The mitochondrial genome of and (Tunicata, Ascidiacea): high genome plasticity at intra-genus level-1

<p><b>Copyright information:</b></p><p>Taken from "The mitochondrial genome of and (Tunicata, Ascidiacea): high genome plasticity at intra-genus level"</p><p>http://www.biomedcentral.com/1471-2148/7/155</p><p>BMC Evolutionary Biology 2007;7():155-155.</p><p>Published online 31 Aug 2007</p><p>PMCID:PMC2220002.</p><p></p> sequences boxed. Gene abbreviations are as in the main text. Non-coding regions are named according to their length (in bp). Underlined sequences indicate inverted repeats

The mitochondrial genome of and (Tunicata, Ascidiacea): high genome plasticity at intra-genus level-2

<p><b>Copyright information:</b></p><p>Taken from "The mitochondrial genome of and (Tunicata, Ascidiacea): high genome plasticity at intra-genus level"</p><p>http://www.biomedcentral.com/1471-2148/7/155</p><p>BMC Evolutionary Biology 2007;7():155-155.</p><p>Published online 31 Aug 2007</p><p>PMCID:PMC2220002.</p><p></p>A-like structures. In the tRNA-like structure, canonical and G-U base pairing are differently indicated. Stop codons are in black background

The mitochondrial genome of and (Tunicata, Ascidiacea): high genome plasticity at intra-genus level-0

<p><b>Copyright information:</b></p><p>Taken from "The mitochondrial genome of and (Tunicata, Ascidiacea): high genome plasticity at intra-genus level"</p><p>http://www.biomedcentral.com/1471-2148/7/155</p><p>BMC Evolutionary Biology 2007;7():155-155.</p><p>Published online 31 Aug 2007</p><p>PMCID:PMC2220002.</p><p></p> pair conserved in all analysed tunicates. Sequences almost identical in the same mtDNA are underlined and linked by a red line. Genes transposed among the three species are underlined and linked by a black line. Non-coding (NC) regions equal or longer that 40 bp are indicated by black background, with numbers corresponding to their size (in bp). Abbreviations for protein-coding and rRNA genes are as in the main text, except for gene (abbreviation: 8). Transfer RNA genes are indicated according to the transported amino acid, except for: G1: Gly(AGR); G2: Gly(GGN); L1: Leu(UUR); L2: Leu(CUN); M1: Met(AUG); M2: Met(AUA); S1: Ser(AGY); S2: Ser(UCN). Diamond: gene of . Star: intra-genome duplicated genes, that is genes in (named I1 and I2), and in . Feature table of mtDNA is as reported in [38]

The Tick-Box motif located downstream of <i>rrnL</i>.

<p>Bold face: species listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047538#pone-0047538-t003" target="_blank">Table 3</a>, for which the 3′-end of the <i>rrnL</i> transcript was experimentally determined by ESTs or 3′ RACE. Bold face only for the genus name: when the DNA sequence of a given species was unknown, the 3′-end of <i>nad1</i> reconstructed by ESTs was mapped on the sequence of a congeneric species. The <i>rrnL</i> 3′-end of <i>Hyalomma anatolicum</i> and <i>marginatum</i> (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047538#pone-0047538-t003" target="_blank">Table 3</a>) were both mapped on the sequence of <i>Hyalomma aegyptium</i> (<i>Hyalomma_ae</i>). Red colour: last DNA-encoded nucleotide preceding the <i>rrnL</i> polyA tail. Dashed line: overlap between <i>rrnL</i> and <i>trnL(CUN)</i>. Genus names were abbreviated to a single letter for <i>Ixodes</i> (I), <i>Haemaphysalis</i> (H), <i>Rhipicephalus</i> (R) and <i>Drosophila</i> (D). Underlined nucleotides: tRNA anticodon; bold lower case nucleotide with grey background: differences to the Tick-Box consensus sequence; blue lines: original annotation of the <i>rrnL</i> 3′-end, with a dot indicating the presence of additional nucleotides; “repeat”: 71 bp-long inverted repeat located in the CR2 and <i>rrnL</i> gene of <i>I. uriae</i> (position 12431–12501 and 12606–12676, respectively, of NC_006078). Degenerate nucleotide symbols according to the IUPAC code. Analyses species and sequence accession numbers are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047538#pone.0047538.s003" target="_blank">Table S1</a>. Gene abbreviations as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047538#pone-0047538-g001" target="_blank">Figure 1</a>.</p

Features of the <i>nad1</i> 3′-end and the downstream non-coding region, mapped on the Ixodida phylogeny.

<p>(A) Ixodida Bayesian tree calculated on the nucleotide sequence of the 13 mt protein-coding genes, and gene order downstream of <i>nad1</i>. Bayesian tree was calculated according to the GTR+I+gamma model, using 13 partitions, and all branches have a posterior probability value equal to 1. In gene order scheme, the genes encoded by the strand opposite to that of <i>nad1</i> are reported in bold. Gene abbreviations as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047538#pone-0047538-g001" target="_blank">Figure 1</a>. (B) Predicted overlap between <i>nad1</i> and the downstream gene, and length of the non-coding region experimentally identified downstream of <i>nad1</i> by transcriptional data. tRNA regions containing the <i>nad1</i> complete stop codon are indicated in brackets, with the following abbreviations: DHU: DHU arm; AA: amino acid acceptor arm; AA-DHU: spacer between the AA and DHU arms. Gene abbreviations as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047538#pone-0047538-g001" target="_blank">Figure 1</a>.</p

Phylogenetic tree of RPB2 protein of <i>P</i>. <i>lycopersici</i> ER1518 and other ten ascomycetes obtained with PhyML 3.0 and drawn with MEGA7.

<p>The tree is drawn to scale, with bootstrap values on branches and branch lengths measured in the number of substitutions per site.</p

Completely sequenced mitochondrial genomes of Ixodida.

<p>Completely sequenced mitochondrial genomes of Ixodida.</p

Circular representation of genomic features.

<p>Circular representation of the assembled sequences (length > 10Kb) of <i>P</i>. <i>lycopersici</i> ER1518 genome reporting the distribution of the following features: A) Repetitive elements count (blue); B) Gene density (green); C) Sequence identity percentage (red) of <i>P</i>. <i>lycopersici</i> ER1211 genomic sequences based on pairwise alignment between genome assemblies performed with MUMmer.</p

Tick-Box for 3′-End Formation of Mitochondrial Transcripts in Ixodida, Basal Chelicerates and <em>Drosophila</em>

<div><p>According to the tRNA punctuation model, the mitochondrial genome (mtDNA) of mammals and arthropods is transcribed as large polycistronic precursors that are maturated by endonucleolytic cleavage at tRNA borders and RNA polyadenylation. Starting from the newly sequenced mtDNA of <em>Ixodes ricinus</em> and using a combination of mitogenomics and transcriptional analyses, we found that in all currently-sequenced tick lineages (Prostriata, Metastriata and Argasidae) the 3′-end of the polyadenylated <em>nad1</em> and <em>rrnL</em> transcripts does not follow the tRNA punctuation model and is located upstream of a degenerate 17-bp DNA motif. A slightly different motif is also present downstream the 3′-end of <em>nad1</em> transcripts in the primitive chelicerate <em>Limulus polyphemus</em> and in <em>Drosophila</em> species, indicating the ancient origin and the evolutionary conservation of this motif in arthropods. The transcriptional analyses suggest that this motif directs the 3′-end formation of the <em>nad1</em>/<em>rrnL</em> mature RNAs, likely working as a transcription termination signal or a processing signal of precursor transcripts. Moreover, as most regulatory elements, this motif is characterized by a taxon-specific evolution. Although this signal is not exclusive of ticks, making a play on words it has been named “Tick-Box”, since it is a check mark that has to be verified for the 3′-end formation of some mt transcripts, and its consensus sequence has been here carefully characterized in ticks. Indeed, in the whole mtDNA of all ticks, the Tick-Box is always present downstream of <em>nad1</em> and <em>rrnL</em>, mainly in non-coding regions (NCRs) and occasionally within <em>trnL(CUN).</em> However, some metastriates present a third Tick-Box at an intriguing site - inside the small NCR located at one end of a 3.4 kb translocated region, the other end of which exhibits the <em>nad1</em> Tick-Box - hinting that this motif could have been involved in metastriate gene order rearrangements.</p> </div

Heatmap of OrthoMCL orthologous groups for the most interesting Pfam protein and CAZymes domains identified in <i>P</i>. <i>lycopersici</i> ER1518 (PLY ER1518) and ten other fungal pathogens.

<p>The heatmap represents the type and the number of domains (rows) for each fungus (columns). The Z-score indicates that the values have been centred and scaled by rows (domains), so that negative z-scores are more likely coloured in red and high z-scores in white. Abbreviations: PLY ER1211, <i>P</i>. <i>lycopersici</i> ER1211; AN, <i>Aspergillus nidulans</i>; BG, <i>Blumeria graminis</i>; CH, <i>Colletotrichum higgisinianum</i>; FO, <i>Fusarium oxysporum</i>; LM, <i>Leptosphaeria maculans</i>; NC, <i>Neurospora crassa</i>; PTT, <i>Pyrenophora teres</i>; PTR, <i>Pyrenophora tritici-repentis</i>; PN, <i>Phaeospheria nodorum</i>. CMB, Carbohydrate-Binding Modules; CE, carbohydrate esterases; GH, Glycoside Hydrolases; GT, Glycosyl-Transferases; PL, Polysaccharide Lyases; HET, HETerokaryon Incompatibility-related domains, NB-ARC, Nucleotide-Binding Adaptor shared by APAF-1, R proteins, and CED-4 domain; NACHT, Neuronal Apoptosis inhibitor; ANK, ankyrin; TPR, tetratricopeptide; ABC, ATP-Binding Cassette transporters; MFS, Major Facilitator domains.</p