularly in relation to their evolutionary history. Nevertheless, giant honeybees have found to occupy distinct habitats and display have remarkable characteristics, which are attracting an increase amount of attention. In this study, we de novo sequenced and then assembled the draft genome sequence of the Himalayan giant honeybee, Apis laboriosa. Phylogenetic analysis based on genomic information indicated that A. laboriosa and its tropical sister species Apis dorsata diverged ∼2.61 million years ago, which supports the speciation hypothesis that link A. laboriosa to geological changes throughout history. Furthermore, we re-sequenced A. laboriosa and A. dorsata samples from five and six regions, respectively, across their population ranges in China. These analysis highlighted major genetic differences for Tibetan A. laboriosa as well as the Hainan Island A. dorsata. The demographic history of most giant honeybee populations has mirrored glacial cycles. More importantly, contrary to what has occurred among human-managed honeybees, the demographic history of these two wild honeybee species indicates a rapid decline in effective population size in the recent past, reflecting their differences in evolutionary histories. Several genes were found to be subject to selection, which may help giant honeybees to adapt to specific local conditions. In summary, our study sheds light on the evolutionary and adaptational characteristics of two wild giant honeybees species, which was useful for giant honeybee conservation.

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Section: Resultssupporting

confidence: 66%

Section: Discussionsupporting

confidence: 70%

Population Structure, Demographic History, and Adaptation of Giant Honeybees in China Revealed by Population Genomic Data

Cao

Dai

Tan

et al. 2023

Genome Biology and Evolution

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“…This led to whole-genome sequencing of other honey bee species, including several Am and A. cerana subspecies. Genome data are currently available in public databases for the following honey bees: A. cerana japonica (Acj) [ 9 ], A. cerana Korean native (Ack) [ 10 ], A. cerana China native (Acc) [ 11 ], A. dorsata (Ad) [ 12 ], A. florea (Af), A. laboriosa (Al) [ 13 ], A. mellifera carnica (Carniolan honey bee) (Amcar), A. mellifera intermissa (Ami) [ 14 ], A. mellifera caucasica (Caucasian honey bee) (Amcau), and A. mellifera (German honey bee) (Amm) ( Table 1 ). Am, A. cerana , Ad, Af are the four major Apis species [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

Revealing Landscapes of Transposable Elements in Apis Species by Meta-Analysis

Yokoi

Kimura

Bono

2022

Insects

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Transposable elements (TEs) are grouped into several families with diverse sequences. Owing to their diversity, studies involving the detection, classification, and annotation of TEs are difficult tasks. Moreover, simple comparisons of TEs among different species with different methods can lead to misinterpretations. The genome data of several honey bee (Apis) species are available in public databases. Therefore, we conducted a meta-analysis of TEs, using 11 sets of genome data for Apis species, in order to establish data of “landscape of TEs”. Consensus TE sequences were constructed and their distributions in the Apis genomes were determined. Our results showed that TEs belonged to four to seven TE families among 13 and 15 families of TEs detected in classes I and II respectively mainly consisted of Apis TEs and that more DNA/TcMar-Mariner consensus sequences and copies were present in all Apis genomes tested. In addition, more consensus sequences and copy numbers of DNA/TcMar-Mariner were detected in Apis mellifera than in other Apis species. These results suggest that TcMar-Mariner might exert A. mellifera-specific effects on the host A. mellifera species. In conclusion, our unified approach enabled comparison of Apis genome sequences to determine the TE landscape, which provide novel evolutionary insights into Apis species.

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“…However, there is no information about morphological comparisons and genetic diversity about intraspecies of this honeybee. Recent study has disclosed the complete mitochondrial genome and whole genome of A. laboriosa (Lin et al, 2021 ; Takahashi et al, 2018 ), which offers the reference to deeply studying the genetic diversity of A. laboriosa .…”

Section: Introductionmentioning

confidence: 99%

Comparison of the mitochondrial genomes of three geographical strains of Apis laboriosa indicates high genetic diversity in the black giant honeybee (Hymenoptera: Apidae)

Tang

Yao

et al. 2023

Ecology and Evolution

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Apis laboriosa is the largest honeybee that lives mainly on cliff faces, with strong migratory ability. In this study, we firstly sequenced and assembled two complete mitochondrial genomes of A. laboriosa isolated from two distant locations in China (Chongqing and Shangri‐La regions). Combined with the published mitochondrial genome of A. laboriosa from Nepal, comparative genomic analyses were conducted to gain insight into the genetic diversity of giant honeybees from different geographical distributions. The mitochondrial genomes of A. laboriosa from Chongqing and Shangri‐La regions were 15,579 and 15,683 bp in length, respectively, both larger than that from Nepal with the length of 15,510 bp. Three mitochondrial genomes all harbor 37 common genes and present the same AT bias and the frequency of codon usage. However, the fragments including COX 1, SSUrRNA, LSUrRNA, and the AT‐rich region of the mitochondrial genome from Shangri‐La region demonstrate distinctive insertions and deletions compared to those from Chongqing and Nepal regions. Phylogenetic trees of mitochondrial genomes show that A. laboriosa from Chongqing is most closely related to that from Nepal, rather than to Shangri‐La. Genetic distance between Shangri‐La and Chongqing or Nepal was even larger than that between the various subspecies of Apis mellifera . Overall, these results unmark that A. laboriosa in different geographical distributions can exhibit high genetic diversity at the mitochondrial genomic level, and therein, A. laboriosa from Shangri‐La may be the subspecies. All these studies will contribute to our understanding of the geographical distribution and genetic differentiation of black giant honeybee in Asian region.

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Comparative Genomics Reveals Recent Adaptive Evolution in Himalayan Giant Honeybee Apis laboriosa

Cited by 8 publications

References 32 publications

Population Structure, Demographic History, and Adaptation of Giant Honeybees in China Revealed by Population Genomic Data

Population Structure, Demographic History, and Adaptation of Giant Honeybees in China Revealed by Population Genomic Data

Revealing Landscapes of Transposable Elements in Apis Species by Meta-Analysis

Comparison of the mitochondrial genomes of three geographical strains of Apis laboriosa indicates high genetic diversity in the black giant honeybee (Hymenoptera: Apidae)

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