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From the Popular Trnaleu-COX2 Intergenic Region to the Mitogenome From the popular tRNAleu-COX2 intergenic region to the mitogenome: insights from diverse honey bee populations of Europe and North Africa Dora Henriques, Júlio Chávez-Galarza, Andreia Quaresma, Cátia José Neves, Ana Rita Lopes, Cecília Costa, Filipe O. Costa, José Rufino, Maria Alice Pinto To cite this version: Dora Henriques, Júlio Chávez-Galarza, Andreia Quaresma, Cátia José Neves, Ana Rita Lopes, et al.. From the popular tRNAleu-COX2 intergenic region to the mitogenome: insights from diverse honey bee populations of Europe and North Africa. Apidologie, Springer Verlag, 2019, 50 (2), pp.215-229. 10.1007/s13592-019-00632-9. hal-02495379 HAL Id: hal-02495379 https://hal.archives-ouvertes.fr/hal-02495379 Submitted on 2 Mar 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Apidologie (2019) 50:215–229 Original article * INRA, DIB and Springer-Verlag France SAS, part of Springer Nature, 2019 DOI: 10.1007/s13592-019-00632-9 From the popular tRNAleu-COX2 intergenic region to the mitogenome: insights from diverse honey bee populations of Europe and North Africa 1 1,2 1 1 Dora HENRIQUES , Júlio CHÁVEZ-GALARZA , Andreia QUARESMA , Cátia José NEVES , 1 3 4 5 1 Ana Rita LOPES , Cecília COSTA , Filipe O. COSTA , José RUFINO , Maria Alice PINTO 1Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal 2Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, La Molina, Lima, Peru 3Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria - Centro di Ricerca Agricoltura e Ambiente (CREA-AA), Via di Saliceto 80, 40128, Bologna, Italy 4Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal 5Research Centre in Digitalization and Intelligent Robotics (CeDRI), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal Received 26 July 2018 – Revised7December2018– Accepted 10 January 2019 Abstract – The tRNAleu-COX2 intergenic region of the mitochondrial DNA has been used for assessing diversity in honey bee (Apis mellifera L.) populations worldwide. However, differential mutation rates in different partitions of the mitogenome may produce incongruent results. In this study, we sequenced 123 mitogenomes of 7 subspecies from lineages A, M, and C. This allowed generating a comprehensive dataset to investigate the phylogenetic and phylogeographic congruence among the mitogenome, individual genes, and the tRNAleu-COX2 region. We showed that the diversity patterns inferred from the tRNAleu-COX2 marker are not fully paralleled by those obtained with the mitogenome and the individual genes; while the three lineages are supported by these, the African sub-lineages and the haplotypes are not. Thus, conclusions drawn from the tRNAleu-COX2 region need to be taken with caution and this marker may not be appropriate to infer phylogenetic relationships between honey bee colonies. Iberian honey bee / tRNAleu-COX2 intergenic region / mitogenome 1. INTRODUCTION organisms have been undertaken using short seg- ments of the cytoplasmatic DNA (reviewed by Since publication in the 1980s of John Avise’s DeSalle et al. 2017). While these short segments seminal paper (Avise 1986) supporting the power of can provide phylogeographical patterns, they may mitochondrial (mtDNA) markers in phylogeograph- have limited resolution to solve very recent events ic inference, thousands of studies on thousands of (Jacobsen et al. 2012). Next-generation sequencing has made the sequencing of the whole mitochondri- Electronic supplementary material The online version of al genome (mitogenome) possible in a time- and this article (https://doi.org/10.1007/s13592-019-00632-9) cost-effective manner. The mitogenome has a higher contains supplementary material, which is available to resolution than single genes and has been examined authorized users. in a variety of phylogenetic and phylogeographic Corresponding author: M. Pinto, [email protected]. Pin- studies to solve shallow evolutionary histories, such to, [email protected] as in the dog (Pang et al. 2009), brown bear (Keis Handling Editor :KlausHartfelder et al. 2013), bank vole (Filipi et al. 2015), and snub- 216 D. Henriques et al. nosed monkey (Hong et al. 2017), as well as many European) previously described by Ruttner other organisms. (1988). Later on, screening of African and Middle In 1985, the Drosophila yakuba mitogenome Eastern populations led to proposal of a novel was first released (Clary and Wolstenholme 1985) mtDNA lineage, dubbed Y, and to partitioning of and since then other insect mitogenomes have been lineage A variation into sub-lineages AI,AII,AIII, sequenced (Simon and Hadrys 2013), including and Z (Alburaki et al. 2011;Francketal.2001). that of the Italian honey bee, Apis mellifera In addition to being able to differentiate line- ligustica (Crozier and Crozier 1993). Like in most ages and African sub-lineages, the Dra Itesthas of the Metazoa, the honey bee mitogenome con- several advantages: haplotype identification re- tains 37 genes, namely, two rDNAs that encode the quires basic equipment available in any small- mitochondrial ribosome RNA components, 22 scale laboratory, it can be done in a time- and tRNAs required for translation of the mitochondrial cost-effective manner, and there is a large catalog proteins, and 13 protein-coding genes encoding the of haplotypes developed from honey bees collect- essential components of the electron transport ed across the world, which allows comparative chain and oxidative phosphorylation. studies (Chávez-Galarza et al. 2017; Rortais Mitochondrial DNA diversity has been sur- et al. 2011; Techer et al. 2017). On the other hand, veyed in honey bee populations around the world the data produced by the Dra Itestarenotwell with a variety of molecular methods, including suited to phylogenetic and phylogeographical in- RFLPs (restriction fragment length polymor- ference due to the large number of indels, the phisms), PCR-RFLPs, and direct sequencing of duplication of large fragments in the tRNAleu- coding regions (Arias and Sheppard 1996; COX2 region, and the uncertainty about whether Chávez-Galarza et al. 2017;Techeretal.2017). this fragment captures the Breal^ maternal history. The early studies examined mtDNA variation by The honey bees from the Iberian Peninsula have digesting the entire molecule with a combination of been intensively surveyed for mtDNA diversity restriction enzymes, allowing for the construction with the Dra I test (Cánovas et al. 2008;Franck of restriction site maps (Garnery et al. 1992;Smith et al. 1998;Migueletal.2007;Pintoetal.2013; and Brown 1988; Smith et al. 1991). Later on, Pinto et al. 2012). These studies revealed maternal restriction enzymes were employed in PCR- patterns of unparalleled complexity, characterized amplified coding regions of the mtDNA such as by geographically structured co-existence of hap- CYTB (cytochrome b; Crozier et al. 1991; Pinto lotypes belonging to lineages M and A, and to sub- et al. 2003), COX1 (cytochrome c oxidase subunit lineages AI,AII,andAIII. In addition, Iberia har- I; Bouga et al. 2005;HallandSmith1991; Nielsen bors the highest levels of diversity reported so far, et al. 2000; Stevanovic et al. 2010), ls-rRNA (large with hundreds of haplotypes (Cánovas et al. 2008; subunit ribosomal RNA; Hall and Smith 1991; Chávez-Galarza et al. 2017;Francketal.1998; Ozdil and Ilhan 2012a; Pinto et al. 2005), and Migueletal.2007; Pinto et al. 2013). Therefore, ND5 (NADH dehydrogenase 5; Bouga et al. this confined area of the A. mellifera distributional 2005; Ozdil and Ilhan 2012b). Among the different range offers a unique stage for studying honey bee PCR-RFLP assays, the most popular is the Dra I genetic diversity patterns. test developed by Garnery et al. (1993). This assay Chávez-Galarza et al. (2017)carriedoutacom- consists of PCR amplification of the highly poly- prehensive survey of maternal variation in Iberia morphic non-coding region located between the by sequencing the tRNAleu-COX2 fragment of tRNAleu and COX2 (cytochrome c oxidase subunit 711 individuals collected across three north- II) genes (originally named COI-COII intergenic south transects. Herein, we generated sequencing region), followed by digestion with Dra I restric- data of the complete mitogenome for 87 individ- tion enzyme. Garnery et al. (1993) showed that the uals selected from the 711 individuals to represent combined length and restriction site polymor- the Iberian variation range and for 36 individuals phisms of this region were able to assign honey from six subspecies belonging to lineages A, M, bee populations to the morphology-based lineages and C. Using this large dataset, we aim to inves- (A, African; M, Western European; C, Eastern tigate the phylogenetic and phylogeographic From the tRNAleu-COX2 region to the mitogenome 217 congruence among the mitogenome, the individ- A. m. siciliana individuals) were obtained from ual coding genes,
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