Additional file 3: Figure S2. of Diagnosis of a malayan filariasis case using a shotgun diagnostic metagenomics assay

Typing of blast hits after analyzing the eye discharge sample and detail of the phylogenetic MEGAN output. (DOC 117 kb

Additional file 1: Figure S1. of Diagnosis of a malayan filariasis case using a shotgun diagnostic metagenomics assay

Histopathological findings in the nodules of the left little finger. (DOC 2022 kb

Codon usage among the 13 energy pathway protein genes and Two ORFs.

*<p>Codon usage among the 13 energy pathway protein genes of <i>C. sowerbyi</i>;</p>#<p>Codon usage of the genes <i>ORF1611</i> and <i>ORF354</i> of <i>C. sowerbyi.</i></p

Mitochondrial Genome of the Freshwater Jellyfish <em>Craspedacusta sowerbyi</em> and Phylogenetics of Medusozoa

<div><p>The 17,922 base pairs (bp) nucleotide sequence of the linear mitochondrial DNA (mtDNA) molecule of the freshwater jellyfish <em>Craspedacusta sowerbyi</em> (Hydrozoa,Trachylina, Limnomedusae) has been determined. This sequence exhibits surprisingly low A+T content (57.1%), containing genes for 13 energy pathway proteins, a small and a large subunit rRNAs, and methionine and tryptophan tRNAs. Mitochondrial ancestral medusozoan gene order (AMGO) was found in the <em>C. sowerbyi</em>, as those found in <em>Cubaia aphrodite</em> (Hydrozoa, Trachylina, Limnomedusae), discomedusan Scyphozoa and Staurozoa. The genes of <em>C. sowerbyi</em> mtDNA are arranged in two clusters with opposite transcriptional polarities, whereby transcription proceeds toward the ends of the DNA molecule. Identical inverted terminal repeats (ITRs) flank the ends of the mitochondrial DNA molecule, a characteristic typical of medusozoans. In addition, two open reading frames (ORFs) of 354 and 1611 bp in length were found downstream of the large subunit rRNA gene, similar to the two ORFs of <em>ORF314</em> and <em>polB</em> discovered in the linear mtDNA of <em>C. aphrodite,</em> discomedusan Scyphozoa and Staurozoa. Phylogenetic analyses of <em>C. sowerbyi</em> and other cnidarians were carried out based on both nucleotide and inferred amino acid sequences of the 13 mitochondrial energy pathway genes. Our working hypothesis supports the monophyletic Medusozoa being a sister group to Octocorallia (Cnidaria, Anthozoa). Within Medusozoa, the phylogenetic analysis suggests that Staurozoa may be the earliest diverging class and the sister group of all other medusozoans. Cubozoa and coronate Scyphozoa form a clade that is the sister group of Hydrozoa plus discomedusan Scyphozoa. Hydrozoa is the sister group of discomedusan Scyphozoa. Semaeostomeae is a paraphyletic clade with Rhizostomeae, while Limnomedusae (Trachylina) is the sister group of hydroidolinans and may be the earliest diverging lineage among Hydrozoa.</p> </div

Nucleotide composition data for different groups of genes, ORFs, and non-coding regions in <i>C. sowerbyi</i> mtDNA.

<p>Nucleotide composition data for different groups of genes, ORFs, and non-coding regions in <i>C. sowerbyi</i> mtDNA.</p

Comparison of the mitochondrial protein coding genes and RNA genes of the freshwater jellyfish <i>C. sowerbyi</i> (<i>C.s</i>), the jellyfish <i>A. aurita</i> (<i>A.a</i>), the hydrozoan <i>H. oligactis</i> (<i>H.o</i>), cubozoan <i>A. moseri</i> (<i>A.m</i>), and the trachyline <i>C. aphrodite</i> (<i>C.a</i>).

<p>“nd” means not determined.</p>a<p>Data for <i>A. aurita</i> are from Shao et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051465#pone.0051465-Smith1" target="_blank">[10]</a>, for <i>H. oligactis</i> are from Kayal and Lavrov <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051465#pone.0051465-Kayal2" target="_blank">[8]</a>, for <i>A. moseri</i> are from Kayal et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051465#pone.0051465-Kayal1" target="_blank">[7]</a>, for <i>C. aphrodite</i> are from Kayal et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051465#pone.0051465-Kayal1" target="_blank">[7]</a>.</p

Secondary structure models predicted for tRNA and intergenic putative control region of <i>C. sowerbyi</i> and <i>C. aphrodite</i>.

<p>Secondary structure models predicted for tRNA and intergenic putative control region of <i>C. sowerbyi</i> and <i>C. aphrodite</i>.</p

Maps of the mitochondrial genomes of <i>C. sowerbyi</i> and <i>C. aphrodite</i>.

<p>Protein and ribosomal genes (large open boxes) are abbreviated as presented in the text; tRNA genes (small hatched boxes) are identified by the one-letter code for their corresponding amino acid. Intergenic regions greater than 100 bp are shown by shaded boxes; ITR shown by two large arrows. Arrows within or under each box show the direction of transcription. Positive numbers at gene boundaries indicate the number of intergenic nucleotides; negative numbers indicate the number of overlapping nucleotides. The dash lines mean that the sequence of this part is not determined.</p

Shared OTU analysis of the different libraries.

<p>Venn diagram showing the unique and shared OTUs (3% distance level) in the different libraries (A) for the GGCC1, GGCC2, and GGCC3 libraries, and (B) for the HMC, CCW, CCDN, GGCM and GGCC libraries. * GGCC represents GGCC1, GGCC2 and GGCC3; GGCC1, GGCC2 and GGCC3 mean intestinal content of different individuals of grass carp. HMC, GGCM, CCDN, and CCW stand for grass carp feed ryegrass, intestinal mucosa of grass carp, pond sediment and pond water, respectively.</p

Rarefaction analysis of the different samples.

<p>Rarefaction curves of OTUs clustered at 97% sequence identity across different environmental samples.</p