The alignment of ribosomal genes is difficult due to insertion and deletion events of nucleotides, making the alignment ambiguous. This can be overcome by using information from the secondary structure of ribosomal genes. The aim of this study was to evaluate the utility of the secondary structure in improving the alignment of the 16S rRNA gene in land snails of the family Orthalicidae. We assessed 10 Orthalicid species (five genera). 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.
|Translated title of the contribution||Analysis of the secondary structure of mitochondrial LSU rRNA of Peruvian land snails (Orthalicidae: Gastropoda)|
|Number of pages||5|
|Journal||Revista Peruana de Biologia|
|State||Published - Apr 2010|
Bibliographical noteFunding Information:
We thank A. Chumbe, C. Congrains, D. Fernández, J. Chirinos, N. Medina, P. Matos, P. Romero, V. Borda and C. Calderón for assistance during laboratory and field work. We are grateful to P. Ramírez for his molecular logistic help and to E. Cano for his logistic help in Ancash. This study is part of Project 061001071 funded by Vicerrectorado de Investigación de la Universidad Nacional Mayor de San Marcos (VRI). Field work in San Martín was carried out as part of Project PEM2007B28 (VRI) and in Ancash with Project 051001041 (VRI). Dr. Lamas provided critical comments that helped to improve the final version of the manuscript.
2 Museo de Historia Natural, Uni- versidad Nacional Mayor de San Marcos. Av. Arenales 1256, Aparta do 14-0434, Lima-14, Perú. Email Jorge Ramirez: firstname.lastname@example.org Trabajo presentado a la XVIII Reunión Científica del Instituto de Investigaciones en Ciencias Bioló-gicas Antonio Raimondi, “200 años del nacimiento de Charles Darwin y el 150 aniversario de la publicación de On the Origin of Species by Means of Natural Selection”. Del 19 al 21 de agosto de 2009.