Dataset Information

CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms.

ABSTRACT: Circular RNAs (circRNAs) are long noncoding RNAs that play a significant role in various biological processes, including embryonic development and stress responses. These regulatory molecules can modulate microRNA activity and are involved in different molecular pathways as indirect regulators of gene expression. Thousands of circRNAs have been described in diverse taxa due to the recent advances in high throughput sequencing technologies, which led to a huge variety of total RNA sequencing being publicly available. A number of circRNA de novo and host gene prediction tools are available to date, but their ability to accurately predict circRNA host genes is limited in the case of low-quality genome assemblies or annotations. Here, we present CircParser, a simple and fast Unix/Linux pipeline that uses the outputs from the most common circular RNAs in silico prediction tools (CIRI, CIRI2, CircExplorer2, find_circ, and circFinder) to annotate circular RNAs, assigning presumptive host genes from local or public databases such as National Center for Biotechnology Information (NCBI). Also, this pipeline can discriminate circular RNAs based on their structural components (exonic, intronic, exon-intronic or intergenic) using a genome annotation file.

SUBMITTER: Nedoluzhko A

PROVIDER: S-EPMC7081776 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms.

Nedoluzhko Artem A Sharko Fedor F Rbbani Md Golam MG Teslyuk Anton A Konstantinidis Ioannis I Fernandes Jorge M O JMO

PeerJ 20200316

Circular RNAs (circRNAs) are long noncoding RNAs that play a significant role in various biological processes, including embryonic development and stress responses. These regulatory molecules can modulate microRNA activity and are involved in different molecular pathways as indirect regulators of gene expression. Thousands of circRNAs have been described in diverse taxa due to the recent advances in high throughput sequencing technologies, which led to a huge variety of total RNA sequencing bein ...[more]

PMID: 32211235

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Project description:BACKGROUND: Molecular characterization of highly diverse gene families can be time consuming, expensive, and difficult, especially when considering the potential for relatively large numbers of paralogs and/or pseudogenes. Here we investigate the utility of Pacific Biosciences single molecule real-time (SMRT) circular consensus sequencing (CCS) as an alternative to traditional cloning and Sanger sequencing PCR amplicons for gene family characterization. We target vomeronasal gene receptors, one of the most diverse gene families in mammals, with the goal of better understanding intra-specific V1R diversity of the gray mouse lemur (Microcebus murinus). Our study compares intragenomic variation for two V1R subfamilies found in the mouse lemur. Specifically, we compare gene copy variation within and between two individuals of M. murinus as characterized by different methods for nucleotide sequencing. By including the same individual animal from which the M. murinus draft genome was derived, we are able to cross-validate gene copy estimates from Sanger sequencing versus CCS methods. RESULTS: We generated 34,088 high quality circular consensus sequences of two diverse V1R subfamilies (here referred to as V1RI and V1RIX) from two individuals of Microcebus murinus. Using a minimum threshold of 7× coverage, we recovered approximately 90% of V1RI sequences previously identified in the draft M. murinus genome (59% being identical at all nucleotide positions). When low coverage sequences were considered (i.e. < 7× coverage) 100% of V1RI sequences identified in the draft genome were recovered. At least 13 putatively novel V1R loci were also identified using CCS technology. CONCLUSIONS: Recent upgrades to the Pacific Biosciences RS instrument have improved the CCS technology and offer an alternative to traditional sequencing approaches. Our results suggest that the Microcebus murinus V1R repertoire has been underestimated in the draft genome. In addition to providing an improved understanding of V1R diversity in the mouse lemur, this study demonstrates the utility of CCS technology for characterizing complex regions of the genome. We anticipate that long-read sequencing technologies such as PacBio SMRT will allow for the assembly of multigene family clusters and serve to more accurately characterize patterns of gene copy variation in large gene families, thus revealing novel micro-evolutionary patterns within non-model organisms.

Dataset Information

CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms.

Publications

CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms.

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