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Li Y, Yao J, Sang H, Wang Q, Su L, Zhao X, Xia Z, Wang F, Wang K, Lou D, Wang G, Waterhouse RM, Wang H, Luo S, Sun C. Pan-genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees. Mol Ecol Resour 2024; 24:e13905. [PMID: 37996991 DOI: 10.1111/1755-0998.13905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/20/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
The Asian honeybee, Apis cerana, is an ecologically and economically important pollinator. Mapping its genetic variation is key to understanding population-level health, histories and potential capacities to respond to environmental changes. However, most efforts to date were focused on single nucleotide polymorphisms (SNPs) based on a single reference genome, thereby ignoring larger scale genomic variation. We employed long-read sequencing technologies to generate a chromosome-scale reference genome for the ancestral group of A. cerana. Integrating this with 525 resequencing data sets, we constructed the first pan-genome of A. cerana, encompassing almost the entire gene content. We found that 31.32% of genes in the pan-genome were variably present across populations, providing a broad gene pool for environmental adaptation. We identified and characterized structural variations (SVs) and found that they were not closely linked with SNP distributions; however, the formation of SVs was closely associated with transposable elements. Furthermore, phylogenetic analysis using SVs revealed a novel A. cerana ecological group not recoverable from the SNP data. Performing environmental association analysis identified a total of 44 SVs likely to be associated with environmental adaptation. Verification and analysis of one of these, a 330 bp deletion in the Atpalpha gene, indicated that this SV may promote the cold adaptation of A. cerana by altering gene expression. Taken together, our study demonstrates the feasibility and utility of applying pan-genome approaches to map and explore genetic feature variations of honeybee populations, and in particular to examine the role of SVs in the evolution and environmental adaptation of A. cerana.
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Affiliation(s)
- Yancan Li
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, China
| | - Jun Yao
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiling Sang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Quangui Wang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Su
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiaomeng Zhao
- College of Animal Science, Shanxi Agricultural University, Shanxi, China
| | - Zhenyu Xia
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feiran Wang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, China
| | - Kai Wang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Delong Lou
- Shandong Provincial Animal Husbandry Station, Jinan, China
| | - Guizhi Wang
- Department of Animal Science, Shandong Agricultural University, Taian, China
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Huihua Wang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shudong Luo
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing, China
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Wakamiya T, Kamioka T, Ishii Y, Takahashi J, Maeda T, Kawata M. Genetic differentiation and local adaptation of the Japanese honeybee, Apis cerana japonica. Ecol Evol 2023; 13:e10573. [PMID: 37780082 PMCID: PMC10541296 DOI: 10.1002/ece3.10573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023] Open
Abstract
We examine the population genetic structure and divergence among the regional populations of the Japanese honeybee, Apis cerana japonica, by re-sequencing the genomes of 105 individuals from the three main Japanese islands with diverse climates. The genetic structure results indicated that these individuals are distinct from the mainland Chinese A. cerana samples. Furthermore, population structure analyses have identified three genetically distinct geographic regions in Japan: Northern (Tohoku-Kanto-Chubu districts), Central (Chugoku district), and Southern (Kyushu district). In some districts, "possible non-native" individuals, likely introduced from other regions in recent years, were discovered. Then, genome-wide scans were conducted to detect candidate genes for adaptation by two different approaches. We performed a population branch statistics (PBS) analysis to identify candidate genes for population-specific divergence. A latent factor mixed model (LFMM) was used to identify genes associated with climatic variables along a geographic gradient. The PBSmax analysis identified 25 candidate genes for population-specific divergence whereas the LFMM analysis identified 73 candidate genes for adaptation to climatic variables along a geographic gradient. However, no common genes were identified by both methods.
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Affiliation(s)
- Takeshi Wakamiya
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
- Department of Biological SciencesTokyo Metropolitan UniversityHachiojiJapan
| | | | - Yuu Ishii
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | | | - Taro Maeda
- Institute for Agro‐Environmental Sciences (NIAES)NAROTsukubaJapan
| | - Masakado Kawata
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
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Zhang Y, Xu H, Wang Z, Jie H, Gao F, Cai M, Wang K, Chen D, Guo R, Lin Z, Niu Q, Ji T. A key gene for the climatic adaptation of Apis cerana populations in China according to selective sweep analysis. BMC Genomics 2023; 24:100. [PMID: 36879226 PMCID: PMC9987060 DOI: 10.1186/s12864-023-09167-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/06/2023] [Indexed: 03/08/2023] Open
Abstract
BACKGROUND Apis cerana is widely distributed in China and, prior to the introduction of western honeybees, was the only bee species kept in China. During the long-term natural evolutionary process, many unique phenotypic variations have occurred among A. cerana populations in different geographical regions under varied climates. Understanding the molecular genetic basis and the effects of climate change on the adaptive evolution of A. cerana can promote A. cerana conservation in face of climate change and allow for the effective utilization of its genetic resources. RESULT To investigate the genetic basis of phenotypic variations and the impact of climate change on adaptive evolution, A. cerana workers from 100 colonies located at similar geographical latitudes or longitudes were analyzed. Our results revealed an important relationship between climate types and the genetic variation of A. cerana in China, and a greater influence of latitude compared with longitude was observed. Upon selection and morphometry analyses combination for populations under different climate types, we identified a key gene RAPTOR, which was deeply involved in developmental processes and influenced the body size. CONCLUSION The selection of RAPTOR at the genomic level during adaptive evolution could allow A. cerana to actively regulate its metabolism, thereby fine-tuning body sizes in response to harsh conditions caused by climate change, such as food shortages and extreme temperatures, which may partially elucidate the size differences of A. cerana populations. This study provides crucial support for the molecular genetic basis of the expansion and evolution of naturally distributed honeybee populations.
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Affiliation(s)
- Yi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Hao Xu
- Sericultural Research Institute, Anhui Academy of Agricultural Science, Hefei, 230061, China
| | - Zhi Wang
- Apiculture Science Institute of Jilin Province, Jilin, 132108, China
| | - Haoliang Jie
- Jinzhong Agriculture and Rural Affairs Bureau, Jinzhong, 030601, China
| | - Fuchao Gao
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, 157043, China
| | - Minqi Cai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Kang Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Dafu Chen
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rui Guo
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zheguang Lin
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Qingsheng Niu
- Apiculture Science Institute of Jilin Province, Jilin, 132108, China.
| | - Ting Ji
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
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Tang X, Yao Y, Li Y, Song H, Luo R, Shi P, Zhou Z, Xu J. Comparison of the mitochondrial genomes of three geographical strains of Apis laboriosa indicates high genetic diversity in the black giant honeybee (Hymenoptera: Apidae). Ecol Evol 2023; 13:e9782. [PMID: 36744074 PMCID: PMC9891905 DOI: 10.1002/ece3.9782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 12/26/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
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 COX1, 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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Affiliation(s)
- Xiang‐You Tang
- College of Life SciencesChongqing Normal UniversityChongqingChina,Key Laboratory of Conservation and Utilization of Pollinator Insect of the Upper Reaches of the Yangtze RiverMinistry of Agriculture and Rural AffairsChongqingChina
| | - Yu‐Xin Yao
- College of Life SciencesChongqing Normal UniversityChongqingChina,Key Laboratory of Conservation and Utilization of Pollinator Insect of the Upper Reaches of the Yangtze RiverMinistry of Agriculture and Rural AffairsChongqingChina
| | - Yao‐Hui Li
- College of Life SciencesChongqing Normal UniversityChongqingChina,Key Laboratory of Conservation and Utilization of Pollinator Insect of the Upper Reaches of the Yangtze RiverMinistry of Agriculture and Rural AffairsChongqingChina
| | - Hua‐Li Song
- College of Life SciencesChongqing Normal UniversityChongqingChina,Key Laboratory of Conservation and Utilization of Pollinator Insect of the Upper Reaches of the Yangtze RiverMinistry of Agriculture and Rural AffairsChongqingChina
| | - Rui Luo
- College of Life SciencesChongqing Normal UniversityChongqingChina
| | - Peng Shi
- College of Life SciencesChongqing Normal UniversityChongqingChina,Key Laboratory of Conservation and Utilization of Pollinator Insect of the Upper Reaches of the Yangtze RiverMinistry of Agriculture and Rural AffairsChongqingChina
| | - Ze‐Yang Zhou
- College of Life SciencesChongqing Normal UniversityChongqingChina,Key Laboratory of Conservation and Utilization of Pollinator Insect of the Upper Reaches of the Yangtze RiverMinistry of Agriculture and Rural AffairsChongqingChina
| | - Jin‐Shan Xu
- College of Life SciencesChongqing Normal UniversityChongqingChina,Key Laboratory of Conservation and Utilization of Pollinator Insect of the Upper Reaches of the Yangtze RiverMinistry of Agriculture and Rural AffairsChongqingChina
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Su T, He B, Zhao F, Jiang K, Lin G, Huang Z. Population genomics and phylogeography of
Colletes gigas
, a wild bee specialized on winter flowering plants. Ecol Evol 2022; 12:e8863. [PMID: 35494503 PMCID: PMC9035574 DOI: 10.1002/ece3.8863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/05/2022] [Indexed: 11/09/2022] Open
Abstract
Diet specialization may affect the population genetic structure of pollinators by reducing gene flow and driving genetic differentiation, especially in pollen‐specialist bees. Colletes gigas is a pollen‐specialist pollinator of Camellia oleifera, one of the most important staple oil crops in China. Ca. oleifera blooms in cold climates and contains special compounds that make it an unusable pollen source to other pollinators. Thus, C. gigas undoubtedly plays a key role as the main pollinator of Ca. oleifera, with biological and economic significance. Here, we use a population genomic approach to analyze the roles of geography and climate on the genetic structure, genetic diversity, and demographic history of C. gigas. A total of 1,035,407 SNPs were identified from a 582.77 Gb dataset. Clustering and phylogenetic analyses revealed a marked genetic structure, with individuals grouped into nine local clusters. A significant isolation by distance was detected by both the Mantel test (R = .866, p = .008) and linear regression (R2 = .616, p < .001). Precipitation and sunshine duration were positively and significantly (R ≥ .765, p ≤ .016) correlated with observed heterozygosity (Ho) and expected heterozygosity (He). These results showed that C. gigas populations had a distinct phylogeographic pattern determined by geographical distance and environmental factors (precipitation and sunshine duration). In addition, an analysis of paleogeographic dynamics indicated that C. gigas populations exhibited patterns of glacial expansion and interglacial contraction, likely resulting from post‐glacial habitat contraction and fragmentation. Our results indicated that the peculiar phylogeographic patterns in C. gigas populations may be related to their specialization under long‐term adaptation to host plants. This work improves our understanding of the population genetics in pollen‐specialist bees. The distinct genetic clusters identified in this study should be taken into consideration for the protection and utilization of this specialized crop pollinator.
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Affiliation(s)
- Tianjuan Su
- School of Life Sciences Jinggangshan University Ji'an China
| | - Bo He
- School of Life Sciences Jinggangshan University Ji'an China
- College of Life Sciences Anhui Normal University Wuhu China
| | - Fang Zhao
- School of Life Sciences Jinggangshan University Ji'an China
| | - Kai Jiang
- School of Life Sciences Jinggangshan University Ji'an China
| | - Gonghua Lin
- School of Life Sciences Jinggangshan University Ji'an China
| | - Zuhao Huang
- School of Life Sciences Jinggangshan University Ji'an China
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Lan L, Shi P, Song H, Tang X, Zhou J, Yang J, Yang M, Xu J. De Novo Genome Assembly of Chinese Plateau Honeybee Unravels Intraspecies Genetic Diversity in the Eastern Honeybee, Apis cerana. INSECTS 2021; 12:insects12100891. [PMID: 34680661 PMCID: PMC8538478 DOI: 10.3390/insects12100891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary In this study, we obtained a chromosome-scale assembly genome of Apis cerana abansis, which lives in the southeastern margin of the Titan Plateau, by using PacBio, Illumina and high-throughput chromatin conformation capture (Hi-C) sequencing technologies. With a more comprehensive annotation pipeline, we obtained an ampler and more accurate Apis cerana genome than previous studies. Comparative genomic analysis was performed to identify the divergence among different A. cerana genomes by studying two aspects: the differential content of repeat content and the gene loss/gain events occurred in chemosensory receptors and immune-related proteins. Our results show that the content of repetitive sequences differ in types and quantity among four A. cerana strains; the gene loss/gain events in chemoreceptor- and immune-related proteins occur in different A. cerana strains, especially in A. cerana abansis (Aba strain). Specifically, while compared with the other three published genomes, the Aba strain contains the largest number of repeat contents and loses the largest number of both chemosensory-receptor- and immune-related proteins, as well as subfamilies, whereas the Baisha strain contains the largest number of chemoreceptor- and immune-related proteins. We hypothesized that gene loss/gain may be evolutionary strategies used by the different A. cerana strains to adapt to their respective environments. Abstract Apis cerana abansis, widely distributed in the southeastern margin of the Qinghai-Tibet Plateau, is considered an excellent model to study the phenotype and genetic variation for highland adaptation of Asian honeybee. Herein, we assembled and annotated the chromosome-scale assembly genome of A. cerana abansis with the help of PacBio, Illumina and Hi-C sequencing technologies in order to identify the genome differences between the A. cerana abansis and the published genomes of different A. cerana strains. The sequencing methods, assembly and annotation strategies of A. cerana abansis were more comprehensive than previously published A. cerana genomes. Then, the intraspecific genetic diversity of A. cerana was revealed at the genomic level. We re-identified the repeat content in the genome of A. cerana abansis, as well as the other three A. cerana strains. The chemosensory and immune-related proteins in different A. cerana strains were carefully re-identified, so that 132 odorant receptor subfamilies, 12 gustatory receptor subfamilies and 22 immune-related pathways were found. We also discovered that, compared with other published genomes, the A. ceranaabansis lost the largest number of chemoreceptors compared to other strains, and hypothesized that gene loss/gain might help different A. cerana strains to adapt to their respective environments. Our work contains more complete and precise assembly and annotation results for the A. cerana genome, thus providing a resource for subsequent in-depth related studies.
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Affiliation(s)
- Lan Lan
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (L.L.); (P.S.); (H.S.); (X.T.); (J.Z.)
- Engineering Research Center of Biotechnology for Active Substances, Ministry of Education, Chongqing 401331, China
| | - Peng Shi
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (L.L.); (P.S.); (H.S.); (X.T.); (J.Z.)
- Engineering Research Center of Biotechnology for Active Substances, Ministry of Education, Chongqing 401331, China
| | - Huali Song
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (L.L.); (P.S.); (H.S.); (X.T.); (J.Z.)
- Engineering Research Center of Biotechnology for Active Substances, Ministry of Education, Chongqing 401331, China
| | - Xiangyou Tang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (L.L.); (P.S.); (H.S.); (X.T.); (J.Z.)
- Engineering Research Center of Biotechnology for Active Substances, Ministry of Education, Chongqing 401331, China
| | - Jianyang Zhou
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (L.L.); (P.S.); (H.S.); (X.T.); (J.Z.)
- Engineering Research Center of Biotechnology for Active Substances, Ministry of Education, Chongqing 401331, China
| | - Jiandong Yang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (M.Y.)
| | - Mingxian Yang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (M.Y.)
| | - Jinshang Xu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (L.L.); (P.S.); (H.S.); (X.T.); (J.Z.)
- Engineering Research Center of Biotechnology for Active Substances, Ministry of Education, Chongqing 401331, China
- Correspondence:
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