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Analysis of the Secondary Structure of Mitochondrial LSU Rrna of Peruvian Land Snails (Orthalicidae: Gastropoda)

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Analysis of the Secondary Structure of Mitochondrial LSU Rrna of Peruvian Land Snails (Orthalicidae: Gastropoda) Rev. peru. biol. 17(1): 053- 057 (Abril 2010) © Facultad de Ciencias Biológicas UNMSM Secondary structure of mitochondrialVersión LSU Online rRNA ISSN of land 1727-9933 snails Analysis of the secondary structure of mitochondrial LSU rRNA of Peruvian land snails (Orthalicidae: Gastropoda) Análisis de la estructura secundaria del LSU rRNA mitocondrial de cara- coles terrestres peruanos (Orthalicidae: Gastropoda) Jorge Ramirez1, 2, Rina Ramírez1, 2 1 Facultad de Ciencias Biológicas, Universidad Nacional Mayor de Abstract San Marcos. The alignment of ribosomal genes is difficult due to insertion and deletion events of nucleotides, making the 2 Museo de Historia Natural, Uni- versidad Nacional Mayor de San alignment ambiguous. This can be overcome by using information from the secondary structure of ribosomal Marcos. Av. Arenales 1256, Aparta- genes. The aim of this study was to evaluate the utility of the secondary structure in improving the alignment of do 14-0434, Lima-14, Perú. the 16S rRNA gene in land snails of the family Orthalicidae. We assessed 10 Orthalicid species (five genera). Email Jorge Ramirez: [email protected] Total DNA was isolated and the partial 16S rRNA gene was amplified and sequenced using internal primers. The sequences were aligned with ClustalX and manually corrected, in DCSE format, using the 16S rRNA secondary structure of Albinaria caerulea (Pulmonata: Clausiliidae). The sequences obtained ranged from 323 to 345 bp corresponding to parts of both domains IV and V of the 16S rRNA gene. The secondary structure was recovered by homology using RnaViz 2.0. Most stems are conserved, and in general the loops are more variable. The compensatory mutations in stems are related to maintenance of the structure. The absence of a bulge-stem-loop in domain V places the family Orthalicidae within the Heterobranchia. Keywords: 16S rRNA, Mollusca, Bulimulinae, DCSE, Compensatory Mutations. Trabajo presentado a la XVIII Resumen http://sisbib.unmsm.edu.pe/BVRevistas/biologia/biologiaNEW.htm Reunión Cien tífica del Instituto de Investigaciones en Ciencias Bioló- El alineamiento de genes ribosomales es dificultoso debido a eventos de inserción y deleción de nucleótidos, gicas Antonio Raimondi, “200 años convirtiendo el alineamiento en ambiguo; esto puede ser superado utilizando la información de la estructura del nacimiento de Charles Darwin y secundaria. El objetivo del presente trabajo es evaluar la utilidad de la estructura secundaria en mejorar el el 150 aniversario de la publicación de On the Origin of Species by alineamiento del gen 16S rRNA de caracoles terrestres de la familia Orthalicidae. Se evaluaron 10 especies Means of Natural Selection”. Del de Orthalicidos (5 géneros). El ADN total fue aislado y parte del gen 16S rRNA fue amplificado y secuenciado 19 al 21 de agosto de 2009. usando primers internos. Las secuencias fueron alineadas con ClustalX y corregidas a mano, en formato DCSE, usando la estructura secundaria del 16S rRNA de Albinaria caerulea (Pulmonata: Clausiliidae). Las secuen- cias obtenidas variaron de 323 a 345 pb correspondiendo a partes del dominio IV y V del gen 16S rRNA. Se pudo recuperar por homología la estructura secundaria para los Orthalicidos usando RnaViz 2.0. La mayoría Publicado impreso: 20/10/2010 de las hélices son conservadas, siendo en general los bucles más variables. El fenómeno de mutaciones Publicado online: 29/09/2010 compensatorias en las hélices, estaría relacionado con la conservación de la estructura. La ausencia de un “bulge-stem-loop” en el dominio V ubica a la familia Orthalicidae dentro de Heterobranchia. Palabras claves: 16S rRNA, Mollusca, Bulimulinae, DCSE, Mutaciones Compensatorias. Introduction or reduction of three regions of the 16S rRNA for all Hetero- Phylogenetic molecular studies aim to recover the historical branchia (Lydeard et al. 2000; 2002). These regions include a signal stored along the evolution in the sequences of nucleotides stem of domain II, the entire domain III (reduced to a single or amino acids. The alignments of these sequences are hypotheses stem in some mollusks) and part of a stem in Domain V (G16) that allow us to infer phylogenetic relationships among a set of (Lydeard et al. 2002). species. Correct alignment is essential for the reconstruction and Heterobranchia is one of the main clades of gastropods, recovery of phylogenetic signals leading to a correct evolutionary containing the largest number of species, which includes Pulmo- hypothesis. The alignment of many genes with abundant phy- nata, Opisthobranchia and the Lower Heterobranchia (Bouchet logenetic information, such as 16S rRNA, becomes difficult by & Rocroi, 2005). The Family Orthalicidae (Heterobranchia: the presence of insertion and deletion events which increase in Pulmonata: Stylommatophora) is the most diverse group of number with the inclusion of more divergent species, making endemic land snails from Peru and South America. Other genera the alignment ambiguous (Lydeard et al. 2000). These difficulties of the superfamily Orthalicoidea are also found in Oceania and can be overcome by using additional information, such as the Africa (Herbert & Mitchell 2009). Based on the 16S rRNA mi- secondary structure of rRNA. Ribosomal RNA sequences form tochondrial marker, Ramirez et al. (2009) found this family to complex secondary structures based on complementarity of the be a monophyletic group,of the “non-achatinoid clade” within bases along the molecule (Lydeard et al. 2002). Most models of a global phylogeny of Stylommatophora, demonstrating the known secondary structure of rRNA have been determined by efficiency of this marker to resolve evolutionary relationships. comparative sequence analysis (Woese et al. 1980; Noller et al. 1981; Gutell et al. 1994). The aim of this study was to evaluate the utility of the in- formation provided by the secondary structure to improve the The molecule of the large subunit rRNA (LSU rRNA or 16S alignments of the 16S rRNA gene in several species of land snails RNA) can be divided in the 5' and 3' sections, each with three of the family Orthalicidae. main structural domains (labeled I-VI) (Gutell et al. 2002) and in turn the stems are listed with letters and numbers (Wuyts et Materials and methods al. 2001). Several studies have shown the phylogenetic value of We used 10 species of the family Orthalicidae (belonging to the rRNA secondary structure (Titus & Frost 1996; Lydeard et five different genera) from different ecosystems of Peru (Table al. 2000; 2002), one of the most significant being the absence 1 and Fig. 1). Voucher specimens are deposited in the scientific Rev. peru. biol. 17(1): 053- 057 (April 2010) 53 Ramirez & Ramírez Table 1. Pulmonate land snail species, collection data and Genbank accession number for the sequences of the 16S rRNA used. Species Localities Department Coordinates Collectors Accession number 12º12´23.8"S, C. Congrains, J. Ramirez, A. Bostryx aguilari Weyrauch 1967 Atocongo Lima 76º53´43"W Chumbe. HM057172 12º12´23.8"S, C. Congrains, J. Ramirez, A. Bostryx conspersus (Sowerby, 1833) Atocongo Lima 76º53´43"W Chumbe. HM057173 12º12´23.8"S, C. Congrains, J. Ramirez, A. Bostryx modestus (Broderip, 1832) Atocongo Lima 76º53´43"W Chumbe. HM057174 11º52'58"S, D. Fernández, C. Congrains, J. Bostryx turritus (Broderip, 1832) Santa Eulalia Lima 76º 39'12"W Ramirez, P. Matos, A. Chumbe HM057175 11º38´36.2"S, Bostryx scalariformis (Broderip, 1832) Pasamayo Lima P. Romero. 77º12´11.9"W HM057181 11º23’55”S, N. Medina, P. Romero, J. Bostryx sordidus (Lesson, 1826) Iguanil Lima 77º14’01.5”W Ramirez, A. Chumbe. HM057176 12º11’43.2”S, D. Fernández, J. Ramirez, A. Scutalus versicolor (Broderip, 1832) Manzano Lima 76º50’03.2”W Chumbe. HM057177 06º35’18.8”S, Drymaeus sp. Juan Guerra San Martín V. Borda, C. Calderón. 76º18’59”W HM057178 09º11'50.6"S, Neopetraeus sp. Piurog Ancash R. Ramírez, A. Cano. 76º57'25.1"W HM057179 06º34'54,4"S, Naesiotus sp. Juan Guerra San Martín V. Borda, C. Calderón. 76º18'50,6"W HM057180 http://sisbib.unmsm.edu.pe/BVRevistas/biologia/biologiaNEW.htm 5 mm Figure 1. Species of Peruvian Orthalicidae. A: Bostryx aguilari. B: B. conspersus. C: B. modestus. D: B. sordidus. E: B. scalariformis. F: B. tur- ritus G: Scutalus versicolor. H: Drymaeus sp. I: Neopetraeus sp. J: Naesiotus sp. Photos: A, H and I: J. Ramirez. B-G: A. Chumbe. J: V. Borda. 54 Rev. peru. biol. 17(1): 053- 057 (Abril 2010) Secondary structure of mitochondrial LSU rRNA of land snails Results C E26U IV G The sequences obtained ranged from 323 to 345 base pairs U G U A C A E27 G and the alignment had 373 positions. It corresponds to part of G U A domains IV and V of the 3' end of the 16S rRNA gene (position G E24 C a g G A U 557 - 873 in the Albinaria caerulea sequence), including stems A A A A A [0-2] G U E27, E28, F1, G2, G3, G6, G7, G9 and G16. Stems E26, E24, a UA A G u UC G UU U G E21, E18, G1 and G17 did not form due to the small size of G C G C g U E28 the fragment analyzed (Fig. 2). G U U U [3-10] G7 A u A [1-12] C The secondary structure was recovered by homology for the U G t a u A U G3 u A A 10 species studied (Fig. 2). The structure of the partial 16S rRNA C G6 C c U u a G G U A G C sequence of B. aguilari is shown in Figure 3. Most of the stems G g [1-3] U g c E21 - E18 G C [0-4] A u are preserved and in general the loops are more variable (Figs. u U [0-4] A U u u u [9-14] u 2 and 3). The more conserved stems were E27 and E28.
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