Open Access Research article

Molecular organization and phylogenetic analysis of 5S rDNA in crustaceans of the genus Pollicipes reveal birth-and-death evolution and strong purifying selection

Alejandra Perina, David Seoane, Ana M González-Tizón, Fernanda Rodríguez-Fariña and Andrés Martínez-Lage*

Author Affiliations

Department of Cell and Molecular Biology. Evolutionary Biology Group (GIBE), Universidade da Coruña, A Fraga 10, E-15008 A Coruña, Spain

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BMC Evolutionary Biology 2011, 11:304  doi:10.1186/1471-2148-11-304

Published: 17 October 2011

Additional files

Additional file 1:

Figure S1: Different 5S rDNA tandem arrangements. Drawings are done to scale. Scheme is as follows: a) last portion of the 5S (88 bp), NTS, 5S (120 pb), NTS, 5S (120 pb), NTS, and the first portion of the contiguous 5S (32 pb) for the trimer; b-g) last portion of the 5S (88 bp), NTS, 5S (120 pb), NTS, and the first portion of the contiguous 5S (32 pb) for dimers. Different colors show different types of NTS. Dotted arrows indicate putative pseudogenes. 5S, 5S rDNA gene; NTS, nontranscribed spacer.

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Additional file 2:

Table S1: Accession numbers and details of barnacle sequences used in this study.

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Additional file 3:

Figure S2: Alignments of different types. F and G types are aligned together. Putative pseudogenes (red) are aligned with C type sequences. Table S2: Values of similarity among NTS types.

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Additional file 4:

Figure S3: Phylogenetic relationships of 5S rDNA for the three main variants in Pollicipes species reconstructed by means of a maximun likelihood trees. Numbers on nodes represent bootstrap values based on 100 replicates. (a) Phylogeny of A type reconstruted by K81uf + I + G model. (b) Phylogeny of E type reconstruted by SYM + I + G model. (c) Phylogeny of F and G types reconstruted by HKY + I + G model. In (b) and (c), asterisks indicate P. pollicipes sequences. Figure S4: Identified regions (not aligned) of 78 nucleotides upstream the transcriptional start site of 5S ribosomal DNA. Three conserved regions were identified. Nucleotides shaded in blue share the motif CGGCCACCGGC, those shaded in red correspond to an AT rich region that it was located about -25 bp, and the TTC sequence (shared with Bombyx mori silkworms) is shaded in green color. Figure S5: 5S ribosomal RNA predicted secondary structures of barnacles. Structures correspond to the b and c types sequences that excluding the primer-annealing regions. (a-h) Sequences used in the predicted consensus secondary structures type I Pollicipes and (i) type II Pollicipes. ((a) El04Tie09b;(b) El03Afu02b; (c) Py02Oly04b; (d) El04Afu04b, El03Afu19b, El05Afu04b, El03Afu02c, El01Tie02b, El01Tie01b; (e) El01Tie03b; (f) Py08Oly03b, Py03Oly01b; (g) El03Afu07b, El04Tie06b; (h) El03Afu16b; (i) Po06Bal01b, Po06Bal02b. Figure S6: 5S alignment. Upper line is the consensus 5S rDNA gene. White boxes represent the internal control regions (ICRs) involved in the transcription of the D. melanogaster 5S rDNA, and grey shading areas correspond to the three sequence elements that regulate transcription activity of X. laevis 5S rDNA (box A, intermediate element, and box C, from left to right). The b and c types sequences represent the second and third unit of the array.

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Additional file 5:

Constraints applied in RNA alifold.

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