Open Access Highly Accessed Research article

An EST screen from the annelid Pomatoceros lamarckii reveals patterns of gene loss and gain in animals

Tokiharu Takahashi14*, Carmel McDougall246, Jolyon Troscianko3, Wei-Chung Chen4, Ahamarshan Jayaraman-Nagarajan5, Sebastian M Shimeld4 and David EK Ferrier24*

Author Affiliations

1 Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, UK

2 The Scottish Oceans Institute, University of St. Andrews, St. Andrews, Fife, UK

3 Centre for Ornithology, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK

4 Department of Zoology, University of Oxford, South Parks Road, Oxford, UK

5 Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK

6 School of Biological Sciences, University of Queensland, St Lucia, Queensland, Australia

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BMC Evolutionary Biology 2009, 9:240  doi:10.1186/1471-2148-9-240

Published: 25 September 2009

Additional files

Additional file 1:

Distribution of Pomatoceros ESTs in the assembled contigs. The data shows the distribution of Pomatoceros EST reads in 521 assembled contigs and the most highly represented putative genes in P. lamarckii cDNA library (more than 10 reads).

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Additional file 2:

A complete list of 59 orthologous proteins that were used for the phylogenetic analysis. The table lists 59 orthologues and their accession numbers that were used for the phylogenetic analysis. Note that the genes are listed as 60 orthologues because in one case (EEF2) the orthologous ESTs from P. lamarckii aligned to discrete regions of this gene. Therefore the two genes are listed as 'a' and 'b' forms.

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Additional file 3:

A table of the evolutionary distance values in Figure 1A and 1B. The table shows the evolutionary distance values from the root where Nematostella and all bilaterian animal species diverge in Figure 1A and 1B. The exact probability values from the distance-based relative rate tests are also provided. The cells of the table are highlighted with red for significantly higher/longer distance values than that of Pomatoceros (P < 0.001) and green for lower/shorter values.

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Additional file 4:

A complete list of 807 unique P. lamarckii EST sequences that are conserved in both the Deuterostomia and the Ecdysozoa. The table lists 807 unique P. lamarckii EST sequences that are significantly (E-value less than 10-10) conserved in both the Deuterostomia and the Ecdysozoa. Sequence description, GO terms and Enzyme code are annotated by Blast2GO. Because the BLASTx matches of pl_xlvo_22e07, pl_xlvo_32f10 and Contig 207 are only predicted proteins from genome data, their sequence descriptions and GO terms are not shown here.

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Additional file 5:

A list of 158 P. lamarckii EST sequences that are conserved uniquely with the Deuterostomia. The table lists 158 P. lamarckii ESTs that are conserved uniquely with the Deuterostomia (E-value less than 10-10). Sequence description, GO terms and Enzyme code are annotated by Blast2GO. The genes for which sequence descriptions and GO terms are not shown here are those that match only predicted proteins from genome data.

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Additional file 6:

A list of 23 P. lamarckii EST sequences that are conserved uniquely with the Ecdysozoa. The table lists 23 P. lamarckii ESTs that are conserved uniquely with the Ecdysozoa (E-value less than 10-10). Sequence description, GO terms and Enzyme code are annotated by Blast2GO. The genes for which sequence descriptions and GO terms are not shown here are those that match only predicted proteins from genome data.

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Additional file 7:

A list of 96 P. lamarckii EST sequences that are conserved only within the Lophotrochozoa. The table lists 96 P. lamarckii ESTs that are conserved only within the Lophotrochozoa (E-value less than 10-10). Domain predictions are from INTERPROSCAN and NCBI Conserved Domains searches. Cellular locations were predicted using PSORT. The ESTs highlighted with blue are only conserved within annelids such as Capitella and Helobdella.

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Additional file 8:

P. lamarckii protein sequences listed in Table 2. P. lamarckii predicted amino acid sequences in Table 2 are provided. The three proteins that are described in Figure 4 are not shown here. A. Pomatoceros -FVamide neuropeptide precursor protein sequence predicted from entire sequence of pl_xlvo_23a09 [GenBank: GQ381306]. RPRFV, RRMFV, RPKFV motifs are highlighted with blue. B. Pomatoceros galactose-binding lectin sequences predicted from pl_xlvo_33f01 and pl_xlvo_58g09 [GenBank: GQ381307]. The G-X-X-X-Q-X-W motifs are highlighted with yellow and related motif with blue. C. Pomatoceros FMRFamide precursor protein sequence predicted from Contig 196. FMRF motifs are highlighted with yellow.

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