Intraspecific Variation in the First Internal Transcribed Spacer (ITS1)
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Intraspecific variation in the first internal transcribed spacer (ITS1) of the nuclear ribosomal DNA in Melipona subnitida (Hymenoptera, Apidae), an endemic stingless bee from northeastern Brazil Darci de Oliveira Cruz, Daniel Macedo de Melo Jorge, Júlio Otávio Portela Pereira, Davi Coe Torres, Carlos Eduardo Alves Soares, Breno Magalhães Freitas, Thalles Barbosa Grangeiro To cite this version: Darci de Oliveira Cruz, Daniel Macedo de Melo Jorge, Júlio Otávio Portela Pereira, Davi Coe Torres, Carlos Eduardo Alves Soares, et al.. Intraspecific variation in the first internal transcribed spacer (ITS1) of the nuclear ribosomal DNA in Melipona subnitida (Hymenoptera, Apidae), an endemic stingless bee from northeastern Brazil. Apidologie, Springer Verlag, 2006, 37 (3), pp.376-386. hal- 00892187 HAL Id: hal-00892187 https://hal.archives-ouvertes.fr/hal-00892187 Submitted on 1 Jan 2006 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 37 (2006) 376–386 © INRA/DIB-AGIB/ EDP Sciences, 2006 DOI: 10.1051/apido:2006003 Original article Intraspecific variation in the first internal transcribed spacer (ITS1) of the nuclear ribosomal DNA in Melipona subnitida (Hymenoptera, Apidae), an endemic stingless bee from northeastern Brazil1 Darci de Oliveira CRUZa, Daniel Macedo de Melo JORGEb, Júlio Otávio Portela PEREIRAa, Davi Coe TORRESb, Carlos Eduardo Alves SOARESb, Breno Magalhães FREITASa, Thalles Barbosa GRANGEIROb* a Grupo de Pesquisa com Abelhas, Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal do Ceará, Fortaleza-CE, Brazil b Laboratório de Citogenética e Genética Molecular, Departamento de Biologia, Bloco 906, Centro de Ciências, Universidade Federal do Ceará, Av. Humberto Monte, s/n, CEP 60.455-970, Fortaleza-CE, Brazil Received 27 June 2005 – revised 20 September 2005 – accepted 27 September 2005 Abstract – Melipona subnitida is endemic to northeastern Brazil where it has been exploited for the production of honey. In this work, partial sequences (about 600 bp) of the first internal transcribed spacer (ITS1) of the ribosomal DNA were obtained from M. subnitida specimens collected in thirteen localities in northeastern Brazil. All the sequences were deposited in GenBank (accession numbers DQ078726- DQ078738). The mean nucleotide divergence (excluding sites with insertions/deletions) in the ITS1 sequences was about 5%, ranging from 0 to 13%. However, when the sites with insertions/deletions were taken into account each sequence was unique, with nucleotide divergences varying from 1.1 to 18%. The intraspecific variation in the M. subnitida ITS1 is therefore greater than most of those previously published studies comprising a wide range of organisms. This high variation is taken as an evidence of isolated populations evolving individually for a long period of time. This information is also of importance for the development of appropriate conservation strategies for this species. Melipona subnitida / stingless bee / nuclear ribosomal DNA / ITS/5.8S region / genetic variability 1. INTRODUCTION as “jandaira”. This bee species, which makes its nests in the trunks of living trees, has been tra- Melipona Illiger 1806 (Hymenoptera: Api- ditionally exploited for the production of honey dae) comprises about 40 neotropical species of (Bruening, 1990; Martins et al., 2004). stingless bees found exclusively in the equato- Despite their ecological relevance there are rial, tropical and subtropical regions of the still a few molecular genetic studies of American continent, with its geographical dis- Melipona species (Fernandes-Salomão et al., tribution ranging from Mexico to Argentina 2002; Waldschmidt et al., 2002; Costa et al., (Schwarz, 1932; Michener and Sakagami, 2005). More recently, the complete sequences 1990; Camargo and Pedro, 1992; Michener, of the first internal transcribed spacer (ITS1) of 2000). Melipona subnitida Ducke is endemic to the nuclear ribosomal DNA (nrDNA) from northeastern Brazil where it is popularly known three Melipona species were determined * Corresponding author: [email protected] 1 Manuscript editor: Klaus Hartfelder Article published by EDP Sciences and available at http://www.edpsciences.org/apido or http://dx.doi.org/10.1051/apido:2006003 Intraspecific variation in Melipona subnitida 377 Figure 1. Map of the Northeast of Brazil showing sampling locations of Melipona subnitida specimens used in the present study. Specimens were collected in thirteen localities across the states of Maranhão (MA), Paraíba (PB), Rio Grande do Norte (RN) and Ceará (CE). The localities were: 1-Quixadá; 2-Sousa; 3-Ocara; 4-Mossoró; 5-Russas; 6-Sobral; 7-Milhã; 8-Quixelô; 9-Aracati; 10-Aracoiaba; 11-João Câmara; 12-Choro- zinho; and 13-Araioses. (Fernandes-Salomão et al., 2005). The relation- 2. MATERIALS AND METHODS ships among eight species from this genus were inferred from partial ITS1 sequences, demon- 2.1. Insect material strating the potential phylogenetic utility of this region (Fernandes-Salomão et al., 2005). How- Adult specimens of M. subnitida were collected in different localities of four states (Ceará, Paraiba, ever, the usefulness of this spacer for intraspe- Rio Grande do Norte and Maranhão) in northeastern cific studies in Melipona has yet to be Brazil (Fig. 1). The Northeast of Brazil is situated determined. In the present work the intraspe- between 1°02’–18°20’ S and 34°47’–48°45’ W, cific sequence variation in the ITS1 was covering an area of 1 644 039 km2, from the state of assessed in M. subnitida specimens from dif- Maranhão to the state of Bahia, which corresponds ferent localities of northeastern Brazil. Infor- to 9.3% of the Brazilian territory (Andrade, 1977). mation on genetic variation is of great Insects were maintained in 100% ethanol until used importance to understand the genetic structure for DNA extraction. Locality data, specimen voucher and GenBank accession numbers are listed as well as the phylogeographical patterns of a in Table I. Voucher specimens from all sampled species. This information is also relevant for localities are housed in the bee collection of the the development of effective conservation Departamento de Zootecnia, Universidade Federal strategies. do Ceará, Fortaleza-Ceará, Brazil. 378 D.O. Cruz et al. Table I. Geographical and voucher data of the specimens of Melipona subnitida used in the present study. Locality1 Sample Coordinates Collection Voucher GenBank (County-State) number2 date number accession number Quixadá-Ceará 1 4°58’17” S, 39°00’55” W 10/10/2003 MGPA0503 DQ078726 Sousa-Paraíba 2 6°45’33” S, 38°13’41” W 11/11/2003 MGPA0703 DQ078727 Ocara-Ceará 3 4°29’27” S, 38°35’48” W 25/08/2003 MGPA1305 DQ078728 Mossoró-Rio Grande 4 5°11’15” S, 37°20’39” W 05/04/2004 MGPA1404 DQ078729 do Norte Russas-Ceará 5 4°56’25” S, 37°58’33” W 30/10/2003 MGPA0603 DQ078730 Sobral-Ceará 6 3°41’10” S, 40°20’59” W 07/09/2003 MGPA0103 DQ078731 Milhã-Ceará 7 5°40’30” S, 39°11’38” W 21/09/2003 MGPA0104 DQ078732 Quixelô-Ceará 8 6°15’16” S, 39°12’07” W 21/09/2003 MGPA0203 DQ078733 Aracati-Ceará 9 4°33’42” S, 37°46’11” W 10/10/2003 MGPA0403 DQ078734 Aracoiaba-Ceará 10 4°22’16” S, 38°48’51” W 21/09/2003 MGPA0303 DQ078735 João Câmara-Rio 11 5°32’15” S, 35°49’11” W 05/04/2004 MGPA1304 DQ078736 Grande do Norte Chorozinho-Ceará 12 4°18’01” S, 38°29’52” W 28/09/2004 MGPA1104 DQ078737 Araioses-Maranhão 13 2°53’24” S, 41°54’11” W 06/07/2004 MGPA1704 DQ078738 General Sampaio-Ceará3 14 4°03’10” S, 39°27’16” W 06/04/2004 MGPA1204 - 1 Specimens were collected in localities of northeastern Brazil; 2 As shown in Table II; 3 ITS1 sequence for specimens collected in this locality was not determined. 2.2. DNA purification 2.3. PCR amplification and DNA sequencing Total genomic DNA was isolated from five spec- imens of each locality using a CTAB-based protocol Amplification reactions were performed in a final (Foster and Twell, 1996). The thorax of each speci- volume of 25 µL containing 500–800 ng of genomic men was ground in liquid nitrogen and digested for DNA (template), 20 mM Tris-HCl, pH 8.4, 50 mM µ 2 h at 60 °C in 500 µL CTAB extraction buffer (2% KCl, 1.5 mM MgCl2, 100 M of each dATP, dCTP, w/v CTAB, 100 mM Tris-HCl, pH 8.0, 20 mM dGTP and dTTP (Amersham Biosciences, Sweden), EDTA, 1.4 M NaCl, 0.2% v/v 2-mercaptoethanol, 5 pmoles of each primer and 0.5 units of Taq DNA 200 µg/mL proteinase K). DNA was then extracted Polymerase (Amersham Biosciences, Sweden). sequentially with 1 volume of phenol:chloro- PCR reactions were carried out in a MJ-Research form:isoamylalcohol (25:24:1) and 1 volume of Inc. (Watertown, Maryland, USA) PTC-100 ther- chloroform:isoamylalcohol (24:1), and precipitated mocycler programmed for an initial denaturation overnight at −20 °C with 2 volumes of 100% ethanol. step (3 min at 94 °C) followed by 45 cycles of 1 min The precipitate was collected by centrifugation at 94 °C, 1 min at 55 °C, and 2 min at 72 °C. The (8 000 rpm, 20 min) and the DNA pellet was washed last cycle was followed by a final incubation of in 70% ethanol, air-dried, and resuspended in 100 µL 10 min at 72 °C. The samples were then stored at of 10 mM Tris-HCl pH 8.0, 1 mM EDTA.