The ML tree analysis was Epub 2021 Aug 6. Blastx was used to search against non-redundant (Nr) and Swissprot databases with an E-value threshold of 103. the analysis was based on 32 morphological characteristics of A. crassicuda native to southwest Iran. Mirshamsi O, Sari A, Elahi E, Hosseinie S. Mesobuthus eupeus (Scorpiones: Buthidae) from Iran: A polytypic species complex. 3). Rep. 6, 18 (2016). This Targeted Locus Study (TLS) project was deposited at DDBJ/EMBL/GenBank under the accession KEPY00000000, associated with the BioProject PRJNA687110 and biosample SAMN17133090. Polymerase chain reaction amplification with 12srRNA (1) and COXI (2) genomes from Androctonus crassicuda, Average genetic distance of Androctonus crassicuda (Makoo, Iran), A. australis (Tunisia), and A. amurexi (Portugal), Maximum likelihood tree resulting from the analysis of the combined sequences of COXI, and 12sRNA genes of Androctonus crassicuda from Khuzestan province and Hottentotta zagrosensis as an outgroup, Maximum likelihood tree resulting from the analysis of sequences of 12SrRNA genes from three genera of Androctonus species. Distribution records of Androctonus crassicauda (Olivier, 1807), Apistobuthus pterygocercus Finnegan 1932, Buthacus nigroaculeatus (Levy, Amitai & Shulov 1973) and Butheolus villosus Hendrixson,. However, the fat-tailed scorpion is able to go months without consuming food. FOIA 472 million clean reads were assembled into 952,725 transcripts (585,177 genes) by Trinity tool using default parameters18,19. 7). Acids Res. All collected scorpions were examined under a stereomicroscope condition. The Arabian fat-tailed scorpion, Androctonus crassicauda, is a species of dangerous scorpion usually found in North Africa and the Middle East. Getting stung by black scorpion Androctonus crassicauda: A case report December 2013 Human & Experimental Toxicology DOI: Authors: Abbas Aghabiklooei Iran University of Medical Sciences Nasim. official website and that any information you provide is encrypted elife 3, e03523 (2014). 6). In the phylogenetic tree, A. crassicuda from the northwest and southwest Sensitivity, specificity, accuracy (ACC), positive predictive value (PPV) and, negative predictive value (NPV) metrics were used to assess classification performance of the computational programs on drosophila melanogaster and Androctonus crassicauda datasets. characteristics, such as pedipalp, mesosoma, metasoma, chelicerae, carapace, femur, and trichobothrium pattern, which lead to limitations in the identification ; Loureno and Qi, 2006 importance of geographical and climate features of the region and genetic distance among the populations. Androctonus crassicauda (Olivier, 1807) - GBIF Toxicon 95, 5261 (2015). MeSH Furthermore, Venn diagrams (http://bioinformatics.psb.ugent.be/webtools/Venn) were utilized to plot the performance of lncRNA prediction tools visually (Fig. A. gonneti (Morocco) and A. amoreuxi (Portugal), respectively. 2021 Nov;7(6):2418-2426. doi: 10.1002/vms3.593. Kong, L. et al. Grabherr, M.G., et al. Also additional annotation programs including CPC2 (coding potential calculator software based on alignment-based algorithms, version 2.0) and PLEK (predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme, version 1.2) were employed. Evol. The Buthidae family with 85 genera and 895 Therefore, the phylogeographic structure of 2000 Feb;62(2):277-83. doi: 10.4269/ajtmh.2000.62.277. PubMed Central There are insufficient data on the toxicity of . To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome. Systematic and computational identification of, https://doi.org/10.1038/s41598-021-83815-8. PubMed Extremely low gene expression is generally considered to be transcriptional noise54. Following trained PLEK, CNIT, Annocript, and CPC2 approaches in scorpion data set, we evaluated the performance of approaches. However, ADS regarding Androctonus crassicauda, which was observed in Kashan, by Olivier in 1807 ( Farzanpay, 1987 Systematic and computational identification of Androctonus crassicauda long non-coding RNAs | Scientific Reports Open Access Published: 25 February 2021 Systematic and computational. The morphological measurements were conducted using digital calipers. J Arthropod Borne Dis. The fatal case described was inadequately treated with antivenom and presented a rare situation of intracranial coagulation in the basal cisterns or low in the cranial subarachnoid space. The Arabian Fat-Tailed Scorpion ( Androctonus crassicauda ) is a venomous arachnid. Clinical manifestations and management of scorpion envenomation. species is the largest of the scorpion families ( Sousa et al., 2017 Two pregnant victims were treated with antivenom with no bad consequences on mothers or foetuses. The smallest genetic distance was between A. crassicuda in Khuzestan and A.crassicuda in west Azerbaijan ({"type":"entrez-nucleotide","attrs":{"text":"KT972133","term_id":"992287553","term_text":"KT972133"}}KT972133). eCollection 2022. Al-Tobasei, R., Paneru, B. ECF pipeline basically filters out any transcript with high coding potential, which estimated with CPC2. First DNA phylogeny of Euscorpius Thorell, 1876 (Scorpiones: Euscorpiidae) and its bearing on taxonomy and biogeography of this genus. Therefore, this study aimed to investigate the geographic morphological . Due to Table 1, Annocript, despite having a long wait presented the best result than CPC, CNIT, and PLEK. Accordingly, they can be [1] Several pharmaceutical companies manufacture an antivenom for treatment of Androctonus envenomations. Bioinform. Abstract Androctonus crassicauda venom has an i.v. Primary transcripts of microRNAs encode regulatory peptides. phylogenetic studies of A. crassicauda is poorly defined in Iran, extensive research is needed to review the classification. PloS one 10, (2015). Accumulating evidence suggests that some aspects of lncRNA function depend on the structural properties of RNA molecules; hence it is important to indicate the sequence properties of lncRNAs. ). At least 44 different sub-fractions were resolved and collected for finger print mass analysis using an electrospray mass spectrometer. The Area Under the Curve (AUC) measures the performance of an algorithm under different thresholds. study of specimens is one of the new approaches due to the limitations of the morphological approaches. Google Scholar. Sci. (2) Building customized databases with local sequences by means of the makeblastdb. comparison of the male (n=10) and female (n=10) scorpions showed that the body length of the females was longer (89.7514.56 mm), and their carapaces were wider On the other hand, metasoma was longer and wider in males than (A,B) Classification of protein-coding and non-coding transcripts of fruit fly using CNIT, CPC2 and, PLEK tools. Cardoso-Arenas S, Clement H, Arenas I, Olvera F, Zamudio F, Caliskan F, Corrales-Garca LL, Corzo G. J Venom Anim Toxins Incl Trop Dis. Salabi, F., Jafari, H., Navidpour, S. et al. Accessibility ; Fet and Braunwalder, 2000 2021 Feb;191:83-103. doi: 10.1016/j.toxicon.2020.12.017. The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Mol. Google Scholar. [7]. Androctonus crassicauda venom has an i.v. Toxicon 70, 7081 (2013). 104, 1942819433 (2007). Novel and known lncRNAs had a mean length of 762.2bp and 504.15bp respectively, while the average length of protein-coding transcripts was 871.9bp. TP means true positive, FN refer to false negative, FP is false positive, and TN represents true negative. There is a large gap in the recognition of the diversity, distribution, and evolution of this In the current study, Sci. The trend of lower protein-coding potential, lower GC content, shorter transcript length, and less number of isoform per gene in lncRNAs sequence over protein-coding transcripts are outstanding features of A. crassicauda lncRNAs transcripts that mean these sequences contain lower stably base-paired structures and therefore, it is more possible to interact with other cellular factors21,37,45,46,47. Ozkan O, Ahmet C, Zafer K. A study on the genetic diversity of Androctonus crassicauda (Olivier, 1807; Scorpiones: Buthidae) from Turkey. Known lncRNA sequences including all validated lncRNAs were downloaded from two lncRNA databases: (1) NONCODE database (http://www.noncode.org/). The obtained results indicated that the ECF pipeline is suited for de novo assembled data sets from scorpion species. To detect high reliable novel lncRNAs, the remaining transcripts were subjected to PLEK tool17. In vitro Scolicidal effects of Androctonus crassicauda (Olivier, 1807 To avoid loss of known lncRNAs, all identified scorpion lncRNAs were initially aligned with known lncRNA sequences of diverse species in RNACentral v14 and NONCODE v3.0 databases using blastn28. They had one terminal and three distal granules in their movable pedipalp Internet Explorer). In this work, 911,471 and 40,503 transcripts were identified to be noncoding and mRNA in PLEK algorithms, respectively. Inclusion in an NLM database does not imply endorsement of, or agreement with, Fattail scorpion or fat-tailed scorpion is the common name given to scorpions of the genus Androctonus, one of the most dangerous groups of scorpion species in the world. 8600 Rockville Pike The ML tree revealed 47, W516W522 (2019). 1840, 10631071 (2014). & Alba, M. M. Long non-coding RNAs as a source of new peptides. Google Scholar. An official website of the United States government. fingers, and their chelae were slender with long fingers. In this work have shown that Annocript be a powerful platform for the identification of scorpion lncRNA transcripts in high-throughput sequencing data. Androctonus crassicauda - Simple English Wikipedia, the free encyclopedia Background: Androctonus crassicauda is the most medically relevant animal and understanding its morphological characteristics is essential in the production of antiscorpion sera. Micro habitat of Androctonus crassicauda (Arachnida: Scorpionida This scorpion can make venom. distance was between A. amoreuxi in Portugal and A. crassicuda in Makoo, while the smallest genetic distance was between A. crassicuda in Makoo and Luna-Ramirez, K., et al., Whole transcriptome of the venom gland from Urodacus yaschenkoi scorpion. ; Ochoa et al., 2013 PubMed of genus, species, and subspecies ( Hjelle, 1990 The results of sequencing were based on a COXI fragment with a length of 671 nucleotides and 12srRNA with a length of 360 nucleotides (Figure 1). Vignoli V, Salomone N, Caruso T, Bernini F. The Euscorpius tergestinus (C.L. This study is the first comprehensive analysis and characterization of lncRNAs in the scorpions. Santibez-Lpez CE, Gonzlez-Santilln E, Monod L, Sharma PP. Genome Biology 21, 123 (2020). We found that, our predicted lncRNA transcripts exhibited lower coding probability than that of protein-coding transcripts (Fig. 6A, we note that the ECF pipeline, CPC2, and CNIT struck a good balance between sensitivity and specificity as well as obtaining a reasonable result. CAS Electrocardiograms recorded simultaneously with blood pressure changes showed evidence of ectopic foci during the hypertensive phase and ischaemia, inferior wall infarction and different degrees of heart block during the late hypotensive phase. Pectinal organ length, pectinal tooth count, and caudal carapace width were the most 3). performed on the basis of morphological characteristics defined by Stahnke (1970) Sci. Ruiz-Orera, J., Messeguer, X., Subirana, J. To extract reliable putative ncRNAs, we set the minimum assembled transcript length to longer than 300bp and those that were300bp in length were removed. The most common parameters for species identification included total body, metasoma, carapace, pedipalp, and telson length, as well as pectinal tooth ) and Turkey ( Ozkan et al., 2006 Text is available under the Creative Commons Attribution-ShareAlike License; additional terms may apply.By . 7, 497 (2011). Nucleic Acids Res. Article Protoc. Androctonus is widespread in North and West Africa, the Middle East and eastwards to the Hindukush region. 1828. 17, 1621 (2012). [9] Once the prey has been stung, it causes paralysis and allows the scorpion to consume it with ease. relationships based on both molecular and morphological characteristic methods with the purpose of determining and assessing the relationships (at 94 C for 30 sec, 42 C for 50 sec, and 72 C for 35 sec) and a final extension of 72 C for 5 min. Similarly, the Latin word for South is australis, from which Androctonus australis, "southern man-killer", derives. The authors declare that they have no conflict of interest. Discrimination of non-protein-coding transcripts from protein-coding mRNA. To eliminate transcripts harboring any protein domains, we implemented various blast search methods; at first, remaining 901,937 transcripts were exposed to Swissprot database, NCBI non-redundant (Nr), and Pfam protein domain databases to find protein-coding transcripts. Conceived and designed the experiments: F.S. Among all assembled transcripts, 904,112 transcripts were classified as non-coding RNAs, while 48,613 transcripts were protein-coding. touchdown PCR protocol. It employed the model trained on the human database to predict the sequences of invertebrates. & Dewey, C. N. RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. Department of Venomous Animals and Anti-Venom Production, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Ahvaz, Iran, Department of Venomous Animals and Anti-Venom Production, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran, Aquaculture Research Center-South of Iran, Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Ahvaz, Iran, You can also search for this author in PubMed Central Sci Rep 11, 4720 (2021). The raw sequences and clean data were subjected to FastQC for quality assessment of sequences (Supplementary figures F1F6). The Androctonus crassicuda is the most diverse scorpion species in the family of Buthidae, Global Biodiversity Information Facility. J. Proteomics 128, 231250 (2015). taxonomy of samples collected from this region. Androctonus crassicauda is from the opportunist group in terms of the selection of. In addition, RNACentral and NONCOD databases were used to predict the known lncRNAs. Expression and purification of recombinant alpha-toxin - Springer were sequenced. 29, S83 (2008). The comparison of the genetic distances of the genus A. crassicuda in Iran showed that Biol. It is now highly recommended to use step-by-step filtering pipeline instead of lncRNA computational prediction programs to identify the lncRNAs of these organisms. The site is secure. Cytochrome c oxidase subunit I was amplified with COXI-F/COXI-R with the primers Article PubMed Central & Salem, M. Genome-wide discovery of long non-coding RNAs in rainbow trout. 35, W345W349 (2007). In total, 10 replicated fragments of 12srRNA and COXI genes from 10 individual genomes (5 males and 5 females) of A. crassicuda Prediction of plant lncRNA by ensemble machine learning classifiers. Briefly, the cleaned reads were assembled using Trinity and then evaluated for protein coding portability with coding potential calculator 2 (CPC2). Background: Androctonus crassicauda is the most medically relevant animal and understanding its morphological characteristics is essential in the production of antiscorpion sera. The phylogenetic study of other species of Androctonus Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. Boghozian A, Nazem H, Fazilati M, Hejazi SH, Sheikh Sajjadieh M. Vet Med Sci. ; Mirshamsi et al., 2011 A. crassicuda in Urmia. After that, the remaining transcripts were subjected to getorf website (http://www.bioinformatics.nl/cgi-bin/emboss/getorf) to find longest ORFs, and those transcripts with ORF longest than300 nt were also discarded. shown that the incidence of scorpionism is higher in Iran than the global average ( Chippaux and Goyffon, 2008 ). The transcripts scored with a probability less than 0.4 were considered noncoding-RNA candidates. To overcome this problem, we tried two methods of predicting lncRNAs. The fat-tailed scorpion's main diet when in captivity consists of cockroaches, grasshoppers, and crickets. [1] Stings from Androctonus species are known to cause several human deaths each year. The housekeeping ncRNAs also were removed. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. segment IV length to height; Met-V_L/W: metasomal segment V length to width; Met-V_L/H: metasomal segment V length to height. 123, 1118 (2013). divergence between the A. crassicuda isolated from northern and southern areas of Iran. Additionally, the pectinal teeth in males were longer and higher in number than in females. The genetic distance value among the species was ; Thompson et al., 1994 Young, R. S. et al. In the present study, the total and metasoma lengths of A. crassicauda were 80-100 and 43-45 mm, respectively. ; Parmakelis et al., 2006 Acta Biomed. To predict long non-coding RNAs, an experimental and computational filtering (ECF) pipeline was carried out (Fig. The remaining ncRNA transcripts were filtered based on coding probability0.4, transcript length 300 nt and, open reading frames (ORFs)300nt. Systematic identification and characterization of Aedes aegypti long noncoding RNAs (lncRNAs). Disclaimer. NCI CPTC Antibody Characterization Program. & Golding, G. B. PLoS Comput. ECF pipeline achieved the highest accuracy of 0.99, specificity 1, sensitively 0.91, PPV 1, and NPV 0.99 on the fruit fly dataset. Analyzed the data: F.S and A.S.S. Scientific data 6, 16 (2019). This result indicated that Annocript performed better in predicting the scorpion data than other programs. Using 952,725 de novo assembled transcripts, 904,743 ncRNAs and a set of 47,982 protein-coding transcripts were obtained. The main steps of the ECF pipeline are similar to previously reported procedures20,21. Androctonus crassicauda - Pet Products The members of this family are found mainly in tropical and subtropical regions, The validity of variant nucleotides at highly conserved positions was confirmed. Androctonus crassicauda (Olivier, 1807) is the most common and medically important species in Arabia and the Middle East. Considering lack of lncRNA genomic coordinates for scorpion, the approaches were trained and tested on drosophila melanogaster dataset retrieved from NONCODE and Ensamble databases, which contains 3976 lncRNAs and 30,588 mRNA sequences. From Simple English Wikipedia, the free encyclopedia, "Living Hazards Database (LHD) Search by Scientific Name", https://simple.wikipedia.org/w/index.php?title=Androctonus_crassicauda&oldid=8765387, Creative Commons Attribution/Share-Alike License. Pharmacological and clinical studies. Based on the results of the phylogenetic tree, A. crassicuda was classified into a monophyletic group. Azlan, A. et al. ). et al. at the southern Zagros mountain with a height of 2,000 meters, as well as the coastline of the Persian Gulf and Oman Sea (at the height of 5 meters). As a library, NLM provides access to scientific literature. Proced. Toxicon 32, 1599-1618, 1994. Androctonus Crassicauda - Academic Accelerator Acad. BMC Bioinform. In this study, we elucidated and compared the venom gland gene expression profiles of adult and juvenile male scorpion A. crassicauda using . The highest and lowest genetic distance of A. crassicuda was compared with the reports obtained in Urmia and west Azerbaijan, Iran. Anatomy and morphology the Biology of Scorpions, Stanford University Press, Stanford, California; 1990. [1], The Arabian fat-tailed scorpion is an Old World scorpion. [10] Interestingly, the fat-tail scorpion can only ingest liquids. By submitting a comment you agree to abide by our Terms and Community Guidelines. Characterization of A. crassicauda lncRNA. inappropriateness of morphological characteristics for the detection of species and subspecies, the result of nuclear and mitochondrial markers was used in solving these challenges ( Gantenbein and Largiadr, 2002 Then in order to distinguish ncRNAs from protein-coding transcripts, we focused on transcripts labeled as noncoding in the output and filtered out any transcripts that had higher coding probability. Trends Plant Sci. The first branch Androctonus crassicauda (Olivier), a dangerous and unduly neglected Moreover, we employed machine learning classifiers and alignment-free software not only to obtain high-confidence predictions of lncRNAs/mRNAs but also to validate our pipeline. Google Scholar. Scorpion (Androctonus crassicauda) venom limits growth of - PubMed Gantenbein B, Soleglad M, Fet V. Euscorpius balearicus Caporiacco, 1950, stat. Mol. The ML tree of Androctonus species, which showed the same phylogenetic tree topology, was constructed As a comparison, at least 6.19, 8.07 and 9.45% of fruit fly non-coding dataset were misclassified as coding by CPC, CNIT and PLEK respectively (Fig. The purpose of study was to examine the cytotoxic and anti-cancer properties along with addressing the plausible pathway followed by scorpion venom to reduce cell viability in SH-SY5Y and MCF-7 cells. Moreover, analysis of the novel lncRNAs indicated a low GC content (42.6%), similar to what was observed in known lncRNAs (43.4%), which is significantly lower than protein coding sequence (50.8%) (Fig. Countries where Androctonus species live include: Egypt, Israel, India, Lebanon, Turkey, Jordan, Saudi Arabia, Yemen, Oman, United Arab Emirates, Qatar, Kuwait, Iraq, Iran, Afghanistan, Bahrain, Pakistan and Morocco. LncRNAs are a new and critical class of ncRNAs with a series of unique features. Please enable it to take advantage of the complete set of features! LncRNA discovery approaches show similarities among different studies (Additional file 1). eCollection 2022 Mar. Guo, J.-C., et al. 105, 169181 (2019). In addition to high accuracy lncRNA prediction pipeline, we provided most comprehensive dataset of scorpion lncRNAs, which is consist of multiple information of scorpion lncRNAs, like expression profile, coding probability distribution, features of predicted lncRNAs, annotation, etc. Figure5 showed that using lncRNAs prediction tools in species without closely related organisms to build ncRNA/mRNA distinguishing model increases the false positive rate compared to database derived dataset. ). Bookshelf [2], They are found throughout the semi-arid and arid regions of the Middle East and Africa. Clipboard, Search History, and several other advanced features are temporarily unavailable. Acta Gen. Subj. Accessibility Various studies about insects investigated the transcriptome in the last decade, with lessened attention to lncRNAs8,9,10,11. 2021 Sep 2;92(4):e2021273. Syst. Distinct patterns of expression and evolution of intronless and intron-containing mammalian genes. Frith, M.C., et al. in females with the same total length. J. Clin. 7D). Rev. Gao, F., Cai, Y., Kapranov, P. & Xu, D. Reverse-genetics studies of lncRNAswhat we have learnt and paths forward. Buthid scorpions of Saudi Arabia, with notes on other families (Scorpiones: Buthidae, Liochelidae, Scorpionidae). In general, we provide a powerful pipeline to predict lncRNAs in the scorpion and closely related species and describe the best lncRNA prediction tool tested on the scorpion dataset.

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