Transcriptome Analysis to Understand the Toxicity of Latrodectus tredecimguttatus Eggs
<p>GO classification of the unigenes from <span class="html-italic">L. tredecimguttatus</span> eggs. Unigenes were annotated within three categories: biological process (<b>A</b>); molecular function (<b>B</b>); and cellular component (<b>C</b>). The <span class="html-italic">x</span>-axis represents the different categories. The number and percent of the unigenes matching GO annotation terms are presented on the <span class="html-italic">y</span>-axis.</p> "> Figure 2
<p>KOG classification of the egg unigenes: 9528 annotated unigenes were classified into 25 KOG categories. The <span class="html-italic">x</span>-axis represents the different KOG categories. The number and percent of unigenes matching KOG classification are presented on the <span class="html-italic">y</span>-axis.</p> "> Figure 3
<p>KEGG classification of the egg unigenes: 3141 unigenes were classified into 317 pathways. The different colors represent different KEGG categories. The number and percent of the unigenes matching KEGG classification are presented on the upper and lower axes, respectively.</p> "> Figure 4
<p>GO enrichment analysis scatterplot for the 280 unigenes encoding toxins. The size of black circle represents the unigene number. Different colors represent different <span class="html-italic">p</span> values for significance test.</p> "> Figure 5
<p>KEGG enrichment analysis scatterplot for the 280 unigenes encoding toxins. The size of black circle represents the unigene number. Different colors represent different <span class="html-italic">p</span> values for significance test.</p> "> Figure 6
<p>Distribution of the egg unigenes. Left pie graph shows the composition of the egg unigenes. “Not annotated” represents the unigenes not annotated in the available databases. Unigenes annotated to encode the proteins matching known toxins are labeled as “Putative toxins”, and those matching other proteins are labeled as “Non-toxins”. The number of the unigenes in each subcategory is given followed by its percentage shown in the bracket. Right pie graph is further classification of the putative toxins. Putative toxins are further divided into four types. The number of the unigenes in each type is given followed by its percentage shown in the bracket. ICK, inhibitor cystine knot.</p> "> Figure 7
<p>Primary and secondary structure analyses of the predicted ICK toxins. The amino acids forming an alpha helix are colored in pink. Yellow arrows represent β-sheet. Red and green rectangles indicate predicted signal peptides and propeptides, respectively. Blue lines show the connecting pattern of disulfide bonds.</p> "> Figure 8
<p>Sequence alignment and phylogenetic analysis of comp21602_c0_seq2. Alignment was performed by DNAman soft. Strictly conserved cysteins are indicated by deep blue and other less conserved amino acids are marked using different colors. Phylogenetic analysis was implemented in MEGA 3.1 using the neighbor-joining method. ArachnoServer accession numbers precede the species name for each sequence. Numbers at the nodes indicate the bootstrap values based on 10,000 replicates.</p> "> Figure 9
<p>Sequence alignment and phylogenetic analysis of comp25199_c0_seq1. Alignment was performed by DNAman soft. Strictly conserved cysteins are indicated by deep blue and other less conserved amino acids are marked using different colors. Phylogenetic analysis was implemented in MEGA 3.1 using the neighbor-joining method. ArachnoServer accession numbers precede the species name for each sequence. Numbers at the nodes indicate the bootstrap values based on 10,000 replicates.</p> "> Figure 10
<p>Amino acid sequence alignment of comp31734_c0_seq1 and comp19276_c0_seq1: (<b>A</b>) Multisequence alignment of comp31734_c0_seq1 with AP00140 and its precursor (GenBank:GJ19999). The underlined amino acid residues indicate a putative signal peptide sequence. (<b>B</b>) Sequence alignment of comp19276_c0_seq1 with AP2030. Identical residues are shaded in blue in both (<b>A</b>) and (<b>B</b>).</p> ">
Abstract
:1. Introduction
2. Results
2.1. Illumina Sequencing and Read Assembly
2.2. Categories and Annotations of Unigenes
2.3. GO and KEGG Pathway Enrichment Analyses of Unigenes
2.4. Proteinaceous Toxins in the Eggs
2.4.1. ICK Motif Peptide Toxins
2.4.2. Non-ICK Motif Peptide Toxins
2.4.3. Antimicrobial Peptides and Precursors
2.4.4. Toxin-Like Proteins or Enzymes
3. Discussion
4. Conclusions
5. Materials and Methods
5.1. cDNA Library Construction, Sequencing and De Novo Assembly
5.2. Annotation and Identification of Proteinaceous Toxins
5.3. Other Bioinformatics Analyses
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Analysis of Read Assembly | Amount |
---|---|
Total number of reads | 47,970,296 |
Total base pairs (bp) | 5,836,590,233 |
Average read length (bp) | 121 |
Total number of transcripts | 69,684 |
Total number of unigenes | 53,284 |
Average length of unigenes (bp) | 738 |
Total number of unigenes >2000 bp in length | 4376 |
Total number of unigenes annotated in at least one database | 14,185 |
Sequence ID | Signal Peptide | Score (Bits) | E-Value | Identity | BLAST Annotation |
---|---|---|---|---|---|
comp24914_c0_seq1 | N | 64.7 (156) | 8 × 10−11 | 34% | gb|AGA82764.1|toxin-like protein 14 precursor (Urodacus yaschenkoi) |
comp6833_c0_seq1 | N | 92.0 (227) | 4 × 10−22 | 56% | gb|ABR21046.1|venom toxin-like peptide-6 (Mesobuthus eupeus) |
comp22890_c0_seq2 | N | 90.9 (224) | 9× 10−22 | 56% | gb|ABR21046.1|venom toxin-like peptide-6 (Mesobuthus eupeus) |
comp17051_c0_seq1 | N | 53.5 (127) | 3× 10−10 | 32% | as: U15-SYTX-Sth1a||1459 Translation of a toxin from the spider Scytodes thoracica with unknown molecular target and function |
comp25199_c0_seq1 | Y | 55.8 (133) | 7× 10−11 | 32% | as: U12-SYTX-Sth1a||1449 Translation of a toxin from the spider Scytodes thoracica with unknown molecular target and function |
comp21232_c0_seq1 | Y | 277 (709) | 5× 10−86 | 98% | gb|ADV40303.1|cystatin-like protein (Latrodectus Hesperus) |
comp20935_c0_seq1 | Y | 102 (255) | 7× 10−25 | 40% | as: U24-ctenitoxin-Pn1a|sp:P84032|Toxin from venom of the spider Phoneutria nigriventer with unknown molecular target |
comp213809_c0_seq1 | Y | 65.5 (158) | 1× 10−13 | 29% | as: U24-ctenitoxin-Pn1a|sp:P84032|Toxin from venom of the spider Phoneutria nigriventer with unknown molecular target |
comp27859_c0_seq1 | Y | 105 (263) | 8× 10−26 | 44% | as: U24-ctenitoxin-Pn1a|sp:P84032|Toxin from venom of the spider Phoneutria nigriventer with unknown molecular target |
comp96908_c0_seq1 | Y | 48.5 (114) | 1× 10−8 | 35% | as: U16-aranetoxin-Av1a_1||2248 Toxin from venom of the spider Araneus ventricosus with unknown molecular target and function |
comp5553_c0_seq1 | Y | 53.1 (126) | 9× 10−7 | 32% | sp|Q8MTX1|TXCA_CAEEX U3-aranetoxin-Ce1a OS = Caerostris extrusa PE = 2 SV = 1 |
Name | Number of Unigenes | Percent of Unigenes (%) | Putative Activities |
---|---|---|---|
Metalloprotease | 62 | 25 | Activating proteinogen or zymogen [46,47] |
Degradating tissue to facilitate the spreading of toxins [46,47] | |||
Serine protease | 55 | 22.2 | Activating proteinogen or zymogen [46,47,48] |
Degradating tissue to facilitate the spreading of toxins [46,47,48] | |||
Phospholipase | 41 | 16.5 | Neurotoxicity, myotoxicity, etc. [46,47,48,49] |
Serpin | 30 | 12.1 | Inhibiting degradation of proteinaceous toxins by protease [46,47,48] |
Acting on ion channels, e.g., K+ channel [50,51] | |||
Phosphatase | 18 | 7.3 | Assisting the liberation of purines [52] |
Cholinesterase | 12 | 4.8 | Blocking the neuromuscular transmission [53] |
Allergen/Lipocalin | 11 | 4.4 | Provoking anaphylaxis [29,46,54,55,56] |
Disrupting hemostasis [57] | |||
Chitinase | 10 | 4 | Degrading the chitin [57] |
CAP superfamily | 5 | 2 | Modulating ion channels [57,58] |
Plancitoxin-1 | 2 | 0.9 | Inducing apoptosis [59,60] |
Hyaluronidase | 1 | 0.4 | Enhancing tissue permeability to allow the spreading of toxins [46,47,48,57] |
Prokineticin/AVIT | 1 | 0.4 | Inhibiting the feeding or inducing hyperalgesia [57,61] |
© 2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
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Xu, D.; Wang, X. Transcriptome Analysis to Understand the Toxicity of Latrodectus tredecimguttatus Eggs. Toxins 2016, 8, 378. https://doi.org/10.3390/toxins8120378
Xu D, Wang X. Transcriptome Analysis to Understand the Toxicity of Latrodectus tredecimguttatus Eggs. Toxins. 2016; 8(12):378. https://doi.org/10.3390/toxins8120378
Chicago/Turabian StyleXu, Dehong, and Xianchun Wang. 2016. "Transcriptome Analysis to Understand the Toxicity of Latrodectus tredecimguttatus Eggs" Toxins 8, no. 12: 378. https://doi.org/10.3390/toxins8120378
APA StyleXu, D., & Wang, X. (2016). Transcriptome Analysis to Understand the Toxicity of Latrodectus tredecimguttatus Eggs. Toxins, 8(12), 378. https://doi.org/10.3390/toxins8120378