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Base composition, selection, and phylogenetic significance of indels in the recombination activating gene-1 in vertebrates

Ylenia Chiari12, Arie van der Meijden3, Ole Madsen4, Miguel Vences5 and Axel Meyer1*

Author Affiliations

1 Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany

2 Institut des Sciences de l'Evolution: ISE-M, Université Montpellier 2, 2, Place Eugène Bataillon, CC064, 34095 Montpellier, cedex 5, France

3 CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal

4 Animal Breeding and Genomics Centre, Wageningen University, P. O. Box 338, 6700AH Wageningen, the Netherlands

5 Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Spielmannstr. 8, 38106 Braunschweig, Germany

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Frontiers in Zoology 2009, 6:32  doi:10.1186/1742-9994-6-32

Published: 16 December 2009

Additional files

Additional file 1:

Used sequences. Genbank accession number and species name for each sequence of the 582 sequences dataset. More than one Genbank accession number indicates that multiple sequences for the same species have been merged together (see Methods for additional explanations). Bold numbers indicate full-length sequences.

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Additional file 2:

Alignment of the 582 vertebrate Rag1 sequences. Alignment of the 582 vertebrate sequences used in this work. The first 105 amino acid have been removed from the alignment (see Methods for additional explanations).

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Additional file 3:

Average nucleotide and amino acid distances. a) Average Tamura-Nei nucleotide distances, and average amino acid p-distances calculated for the 582 sequence dataset and for each part (5' and 3'-ends) of the entire fragment length of the gene. "N" indicates the number of sequences used. Check Table 1 to see the length range of the sequences included. "Bp" indicates the number of base pairs in the fragment analyzed after the within group alignment. Note that for Actinopterygii and Chondrichthyes only the 3' -end of the gene is provided. "F", "5"' and "3"' indicate the full gene and the 5' and 3' -ends of the gene, respectively.b) Average Tamura-Nei nucleotide distances, and amino acid p-distances for the functional zinc-finger and DNA binding domains in the 5' -end of the gene. "ZF" and "DB" indicate the zinc finger and DNA binding domains, respectively (Figure 1). See Methods for any additional information on the gene divisions and data available for each gene division.

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Additional file 4:

AT and GC skew. Average GC content (in % round up to higher integer) and base compositional skew for each codon position for each vertebrate group, based on the 582 sequences alignment. For the complete alignment across vertebrates 582 sequences have been used without the first 105 amino acid. See Methods for additional information about how the base compositional skew has been calculated.

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Open Data