ITS-1 alignment

Alignment of 133 internal transcribed spacer 1 sequences (130 of Cephaloflexa bergi species and 3 of Cephaloflexa sp. as outgroup) used for the phylogenetic analyses

COI alignment

Alignment of cytochrome oxidase I sequences resulted in an 822 bp matrix with no gaps used for phylogenetic analyses

Summary of <i>N. vitripennis</i> OBPs. Unless otherwise indicated, the “Status” is protein coding and “EST support” is full.

*<p>OBP only has some vestiges of its second domain.</p>(a)<p>On its first domain only.</p

Phylogenetic relationships of <i>Nasonia</i>'s double-domain OBPs with their closest Classic OBPs.

<p>Double-domain OBPs were split in the two encompassing domains (domain 1 in dark blue; domain 2 in dark orange).</p

Mid-point rooted phylogenetic relationships of <i>Nasonia vitripennis</i> (light brown) and <i>Apis mellifera</i> (orange) OBPs.

<p>The outer ring shows the intron/exon structure in the coding region (intron phases are represented by colour-coded crossed bars: dark orange, phase 0; blue, phase 1; black, phase 2. The scale bar represents 1 amino acid substitution per site. The tree is displayed using the iTOL webserver (Letunic and Bork 2007). The accession numbers of OBPs used are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043034#pone.0043034.s005" target="_blank">Table S1</a>.</p

Conserved cysteine residue losses in OBPs.

*<p>Cysteine pairs forming disulphide bonds in the OBPs. Incomplete sequences were excluded.</p

Nucleotide composition bias in the Platyhelminthes analyzed.

<p>A) Relationship between A+T content and NB3 (NB at the third position of four-fold degenerate codons) values. Green squares and red circles indicate free-living and parasitic platyhelminths, respectively. The surveyed species are shown in numbers: 1, <i>T</i>. <i>sigani</i>; 2, <i>F</i>. <i>hepatica</i>; 3, <i>D</i>. <i>balaenopterae</i>; 4, <i>B</i>. <i>hoshinai</i>; 5, <i>T</i>. <i>saginata</i>; 6, <i>S</i>. <i>japonicum</i>; 7, <i>C</i>. <i>alpina</i>; 8, <i>Obama</i> sp.; 9, <i>S</i>. <i>mediterranea</i>; 10, <i>D</i>. <i>japonica</i>. B) Values of the different NB-based statistic across species. C) Relationship between A+T content for different genome portions and A+T content for the third positions.</p

Relationship between different codon bias measures.

<p>A) Relationship between ENC and SC values. B) Relationship between SC and A+T% values. C) SC values across species (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120081#sec002" target="_blank">Material and Methods</a> text for acronym description). Green squares and red circles indicate free-living and parasitic Platyhelminthes, respectively. The surveyed species are shown in numbers: 1, <i>T</i>. <i>sigani</i>; 2, <i>F</i>. <i>hepatica</i>; 3, <i>D</i>. <i>balaenopterae</i>; 4, <i>B</i>. <i>hoshinai</i>; 5, <i>T</i>. <i>saginata</i>; 6, <i>S</i>. <i>japonicum</i>; 7, <i>C</i>. <i>alpina</i>; 8, <i>Obama</i> sp.; 9, <i>S</i>. <i>mediterranea</i>; 10, <i>D</i>. <i>japonica</i>.</p

Overlapping transcripts.

<p>In green: <i>Nasonia vitripenis</i> ESTs, in blue: gene models predicted based on these ESTs.</p

Multiple Sequence Alignment (MSA) of all 90 <i>Nasonia</i> OBP sequences.

<p>The signal peptides are in skyblue boxes, the conserved residues are highlighted, the characteristic cysteines indicated in purple boxes. The splice sites are labelled with orange separators: vertical ones indicate splice sites between codons; backward slanted separators indicate splice sites within codons after the first base. The double-domain OBPs are NvitOBP38-NvitOBP46 and NvitOBP48.</p