Open Access Research article

The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays

Danillo Pinhal, Tatiana S Yoshimura, Carlos S Araki and Cesar Martins*

Author Affiliations

UNESP - Universidade Estadual Paulista, Instituto de Biociências, Departamento de Morfologia, Botucatu, SP, Brazil

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BMC Evolutionary Biology 2011, 11:151  doi:10.1186/1471-2148-11-151

Published: 31 May 2011

Additional files

Additional file 1:

Final alignment of nucleotide sequences encompassing the class I and class II 5S rRNA genes from the three Potamotrygonidae stingrays. Species are referred to as follows: Pfalkneri = Potamotrygon falkneri, Pmotoro = P. motoro, Paireba = Paratrygon aiereba. Dots represent sequence identity, gray shadowed nucleotides are indicative of distinctive sites between 5S genes found in the two 5S rDNA arrays. The internal control regions (A box, IE and C box) are highlighted in black. a, 5S rRNA genes class II; b, 5S rRNA genes class I.

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Additional file 2:

NTS class I and NTS class II nucleotide sequences from the stingray species included in this study. a) Nucleotide sequence alignment of short NTS repetitions of class I; (b) partial nucleotide sequence alignments of long NTS repetitions of class II obtained from the stingrays genome. Species are referred to as follows: Pfalkneri = Potamotrygon falkneri, Pmotoro = P. motoro, Paireba = Paratrygon aiereba. Dots represent conserved nucleotides and hyphens report indels. The microrepetition TCCC expanded in the P. aiereba genome is indicated in gray shading. Dots represent conserved bases and hyphens report indels.

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Additional file 3:

Alignment of 5S rRNA gene sequences from several vertebrates. The 5S gene of lampreys and diverse bony fish orders are majority-rule consensus (MRC) sequences obtained from data source listed in Additional file 1. (s) somatic type; (o) oocyte type. Sequences generated in the present study are underlined.

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Additional file 4:

Compilation of information regarding 5S rDNA nucleotide sequence in vertebrates. 5S rDNA information of several vertebrate groups (except stingrays sequences) were retrieved from GenBank/EMBL/DDBJ and used in the present study.

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