Careful with understudied phyla: The case of chaetognath

Additional file 7:

Unit of the 5S cluster including the two splice-leader genes organized in tandem, the splice-leader sequences and the outrons. Primers employed for amplification are also specified.

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Additional file 1:

Examples of unrelated trans-spliced genes retrieved in the S. cephaloptera EST library. The presence of the TAC and TTT classes of splice-leaders is indicated for both ribosomal protein genes and other genes.

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Additional file 2:

Structure of the ribosomal protein S8 gene with alignment of used primers, transcript sequences from the EST library and genomic sequence deduced from sequencing of PCR products. The alignment especially stresses the absence of the splice-leader sequence from the 5'UTR and upstream promoter region.

Format: FAST Size: 30KB Download file

Additional file 3:

Description of the composite taxa employed in phylogenomic analysis. The amount of missing data was determined for the final Gblocked alignment of 12,764 amino acid positions. p-values are from the chi-square test, which tests whether the amino acid composition of each sequence is identical to the average amino acid composition of the whole alignment. The number of species included in the taxons is specified, as well as the name of the principal species.

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Additional file 4:

List of ribosomal proteins available in the chaetognaths Flaccisagitta enflata (Fe) and Spadella cephaloptera (Sc) and their divergence rates. The molecular divergence of each alternative form is indicated as ML patristic distance to the root (assuming WAG+Γ₄+I) as well as the content of best contig (least divergient of all species and variants), shorter contig (least divergent variant of S. cephaloptera) and longer contig (most divergent variant of S. cephaloptera).

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Additional file 5:

Bayesian trees calculated using Phylobayes implementing the CAT model for the shorter contig (A), longer contig (B) and both of them (C) from S. cephaloptera, as described in Additional file 3. Significant posterior probability values (pp > 0.95) are retrieved for all nodes and only lower ones are displayed in plain text. Both topology and support values remain unaffected by the use of variants of ribosomal proteins.

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Additional file 6:

PCR Primers and annealing conditions used for PCR experiments.

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