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Open Access Highly Accessed Research article

Evolution of the multifaceted eukaryotic akirin gene family

Daniel J Macqueen and Ian A Johnston*

Author Affiliations

Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK

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BMC Evolutionary Biology 2009, 9:34  doi:10.1186/1471-2148-9-34

Published: 6 February 2009

Additional files

Additional file 1:

Detailed information on akirin orthologues identified in a broad range of metazoans. The table provides exhaustive data on akirin sequences identified in a screen of genome and transcriptome databases for 22 metazoan phyla. It should be noted that the absence of a sequence from specific lineages does not, in most cases, distinguish between artefacts of insufficient sequencing data and gene non-functionalization.

Format: XLS Size: 34KB Download file

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Additional file 2:

Alignment of Akirin proteins used for evolutionary analyses. The file, which is in Fasta format, is the amino acid alignment of Akirin sequences used for phylogenetic reconstructions, the DIVERGE analysis and the likelihood ratio test. Accession numbers and other identifiers are shown next to each sequence.

Format: TXT Size: 6KB Download file

Open Data

Additional file 3:

Protein alignments of seven gene families found in chromosomal proximity to akirin1 and akirin2. The text file provides Fasta format amino acid alignments used for phylogenetic reconstructions of seven gene families that were located in the genomic neighbourhood of both akirin1 and akirin2 in multiple vertebrate classes. Sequences were mainly obtained from Ensembl release 52 genome databases and are shown with gene identifiers and their chromosomal location. Alternatively, NCBI accession numbers are provided.

Format: TXT Size: 46KB Download file

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Additional file 4:

Pairwise synonymous and non-synonymous substitution rates for Akirin1 and Akirin2 orthologues. The table provides separate estimates of pairwise synonymous (dS) and non-synonymous (dN) substitution rates for Akirin1 and Akirin2 orthologues from mammals, birds, amphibians and teleost fishes as performed by two methods (see main text). Also shown are the accompanying dN/dS ratios.

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Open Data

Additional file 5:

Amino acid alignment of 27 Akirin sequences showing the full results of the rate-shift likelihood ratio test. This file shows an output from the rate-shift analysis server http://www.daimi.au.dk/~compbio/rateshift/protein.html webcite where the LRT (ref [29] in the main text) was performed. Sites highlighted as red or blue in both Akirin1 and Akirin2 have evolved at a respective faster and slower rate for both paralogues, relative to the average for all positions in the alignment. Sites highlighted in either red or blue in one Akirin paralogue or the other were calculated to have evolved at a respective faster or slower rate in one paralogue and are likely to have contributed to functional divergence after the Akirin duplication. Alignment name abbreviations are: P.m (P. marinus), H.s (H. sapiens), X.t (X. tropicalis), D.r (D. rerio), T.r (Takifugu rubripes), G.g (G. gallus), G.a (G. aculeatus), O.l (Oryzias latipes), P.p (P. promelas), S.a (Sparus aurata).

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