Table 1.
Summary of assembly statistics after Illumina sequencing.
Table 2.
Unique sequences encoded by 210 transcripts of the Urodacus yaschenkoi transcriptome.
Fig 1.
Statistics of Go term annotation of unigenes found in the transcriptome of the venom gland of Urodacus yaschenkoi scorpion.
The three Go terms domains are plotted with the number of annotated unigenes and also, the variety within each domain is showed (different categories of Go term per domain).
Fig 2.
Most abundant categories within every GO-term found in the Urodacus yaschenkoi whole transcriptome dataset.
The biological process (BP) category was the most abundant, followed by cellular component (CC) and the molecular function (MF) was the least abundant.
Fig 3.
Subfamilies of scorpion toxins and enzymes found in the whole transcriptome of the venom gland of U. yaschenkoi.
A total of 62,505 unigenes were searched against the NCBI-nr database, only 51% had an identity against the databases; from those 3900 were related to venom components and housekeeping genes and 210 sequences codify toxins and enzymes in scorpion venom were identified. The diagram shows the relative proportion expressed as percentages, of each subfamily of scorpion toxins found in the analysis of the transcripts from U. yaschenkoi venom gland transcriptome.
Fig 4.
Sequence comparison of putative antimicrobial peptides from U. yaschenkoi and U. manicatus.
Multiple alignment of sequences obtained from the transcriptome of U. yaschenkoi that codify antimicrobial peptides from the subfamily NDBP-5. These sequences are compared with CYLIP-Uro-1 (GenBank: GALI01000003.1), CYLIP-Uro-2 (GenBank: GALI01000004.1), CYLIP-Uro-3 (GenBank: GALI01000005.1), CYLIP-Uro-4 (GenBank: GALI01000006.1) and CYLIP-Uro-5 (GenBank: GALI01000007.1) from U. manicatus [49]. The predicted signal peptide is underlined; the mature peptide is in bold and highlighted in yellow, the conserved proteolytic site GKR is in italics and underlined and the propetide in italics. The hyphen (-) in the name of U. yaschenkoi sequences indicates that the amino acid sequence was found within different nucleotide sequences (transcripts), for example: comp17_c0_seq1-4 means that four different nucleotide sequences codify the same peptide. The percentage of identity of the mature peptide is indicated at the right (% Identity) with respect to the peptide encoded by comp17_c0_seq1-4; additionally, at the far right, the theoretical molecular weights of the antimicrobial peptides for U. yaschenkoi are shown. The theoretical molecular weight of the peptide encoded by the sequences comp17_c0_seq1-4 (in bold) has a perfect match with the U. yaschenkoi proteome previously reported by [41] at the retention time 13.88. Note: several sequences of transcripts found in the U. yaschenkoi transcriptome codify the same precursors, such as: comp17_c0_seq1-4 and comp18_c0_seq1-2 (not shown); comp17_c0_seq5 and comp18_c0_seq3-4 (not shown); comp192_c0_seq1-2, comp192_c0_seq4-5 (not shown), comp192_c0_seq7-9 (not shown) and comp196_c0_seq1-7 (not shown) codify the same precursor.
Fig 5.
Scorpine-like peptides found in the Urodacus yaschenkoi transcriptome.
A) The sequence obtained from the U. yaschenkoi transcriptome that codifies for a scorpine type 1 is shown and it is aligned with the reference scorpine Hg-scorpine-like1 from Hadrurus gertschi. Sequence CSab-Uro-4 from Urodacus manicatus [49] codifies as well for a scorpine type 1 and is included in the alignment. B) The sequence comp324_c0_seq1 found in the U. yaschenkoi transcriptome that codes for a scorpine type 2 is shown and aligned with Hg-scorpine-like2 from H. gertschi. Also, sequence CSab-Uro-3 from U. manicatus [49] is included. Both alignments show the percentage of identity of each sequence with respect to the reference sequence. The cysteine pattern (6 Cys) is highlighted in yellow. Note: comp42_c0_seq1 and comp47_c0_seq1 (not shown) code for the same precursor, comp324_c0_seq1 and comp336_c0_seq1 (not shown), code for the same precursor.
Fig 6.
Putative alpha-KTx toxins from U. yaschenkoi.
(A) Alignment of sequences found in the transcriptome of U. yaschenkoi that code for putative α-KTXs with six cysteines. These sequences are compared against the alpha-toxin KTx8 (UniProtKB/Swiss-Prot: A9QLM3.1) from Lychas mucronatus. Note: The precursor encoded by comp2100_c0_seq1 is also encoded by sequences comp1991_c0_seq1 to seq5 (not shown). (B) Alignment of sequences from U. yaschenkoi that code for alpha-potassium toxins with eight cysteines compared against the α-KTx 6.10 toxin (UniProtKB/Swiss-Prot: Q6XLL5.1) from Opistophthalamus carinatus. For all sequences, the percentage of identity of U. yaschenkoi mature peptides (%I) is shown in relation to the toxin of reference. The theoretical molecular weight (MW) of each U. yaschenkoi peptide is also shown. The signal peptide is underlined; the mature peptide is in bold; the residues probably involved in amidation and the propeptide are indicated in italics. The conserved cysteines are highlighted in yellow. The symbol “&” indicates that the sequence was encoded by two different nucleotide sequences (transcripts). MW in bold indicates that this molecular weight was found in the venom mass fingerprint previously reported [41] and is indicated the retention time (RT) in which it was found. Note: comp849_c0_seq6 (not shown) codes for the same precursor as sequence comp1069_c0_seq1; comp1069_c0_seq5 (no t shown) codes for the same precursor as sequence comp849_c0_seq3&8; comp1069_c0_seq3 (not shown) and comp849_c0_seq5 (not shown) code for the same precursor as comp849_c0_seq1; comp2981_c0_seq1 (not shown) codes for the same precursor as comp2965_c0_seq1.
Fig 7.
Putative β-KTxs found in U. yaschenkoi transcriptome.
Multiple alignments of U. yaschenkoi sequences that code for putative β-KTx. These sequences belong to the long chain scorpion toxin family, Class 2 subfamily. U. yaschenkoi β-KTx sequences are compared against CSab-Uro-2 from U. manicatus and with the Hge-β-KTx from Hadrurus gertschi. All these sequences have 6 cysteines (highlighted in yellow). The percentage of identity (%I) is shown in relation to Hge-β-KTx. The theoretical molecular weight (MW) of U. yaschenkoi toxins is shown. In bold, the MW found in the mass fingerprint previously reported [41]. The retention time (RT) of this component is also indicated. Note: Sequence comp596_c0_seq1 (not shown) codes for the same mature peptide as the sequence comp588_c0_seq1 from this alignment.
Fig 8.
Putative calcium channel specific toxins found in U. yaschenkoi transcriptome.
Three different multiple alignments of sequences are shown that code for: (A) calcins. Comp749_c0_seq1 codes for a calcin of 33 amino acid similar to other scorpion calcins as Hadrucalcin (UniProtKB/Swiss-Prot: B8QG00.1) from Hadrurus gertschi, Imperatoxin-A (UniProtKB/Swiss-Prot: P59868.1) from Pandinus imperator, Maurocalcin (UniProtKB/Swiss-Prot: P60254.1) from Scorpio maurus palmatus and Opicalcin-1 (UniProtKB/Swiss-Prot: P60252.1) from Opistophthalmus carinatus. All of them have 6 conserved cysteine; (B) LaIT1-like calcins. Sequence comp10032_c0_seq1 of U. yaschenkoi is compared with DDH-Uro-1 (GenBank: GALI01000015.1), DDH-Uro-2 (GenBank: GALI01000016.1) and DDH-Uro-3 (GenBank: GALI01000017.1) from U. manicatus, Insecticidal toxin LaIT1 from Liocheles australasiae (UniProtKB/Swiss-Prot: P0C5F2.1) and Phi-liotoxin-Lw1a (UniProtKB/Swiss-Prot: P0DJ08.1) from Liocheles waigiensis. This class of calcins has four cysteines. The sequence reported for DDH-Uro-3 contains undefined nucleotides and therefore the XX undefined amino acids. Finally, (C) Omega Agatoxin-like calcins. Putative calcium channel specific toxins encoded by sequences Comp27527_c0_seq1 and comp104104_c0_seq1 from U. yaschenkoi are shown and compared with DAPPUDRAFT_310236 of Daphnia pulex, LOC100163563 of insect Acyrthosiphon pisum and Omega Agatoxin IVB (Omega-Aga-IVB; GenBank: P37045) of spider Agelenopsis aperta. This class of calcin has eight cysteines. The percentage of identity (% Identity) is shown for all alignments with respect to the first sequence of each alignment. Conserved cysteines and amino acids are highlighted in yellow and bold, respectively.
Fig 9.
La-1-like peptides found in the U. yaschenkoi transcriptome.
The alignment compares the La-1-like peptides encoded by U. yaschenkoi transcripts with the model La1 peptide from Liocheles australasiae. La1 is amidated with a molecular weight of 7781.6 Da. Only the theoretical molecular weight amidated of comp12_c0_seq1 (in bold) was detected in the proteome of U. yaschenkoi [41], in retention time 30.59. La1 peptide has eight cysteines that are conserved in all the putative La-1-like peptides found herein (highlighted in yellow). The percentage of identity with respect to La1 is shown. Note: comp12_c0_seq1 and comp15_c0_seq1 (not shown) encode the same peptide; comp3687_c0_seq2 and comp4167_c0_seq2 (not shown) encode the same peptide; comp3687_c0_seq1 and comp4167_c0_seq1 (not shown) code for the same peptide and comp13_c0_seq1 and comp16_c0_seq1 (not shown) code for the same peptide.
Fig 10.
Comparison of Ascaris-type protease inhibitor peptides found in U. yaschenkoi transcriptome.
Multiple alignment of U. yaschenkoi sequences that code for ascaris-type protease inhibitor compared against the ascaris-type protease inhibitor precursor from Scorpiops jendeki scorpion (SjAPI; GenBank: P0DM55). The sequence of comp75842_c0_seq1 is partial. The predicted signal peptide is underlined; putative propeptides is in italics and the common trypsin inhibitor like cysteine rich domain in bold with its ten cysteines highlighted in yellow. The percentage of identity (%I) with respect to SjAPI is shown. Note. Sequence comp4363_c0_seq1 encodes the same precursor as sequence comp4053_c0_seq1 (not shown); comp5534_c0_seq1 encodes the same precursor as comp4356_c0_seq1 (not shown) and comp135491_c0_seq1 (not shown) codes for the same partial sequence as comp75842_c0_seq1.
Table 3.
Correlation between theoretical molecular weight of transcriptome sequences and experimental molecular weight obtained from the proteome venom of Urodacus yaschenkoi.