RAD tag (SgrAI) derived SNPs from Bombus impatiens

RAD tag (SgrAI) derived SNPs from Bombus impatiens from Sadd et al. (2015) "The genomes of two key bumblebee species with primitive eusocial organisation

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

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

Homeobox gene clusters.

<p>(A) The Hox gene cluster of <i>S. maritima</i> compared to the cluster that can be deduced for the ancestral arthropod. <i>S. maritima</i> provides the first instance of an arthropod Hox cluster with tight linkage of an <i>Even-skipped (Eve)</i> gene (see text). Hox3 is the only gene missing from the <i>S. maritima</i> Hox cluster, but may be present elsewhere in the genome on a separate scaffold (see main text and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005.s072" target="_blank">Text S1</a> for details). The <i>S. maritima</i> cluster is drawn approximately to scale and spans 457 kb from the start codon of <i>labial (lab)</i> to the start codon of <i>Eve-b</i>. Arrows denote the transcriptional orientation. (B) Remains of clustering and linkage of ANTP class genes in <i>S. maritima</i>. The blue boxes are genes belonging to the ANTP class. The brown box is a gene belonging to the HNF class. The orange box is a gene belonging to the SINE class. The intergenic distances are indicated in kb. (C) Clusters of non-ANTP class homeobox genes in <i>S. maritima</i>. The green boxes are genes belonging to the TALE class. The red boxes are genes belonging to the PRD class. The intergenic distances are indicated in kb, except in the case of Rx-Hbn as these genes are overlapping but with opposite transcriptional orientations. All scaffold numbers are indicated in brackets.</p

Plot showing that DNA from a male individual contains a distinct fraction of scaffolds that is underrepresented (black arrow), and presumably derives from heterogametic sex chromosomes.

<p>No such fraction is present in the sequenced DNA of two individual females. The data underlying this plot is presented in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005.s068" target="_blank">File S4</a>.</p

Instances of homeobox gene clustering and linkage.

<p>Instances of homeobox gene clustering and linkage.</p

Conserved macro synteny signal between <i>S. maritima</i> and the chordate lancelet <i>B. floridae</i> clustered into ancestral linkage groups.

<p>Each dot represents a pair of genes, one in <i>B. floridae</i>, one in <i>S. maritima</i>, assigned to the same gene family by our orthology analysis. The ancestral linkage group identifiers refer to groups of scaffolds from the <i>S. maritima</i> (SmALG) or <i>B. floridae</i> (BfALG) assemblies, as detailed in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005.s066" target="_blank">File S2</a>. The identification of ALGs is described in the SI. Note that two <i>S. maritima</i> scaffolds were divided across ALGs, and so appear multiple times in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005.s066" target="_blank">File S2</a>.</p

Expansion of chemosensory receptor families.

<p>(A) Phylogenetic relationships among <i>S. maritima</i> (Smar), <i>I. scapularis</i> (Isca), <i>D. pulex</i> (Dpul), and a few insect GRs that encode for sugar, fructose, and carbon dioxide receptors (Dmel, <i>D. melanogaster</i>, and Amel, <i>A. mellifera</i>). (B) Phylogenetic relationships among <i>S. maritima</i>, <i>I. scapularis</i>, and a few <i>D. melanogaster</i> IRs and IgluR genes (the suffix at the end of the protein names indicates: i, incomplete and p, pseudogene).</p