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Carvalho LR, Nunes R, Sobreiro MB, Dias RO, Corvalán LCJ, Braga-Ferreira RS, Targueta CP, Telles MPC. The complete chloroplast genome sequence of Eugenia klotzschiana O. Berg unveils the evolutionary dynamics in plastomes of Myrteae DC. tribe (Myrtaceae). Gene 2023:147488. [PMID: 37196890 DOI: 10.1016/j.gene.2023.147488] [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: 12/08/2022] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
Myrteae is the most diversified tribe in the Myrtaceae family and has great ecological and economic importance. Here, we performed the assembly and annotation of the chloroplast genome of Eugenia klotzschiana O. Berg and used this in a comparative analysis with other 13 species from the Myrteae tribe. The E. klotzschiana plastome exhibited a length of 158,977 bp and a very conserved structure and gene composition when compared with other Myrteae genomes. We identified 34 large repetitive sequences and 94 SSR repeats in E. klotzschiana plastome. The trnT-trnL, rpl32-trnL, ndhF-rpl32, psbE-petL, and ycf1 regions were identified as mutational hotspots. A negative selection signal was detected in 74 protein-coding genes while neutral selection was detected in two genes (rps12 and psaI). Furthermore, 222 RNA editing sites were identified in the E. klotzschiana plastome. We also obtained a plastome-based Myrtales phylogenetic tree, including E. klotzschiana for the first time in a molecular phylogeny, recovering its sister relationship for all other Eugenia species. Our results illuminate how evolution shaped the chloroplast genome structure and composition in the Myrteae tribe, especially in the E. klotzschiana plastome.
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Affiliation(s)
- Larissa R Carvalho
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - Rhewter Nunes
- Instituto Federal de Goiás - Campus Cidade de Goiás, Goiás, GO, Brasil.
| | - Mariane B Sobreiro
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - Renata O Dias
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - Leonardo C J Corvalán
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | | | - Cíntia P Targueta
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - Mariana P C Telles
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brasil; Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiânia, GO, Brasil
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2
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Giaretta A, Murphy B, Maurin O, Mazine FF, Sano P, Lucas E. Phylogenetic Relationships Within the Hyper-Diverse Genus Eugenia (Myrtaceae: Myrteae) Based on Target Enrichment Sequencing. FRONTIERS IN PLANT SCIENCE 2022; 12:759460. [PMID: 35185945 PMCID: PMC8855041 DOI: 10.3389/fpls.2021.759460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Eugenia is one of the most taxonomically challenging lineages of flowering plants, in which morphological delimitation has changed over the last few years resulting from recent phylogenetic study based on molecular data. Efforts, until now, have been limited to Sanger sequencing of mostly plastid markers. These phylogenetic studies indicate 11 clades formalized as infrageneric groups. However, relationships among these clades are poorly supported at key nodes and inconsistent between studies, particularly along the backbone and within Eugenia sect. Umbellatae encompasses ca. 700 species. To resolve and better understand systematic discordance, 54 Eugenia taxa were subjected to phylogenomic Hyb-Seq using 353 low-copy nuclear genes. Twenty species trees based on coding and non-coding loci of nuclear and plastid datasets were recovered using coalescent and concatenated approaches. Concordant and conflicting topologies were assessed by comparing tree landscapes, topology tests, and gene and site concordance factors. The topologies are similar except between nuclear and plastid datasets. The coalescent trees better accommodate disparity in the intron dataset, which contains more parsimony informative sites, while concatenated trees recover more conservative topologies, as they have narrower distribution in the tree landscape. This suggests that highly supported phylogenetic relationships determined in previous studies do not necessarily indicate overwhelming concordant signal. Congruence must be interpreted carefully especially in concatenated datasets. Despite this, the congruence between the multi-species coalescent (MSC) approach and concatenated tree topologies found here is notable. Our analysis does not support Eugenia subg. Pseudeugenia or sect. Pilothecium, as currently circumscribed, suggesting necessary taxonomic reassessment. Five clades are further discussed within Eugenia sect. Umbellatae progress toward its division into workable clades. While targeted sequencing provides a massive quantity of data that improves phylogenetic resolution in Eugenia, uncertainty still remains in Eugenia sect. Umbellatae. The general pattern of higher site coefficient factor (CF) than gene CF in the backbone of Eugenia suggests stochastic error from limited signal. Tree landscapes in combination with concordance factor scores, as implemented here, provide a comprehensive approach that incorporates several phylogenetic hypotheses. We believe the protocols employed here will be of use for future investigations on the evolutionary history of Myrtaceae.
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Affiliation(s)
- Augusto Giaretta
- Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados, Unidade II, Dourados, Brazil
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Bruce Murphy
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey, United Kingdom
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Olivier Maurin
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey, United Kingdom
| | - Fiorella F. Mazine
- Centro de Ciências e Tecnologias para a Sustentabilidade, Universidade Federal de São Carlos, Campus Sorocaba, Sorocaba, Brazil
| | - Paulo Sano
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Eve Lucas
- Herbarium, Royal Botanic Gardens, Kew, Surrey, United Kingdom
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3
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Machado LDO, Stefenon VM, Vieira LDN, Nodari RO. Structural and evolutive features of the Plinia phitrantha and P. cauliflora plastid genomes and evolutionary relationships within tribe Myrteae (Myrtaceae). Genet Mol Biol 2022; 45:e20210193. [PMID: 35103747 PMCID: PMC8805445 DOI: 10.1590/1678-4685-gmb-2021-0193] [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: 06/05/2021] [Accepted: 11/20/2021] [Indexed: 11/22/2022] Open
Abstract
Plinia phitrantha and P. cauliflora are Myrtaceae species with recognized horticultural and pharmacological potential. Nevertheless, studies on molecular genetics and the evolution of these species are absent in the literature. In this study, we report the complete plastid genome sequence of these species and an analysis of structural and evolutive features of the plastid genome within the tribe Myrteae. The two plastid genomes present the conserved quadripartite structure and are similar to already reported plastid genomes of Myrteae species concerning the size, number, and order of the genes. A total of 69-70 SSR loci, 353 single nucleotide polymorphisms, and 574 indels were identified in P. phitrantha and P. caulifora. Observed evolutive features of the plastid genomes support the development of programs for the conservation and breeding of Plinia. The phylogenomic analysis based on the complete plastid genome sequence of 15 Myrteae species presented a robust phylogenetic signal and evolutive traits of the tribe. Ten hotspots of nucleotide diversity were identified, evidence of purifying selection was observed in 27 genes, and relative conservation of the plastid genomes was confirmed for Myrteae. Altogether, the outcomes of the present study provide support for planning conservation, breeding, and biotechnological programs for Plinia species.
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Affiliation(s)
- Lilian de Oliveira Machado
- Universidade Federal de Santa Catarina, Departamento de Fitotecnia, Programa de Pós-graduação em Recursos Genéticos Vegetais, Florianópolis, SC, Brazil
| | - Valdir Marcos Stefenon
- Universidade Federal de Santa Catarina, Departamento de Fitotecnia, Programa de Pós-graduação em Recursos Genéticos Vegetais, Florianópolis, SC, Brazil
| | | | - Rubens Onofre Nodari
- Universidade Federal de Santa Catarina, Departamento de Fitotecnia, Programa de Pós-graduação em Recursos Genéticos Vegetais, Florianópolis, SC, Brazil
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Balbinott N, Rodrigues NF, Guzman FL, Turchetto-Zolet AC, Margis R. Perspectives in Myrtaceae evolution from plastomes and nuclear phylogenies. Genet Mol Biol 2022; 45:e20210191. [PMID: 35088818 PMCID: PMC8796035 DOI: 10.1590/1678-4685-gmb-2021-0191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/20/2021] [Indexed: 05/05/2023] Open
Abstract
Myrtaceae is a large and species-rich family of woody eudicots, with prevalent
distribution in the Southern Hemisphere. Classification and taxonomy of species
belonging to this family is quite challenging, sometimes with difficulty in
species identification and producing phylogenies with low support for species
relationships. Most of the current knowledge comes from few molecular markers,
such as plastid genes and intergenic regions, which can be difficult to handle
and produce conflicting results. Based on plastid protein-coding sequences and
nuclear markers, we present a topology for the phylogenetic relationships among
Myrtaceae tribes. Our phylogenetic estimate offers a contrasting topology over
previous analysis with fewer markers. Plastome phylogeny groups the tribes
Syzygieae and Eucalypteae and individual chloroplast genes produce divergent
topologies, especially among species within Myrteae tribe, but also in regard to
the grouping of Syzygieae and Eucalypteae. Results are consistent and
reproducible with both nuclear and organellar datasets. It confronts previous
data about the deep nodes of Myrtaceae phylogeny.
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Affiliation(s)
- Natalia Balbinott
- Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil
| | | | - Frank Lino Guzman
- Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Innovación Agraria, Perú
| | | | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil
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Zhou J, Zhang S, Wang J, Shen H, Ai B, Gao W, Zhang C, Fei Q, Yuan D, Wu Z, Tembrock LR, Li S, Gu C, Liao X. Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution. Sci Rep 2021; 11:9471. [PMID: 33947883 PMCID: PMC8096831 DOI: 10.1038/s41598-021-88160-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/06/2021] [Indexed: 02/02/2023] Open
Abstract
The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference.
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Affiliation(s)
- Jiawei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Shuo Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- School of Landscape and Architecture, Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
| | - Hongmei Shen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- The Second Peoples's Hospital of Nantong, Nantong, 226000, Jiangsu, China
| | - Bin Ai
- Foshan Green Development Innovation Research Institute, Foshan, 528000, Guangdong, China
| | - Wei Gao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Cuijun Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Qili Fei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhiqiang Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- The College of Horticulture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Sen Li
- The College of Horticulture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
| | - Cuihua Gu
- School of Landscape and Architecture, Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China.
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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6
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Rodrigues NF, Balbinott N, Paim I, Guzman F, Margis R. Comparative analysis of the complete chloroplast genomes from six Neotropical species of Myrteae (Myrtaceae). Genet Mol Biol 2020; 43:e20190302. [PMID: 32384134 PMCID: PMC7212760 DOI: 10.1590/1678-4685-gmb-2019-0302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/29/2020] [Indexed: 01/15/2023] Open
Abstract
Myrteae is the largest and most diverse tribe within Myrtaceae and represents the majority of its diversity in the Neotropics. Members of Myrteae hold ecological importance in tropical biomes for the provision of food sources for many animal species. Thus, due to its several roles, a growing interest has been addressed to this group. In this study, we report the sequencing and de novo assembly of the complete chloroplast (cp) genomes of six Myrteae species: Eugenia brasiliensis, E. pyriformis, E. nitida, Myrcianthes pungens, Plinia edulis and Psidium cattleianum. We characterized genome structure, gene content, and identified SSRs to detect variation within Neotropical Myrteae. The six newly sequenced plastomes exhibit a typical quadripartite structure, gene content and organization highly conserved among Myrtaceae species. Some differences in genome length, protein-coding genes and non-coding regions were found. Besides, IR boundaries present structural changes among species. Increased sequence diversity was observed in some intergenic regions, suggesting their suitability for investigating intraand interspecific genetic diversity in populational studies. These data also contribute to the improvement of taxa sampling in further phylogenetic investigations to understand Myrtaceae evolution.
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Affiliation(s)
- Nureyev F Rodrigues
- Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul , Centro de Biotecnologia, PPGBCM, Porto Alegre, RS, Brazil
| | - Natalia Balbinott
- Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul , Centro de Biotecnologia, PPGBCM, Porto Alegre, RS, Brazil
| | - Igor Paim
- Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Porto Alegre, RS, Brazil
| | - Frank Guzman
- Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul , Centro de Biotecnologia, PPGBCM, Porto Alegre, RS, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul , Centro de Biotecnologia, PPGBCM, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Porto Alegre, RS, Brazil
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7
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Ding L, Zhao X, Su L, Peng H, Sun C. The complete chloroplast genome of copper-tolerance plant Elsholtzia splendens. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2729-2730. [PMID: 33365703 PMCID: PMC7706683 DOI: 10.1080/23802359.2019.1644241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Elsholtzia splendens is a copper-tolerance plant colonized in copper mines in southern China. In this study, we sequenced and de novo assembled the complete chloroplast genome of E. splendens. The complete chloroplast genome is 150,761 bp (37.8% of GC) in length and contains 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis revealed that among the 11 Lamiaceae species, Perilla citriodor is the closest relative of E. splendens. The complete chloroplast genome of E. splendens provides a valuable resource for comparative and evolutionary analysis among Lamiaceae species and may be helpful in understanding the molecular mechanism of copper tolerance in E. splendens.
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Affiliation(s)
- Lele Ding
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Xiaomeng Zhao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Su
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongyun Peng
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Cheng Sun
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
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