20 Bionatura • Volumen 1 / Número 1 • http://www.revistabionatura.com INVESTIGACIÒN Non-coding chloroplast regions analysis within the Orchidaceae family in Southern Ecuador Análisis de regiones del cloroplasto no codifcante dentro de la familia Orchidaceae en el sur de Ecuador Ludeña Bertha 1, 4 , Cueva Augusta 2 , Riofrio Lorena 2 , Naranjo Carlos 2 , Bastdas Cristan 2 , Pintaud Jean-Christophe 3 , Suárez Juan-Pablo 2 ABSTRACT Non-coding regions of the chloroplast genome offer interesting levels of nucleotide variation which are very useful for molecular genetics, population and phylogenetic analysis. The family Orchidaceae is represented by ca. 500 species in Southern Ecuador. In order to determine the genetic variability present in members of this family belonging to the genera Cyrtochilum, Masdevallia, Epidendrum, Polystachya, Stelis and Zelenchoa, we have analyzed four chloroplas- tic intergenic spacers: atpH - atpI, trnL - trnF, trnF- ndhJ and rps16 - trnQ. All these markers have shown high richness in   simple sequence repeats (SSR), indels and substitutions. They resulted to be useful for species identifcation, phylogenetic analysis and population structure studies. Moreover the information provided by this analysis suggests that the endemic species Masdevallia deformis must be considered vulnerable and conservation strategies need to be adopted for its protection. Keywords: Chloroplast intergenic spacers, conservation, genetic variability, Orchidaceae, Southern Ecuador. RESUMEN Regiones del genoma del cloroplasto no codifcante ofrecen niveles interesantes de variación de nucleótidos que son muy útiles para la genética molecular, la población y el análisis flogenético. La familia Orchidaceae está representada por casi 500 especies en el sur de Ecuador. Con el fn de determinar la variabi- lidad genética presente en los miembros de esta familia pertenecientes a los géneros Cyrtochilum, Masdevallia, Epidendrum, Polystachya, Stelis y Zelenchoa, se han analizado cuatro espaciadores intergénicas cloroplásticos: atpH - atpI, trnL - TRNF, trnF- ndhJ y rps16 - trnQ. Todos estos marcadores han demostrado una alta riqueza en simples repeticiones de secuencia (SSR), indeles y sustituciones. Ellos resultaron ser útiles para la identifcación de las especies, el análisis flogenético y los estudios de estructura de la población. Además la información proporcionada por este análisis sugiere que las especies endémicas deformis Masdevallia deben ser considerados vulnerables y deben adoptarse estrategias de conservación para su protección. Palabras clave: espaciadores intergénicas, conservación, variabilidad genética, Orchidaceae, sur de Ecuador. T he Orchidaceae family encloses members with the most beautiful reproductive organs within Plantae kingdom. Tis monophyletic family is one of the largest with 765 genera and approximately 26500 species worldwide dis- tributed (World Checklist of Selected Plant Families). Orchids exhibit a large panoply of adaptation, ecological and morphological patterns which explain their capacity to colonize all land habitats. Tey constitute one of the most interesting bio- logical models to assess evolutionary, phylogenetic and ecological studies. Orchids represent around 25% of plants in Ecuador and they are the most important family of vascular plants in this country. 1 One third of species of this group is endemic. About 500 members of the Orchidaceae family have been described for the Southern Ecuadorian sierra. 2 In Ecuador the deforestation index is particu- larly high. 3 Epiphytic orchids are sensitive to this kind of anthro- pogenic activity. 4 Te southern province of Zamora-Chinchipe in Ecuador will be the focus of an intensive mining activity with harmful ecologi- cal consequences for its territory and neighbouring provinces. In this context a genetic approach to evaluate variability in the Orchi- 1 Universidad Técnica Partcular de Loja. Prometeo-Senescyt. Ecuador. 2 Universidad Técnica Partcular de Loja. San Cayetano Alto s/n Loja Ecuador. 3 IRD. Insttut de Recherche pour le Développement. Av. Agropolis 911. Montpellier France. 4 Yachay-Tech University. School of Biology. Urcuqui. Ecuador. daceae family in Southern Ecuador, in order to establish levels of biological resistence to habitat modifcation, is a priority. Te chloroplast genome has demonstrated to be a source of important information for population and conservation genetics, phylogenetic inference and species identifcation (bar-coding) studies. 5-7 Plastid genome shows a very conserved size, structure, gene content and arrangement of genes within terrestrial plants. 7  Te most common structural  pattern of this genome consist of two inverted repeats (IR) zones (25 Kb each one) separated by a long single copy (LSC) and a short single copy (SSC) regions respec- tively. Te latter two accumulate mutations at a higher rate than the rest of the organelle genome. 8 Seven orchids chloroplast genomes have been recently se- quenced: Phalaenopsis Aphrodite, 9  Oncidium sp. Gower Ramsey, 10 Rhyzantella gardneri, 11  Neottia nidus-avis, 12  Erycina pusilla. 13 , Corallorhiza striata 14 Cypripedium macranthos and Dendrobium ofcinale. 15 Chloroplastic regions with phylogenetical signal were identi- fed around 1990’s. 16  Moreover, Shaw has developped interesting