1
|
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.
Collapse
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
| |
Collapse
|
2
|
Hwang J, Choi EH, Park B, Kim G, Shin C, Lee JH, Hwang JS, Hwang UW. Transcriptome profiling for developmental stages Protaetia brevitarsis seulensis with focus on wing development and metamorphosis. PLoS One 2023; 18:e0277815. [PMID: 36857331 PMCID: PMC9977060 DOI: 10.1371/journal.pone.0277815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 11/04/2022] [Indexed: 03/02/2023] Open
Abstract
A white-spotted flower chafer Protaetia brevitarsis seulensis widely distributed in Asian countries is traditionally used in oriental medicine. This study explored gene expression abundance with respect to wing development and metamorphosis in P. b. seulensis based on the large-scale RNA-seq data. The transcriptome assembly consists of 23,551 high-quality transcripts which are approximately 96.7% covered. We found 265 wing development genes, 19 metamorphosis genes, and 1,314 candidates. Of the 1,598 genes, 1,594 are included exclusively in cluster 4 with similar gene co-expression patterns. The network centrality analyses showed that wing development- and metamorphosis-related genes have a high degree of betweenness centrality and are expressed most highly in eggs, moderately in pupa and adults, and lowest in larva. This study provides some meaningful clues for elucidating the genetic modulation mechanism of wing development and metamorphosis in P. b. seulensis.
Collapse
Affiliation(s)
- Jihye Hwang
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, Korea
- Phylomics Inc., Daegu, South Korea
| | - Eun Hwa Choi
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, Korea
- Phylomics Inc., Daegu, South Korea
| | - Bia Park
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, Korea
| | - Gyeongmin Kim
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, Korea
- School of Life Sciences, Graduate School, Kyungpook National University, Daegu, South Korea
| | - Chorong Shin
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, Korea
- School of Industrial Technology Advances, Kyungpook National University, Daegu, South Korea
| | - Joon Ha Lee
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Jae Sam Hwang
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Ui Wook Hwang
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, Korea
- Phylomics Inc., Daegu, South Korea
- School of Life Sciences, Graduate School, Kyungpook National University, Daegu, South Korea
- School of Industrial Technology Advances, Kyungpook National University, Daegu, South Korea
- Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, South Korea
- * E-mail:
| |
Collapse
|
3
|
Chen C, Parejo M, Momeni J, Langa J, Nielsen RO, Shi W, Vingborg R, Kryger P, Bouga M, Estonba A, Meixner M. Population Structure and Diversity in European Honey Bees ( Apismellifera L.)-An Empirical Comparison of Pool and Individual Whole-Genome Sequencing. Genes (Basel) 2022; 13:182. [PMID: 35205227 PMCID: PMC8872436 DOI: 10.3390/genes13020182] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Whole-genome sequencing has become routine for population genetic studies. Sequencing of individuals provides maximal data but is rather expensive and fewer samples can be studied. In contrast, sequencing a pool of samples (pool-seq) can provide sufficient data, while presenting less of an economic challenge. Few studies have compared the two approaches to infer population genetic structure and diversity in real datasets. Here, we apply individual sequencing (ind-seq) and pool-seq to the study of Western honey bees (Apis mellifera). METHODS We collected honey bee workers that belonged to 14 populations, including 13 subspecies, totaling 1347 colonies, who were individually (139 individuals) and pool-sequenced (14 pools). We compared allele frequencies, genetic diversity estimates, and population structure as inferred by the two approaches. RESULTS Pool-seq and ind-seq revealed near identical population structure and genetic diversities, albeit at different costs. While pool-seq provides genome-wide polymorphism data at considerably lower costs, ind-seq can provide additional information, including the identification of population substructures, hybridization, or individual outliers. CONCLUSIONS If costs are not the limiting factor, we recommend using ind-seq, as population genetic structure can be inferred similarly well, with the advantage gained from individual genetic information. Not least, it also significantly reduces the effort required for the collection of numerous samples and their further processing in the laboratory.
Collapse
Affiliation(s)
- Chao Chen
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China;
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture and Rural Affairs, Beijing 100093, China
| | - Melanie Parejo
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.L.); (A.E.)
- Swiss Bee Research Center, Agroscope, 3003 Bern, Switzerland
| | - Jamal Momeni
- Eurofins Genomics, 8200 Aarhus, Denmark; (J.M.); (R.O.N.); (R.V.)
| | - Jorge Langa
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.L.); (A.E.)
| | | | - Wei Shi
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China;
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture and Rural Affairs, Beijing 100093, China
| | | | - Rikke Vingborg
- Eurofins Genomics, 8200 Aarhus, Denmark; (J.M.); (R.O.N.); (R.V.)
| | - Per Kryger
- Department of Agroecology, Aarhus University, 4200 Slagelse, Denmark;
| | - Maria Bouga
- Lab of Agricultural Zoology and Entomology, Agricultural University of Athens, 11855 Athens, Greece;
| | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.L.); (A.E.)
| | | |
Collapse
|
4
|
Ostroverkhova NV. Association between the Microsatellite Ap243, AC117 and SV185 Polymorphisms and Nosema Disease in the Dark Forest Bee Apis mellifera mellifera. Vet Sci 2020; 8:vetsci8010002. [PMID: 33383841 PMCID: PMC7823830 DOI: 10.3390/vetsci8010002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 12/24/2020] [Indexed: 12/28/2022] Open
Abstract
The microsporidian Nosema parasites, primarily Nosema ceranae, remain critical threats to the health of the honey bee Apis mellifera. One promising intervention approach is the breeding of Nosema-resistant honey bee colonies using molecular technologies, for example marker-assisted selection (MAS). For this, specific genetic markers used in bee selection should be developed. The objective of the paper is to search for associations between some microsatellite markers and Nosema disease in a dark forest bee Apis mellifera mellifera. For the dark forest bee, the most promising molecular genetic markers for determining resistance to nosemosis are microsatellite loci AC117, Ap243 and SV185, the alleles of which (“177”, “263” and “269”, respectively) were associated with a low level of Nosema infection. This article is the first associative study aimed at finding DNA loci of resistance to nosemosis in the dark forest bee. Nevertheless, microsatellite markers identified can be used to predict the risk of developing the Nosema disease.
Collapse
Affiliation(s)
- Nadezhda V. Ostroverkhova
- Invertebrate Zoology Department, Biology Institute, National Research Tomsk State University, 36 Lenina Avenue, 634050 Tomsk, Russia; ; Tel.: +7-3822-529-461
- Department of Biology and Genetics, Siberian State Medical University, 2 Moskovsky Trakt, 634055 Tomsk, Russia
| |
Collapse
|
5
|
Tihelka E, Cai C, Pisani D, Donoghue PCJ. Mitochondrial genomes illuminate the evolutionary history of the Western honey bee (Apis mellifera). Sci Rep 2020; 10:14515. [PMID: 32884034 PMCID: PMC7471700 DOI: 10.1038/s41598-020-71393-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/11/2020] [Indexed: 12/21/2022] Open
Abstract
Western honey bees (Apis mellifera) are one of the most important pollinators of agricultural crops and wild plants. Despite the growth in the availability of sequence data for honey bees, the phylogeny of the species remains a subject of controversy. Most notably, the geographic origin of honey bees is uncertain, as are the relationships among its constituent lineages and subspecies. We aim to infer the evolutionary and biogeographical history of the honey bee from mitochondrial genomes. Here we analyse the full mitochondrial genomes of 18 A. mellifera subspecies, belonging to all major lineages, using a range of gene sampling strategies and inference models to identify factors that may have contributed to the recovery of incongruent results in previous studies. Our analyses support a northern African or Middle Eastern origin of A. mellifera. We show that the previously suggested European and Afrotropical cradles of honey bees are the result of phylogenetic error. Monophyly of the M, C, and O lineages is strongly supported, but the A lineage appears paraphyletic. A. mellifera colonised Europe through at least two pathways, across the Strait of Gibraltar and via Asia Minor.
Collapse
Affiliation(s)
- Erik Tihelka
- Department of Animal Science, Hartpury College, Hartpury, GL19 3BE, UK.
| | - Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, 210008, China.
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK.
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| |
Collapse
|