Phylogenetic positions of <i>A</i>. <i>menetriesi</i> and <i>C</i>. <i>maculatus</i>.

<p>A) Cladogram of Coleoptera simplified from that determined by [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167431#pone.0167431.ref016" target="_blank">16</a>]. Black asterisk indicates the superfamily in which the Chrysomelidae are located. B) Cladogram of Chrysomelidae simplified from that determined by [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167431#pone.0167431.ref021" target="_blank">21</a>]. Black and grey asterisks indicate the sub-families in which <i>A</i>. <i>menetriesi</i> and <i>C</i>. <i>maculatus</i> are located (respectively). C) <i>A</i>. <i>menetriesi</i> and D) <i>C</i>. <i>maculatus</i> adults.</p

Phylogenetic inter-relationships of ANTP HOXL class genes.

<p>Phylogenetic relationships were reconstructed using MEGA 6 using the LG+Freqs model with 4 gamma categories and invariant sites, based on a 59 amino acid alignment spanning the homeodomain. Numbers at base of nodes represent bootstrap percentages of 1000 replicates. Scale bar at base of phylogeny gives substitutions per site at given unit distance. Red underline indicates <i>A</i>. <i>menetriesi</i> and <i>C</i>. <i>maculatus</i> sequences, coloured boxes are used to delineate known gene families (and in the case of Hox 6/7/8, a superfamily).</p

Summary of RNA sources, life stages sampled and sequencing results.

<p><i>A</i>.<i>menetriesi</i> data is presented at left and <i>C</i>. <i>maculatus</i> data at right.</p

Genes identified by manual annotation.

<p>Genes identified by manual annotation.</p

Assembly metrics for individual time point and combined transcriptomic resources.

<p>Assembly metrics for individual time point and combined transcriptomic resources.</p

All sequences and alignments used in study

Zipped sequences (fasta) and alignments (multiple formats) for all genes used in analyse

Ancestral protein kinases are extensively lost during arthropod evolution.

<p><i>S. maritima</i> is an exception and retains the largest number of ancestral kinases. Numbers of kinase subfamilies in selected species are shown in parentheses after species names. The gains, losses, and inferred content of common ancestors are listed on internal branches. Kinases found in at least two species from human, <i>C. elegans</i> and <i>Nematostella vectenesis</i> were used as an outgroup.</p

Presence and absence of immunity genes in different arthropods.

<p>Counts of immune genes are shown for <i>S. maritima</i>, <i>D. pulex</i><a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005-McTaggart1" target="_blank">[131]</a>, <i>A. mellifera</i><a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005-Evans1" target="_blank">[86]</a>, <i>T. castaneum</i>, <i>Anopheles gambiae</i>, and <i>D. melanogaster</i><a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005-Dasmahapatra1" target="_blank">[132]</a>. ∼, identity of the gene is uncertain; -, not investigated.</p

Dscam diversity caused either by gene and/or exon duplication in different Metazoa.

<p>^aOnly canonical Dscam paralogues were considered. ^bIn <i>D. melanogaster</i> and <i>D. pulex</i> the paralogue Dscam-L2 has two Ig7 alternative coding exons. ^cPotential number of Dscam isoforms, circulating in one individual, produced by mutually exclusive alternative splicing of duplicated exons.</p

Frequency histogram of CpG_(o/e) observed in <i>S. maritima</i> gene bodies.

<p>The y-axis depicts the number of genes with the specific CpG_(o/e) values given on the x-axis. The distribution of CpG_(o/e) in <i>S. maritima</i> is a trimodal distribution, with a low-CpG_(o/e) peak consistent with the presence of historical DNA methylation in <i>S. maritima</i> and the presence of a high CpG_(o/e) peak. The data underlying this plot are available in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005.s068" target="_blank">File S4</a>.</p