Systematic and computational identification of Androctonus crassicauda long non-coding RNAs

Abstract The potential function of long non-coding RNAs in regulating neighbor protein-coding genes has attracted scientists’ attention. Despite the important role of lncRNAs in biological processes, a limited number of studies focus on non-model animal lncRNAs. In this study, we used a stringent st...

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Autores principales:	Fatemeh Salabi, Hedieh Jafari, Shahrokh Navidpour, Ayeh Sadat Sadr
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7580d588b7514dfcbe292eb13ffaaf38
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spelling	oai:doaj.org-article:7580d588b7514dfcbe292eb13ffaaf382021-12-02T15:53:02ZSystematic and computational identification of Androctonus crassicauda long non-coding RNAs10.1038/s41598-021-83815-82045-2322https://doaj.org/article/7580d588b7514dfcbe292eb13ffaaf382021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83815-8https://doaj.org/toc/2045-2322Abstract The potential function of long non-coding RNAs in regulating neighbor protein-coding genes has attracted scientists’ attention. Despite the important role of lncRNAs in biological processes, a limited number of studies focus on non-model animal lncRNAs. In this study, we used a stringent step-by-step filtering pipeline and machine learning-based tools to identify the specific Androctonus crassicauda lncRNAs and analyze the features of predicted scorpion lncRNAs. 13,401 lncRNAs were detected using pipeline in A. crassicauda transcriptome. The blast results indicated that the majority of these lncRNAs sequences (12,642) have no identifiable orthologs even in closely related species and those considered as novel lncRNAs. Compared to lncRNA prediction tools indicated that our pipeline is a helpful approach to distinguish protein-coding and non-coding transcripts from RNA sequencing data of species without reference genomes. Moreover, analyzing lncRNA characteristics in A. crassicauda uncovered that lower protein-coding potential, lower GC content, shorter transcript length, and less number of isoform per gene are outstanding features of A. crassicauda lncRNAs transcripts.Fatemeh SalabiHedieh JafariShahrokh NavidpourAyeh Sadat SadrNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Fatemeh Salabi Hedieh Jafari Shahrokh Navidpour Ayeh Sadat Sadr Systematic and computational identification of Androctonus crassicauda long non-coding RNAs
description	Abstract The potential function of long non-coding RNAs in regulating neighbor protein-coding genes has attracted scientists’ attention. Despite the important role of lncRNAs in biological processes, a limited number of studies focus on non-model animal lncRNAs. In this study, we used a stringent step-by-step filtering pipeline and machine learning-based tools to identify the specific Androctonus crassicauda lncRNAs and analyze the features of predicted scorpion lncRNAs. 13,401 lncRNAs were detected using pipeline in A. crassicauda transcriptome. The blast results indicated that the majority of these lncRNAs sequences (12,642) have no identifiable orthologs even in closely related species and those considered as novel lncRNAs. Compared to lncRNA prediction tools indicated that our pipeline is a helpful approach to distinguish protein-coding and non-coding transcripts from RNA sequencing data of species without reference genomes. Moreover, analyzing lncRNA characteristics in A. crassicauda uncovered that lower protein-coding potential, lower GC content, shorter transcript length, and less number of isoform per gene are outstanding features of A. crassicauda lncRNAs transcripts.
format	article
author	Fatemeh Salabi Hedieh Jafari Shahrokh Navidpour Ayeh Sadat Sadr
author_facet	Fatemeh Salabi Hedieh Jafari Shahrokh Navidpour Ayeh Sadat Sadr
author_sort	Fatemeh Salabi
title	Systematic and computational identification of Androctonus crassicauda long non-coding RNAs
title_short	Systematic and computational identification of Androctonus crassicauda long non-coding RNAs
title_full	Systematic and computational identification of Androctonus crassicauda long non-coding RNAs
title_fullStr	Systematic and computational identification of Androctonus crassicauda long non-coding RNAs
title_full_unstemmed	Systematic and computational identification of Androctonus crassicauda long non-coding RNAs
title_sort	systematic and computational identification of androctonus crassicauda long non-coding rnas
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/7580d588b7514dfcbe292eb13ffaaf38
work_keys_str_mv	AT fatemehsalabi systematicandcomputationalidentificationofandroctonuscrassicaudalongnoncodingrnas AT hediehjafari systematicandcomputationalidentificationofandroctonuscrassicaudalongnoncodingrnas AT shahrokhnavidpour systematicandcomputationalidentificationofandroctonuscrassicaudalongnoncodingrnas AT ayehsadatsadr systematicandcomputationalidentificationofandroctonuscrassicaudalongnoncodingrnas
_version_	1718385516383043584

Systematic and computational identification of Androctonus crassicauda long non-coding RNAs

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