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2020 | OriginalPaper | Buchkapitel

Micro-Variations from RNA-seq Experiments for Non-model Organisms

verfasst von : Elena Espinosa, Macarena Arroyo, Rafael Larrosa, Manuel Manchado, M. Gonzalo Claros, Rocí­o Bautista

Erschienen in: Bioinformatics and Biomedical Engineering

Verlag: Springer International Publishing

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Abstract

RNA-based high-throughput sequencing technologies provide a huge amount of reads from transcripts. In addition to expression analyses, transcriptome reconstruction, or isoform detection, they could be useful for detection of gene variations, in particular micro-variations (single nucleotide polymorphisms [SNPs] and indels). Gene variations are usually based on homogenous (one single individual) DNA-seq data, but this study aims the usage of heterogeneous (several individuals) RNA-seq data to obtain clues about gene variability of a population. Therefore, new algorithms or workflows are required to fill this gap, usually disregarded. Here it is presented an automated workflow based on existing software to predict micro-variations from RNA-seq data using a genome or a transcriptome as reference. It can deal with organism whose genome sequence is known and well-annotated, as well as non-model organism where only draft genomes or transcriptomes are available. Mapping is based on STAR in both cases. Micro-variation detection relies on GATK (combining Mutect2 and HaplotypeCaller) and VarScan since they are able to provide reliable results from RNA-seq reads. The workflow has been tested with reads from normal and diseased lung from patients having small-cell lung carcinoma. Human genome, as well as human transcriptome, were used as reference and then compared: from the initial 120 000 micro-variations, only 267 were predicted by at least two algorithm in the exome of patients. The workflow was tested in non-model organisms such as Senegalese sole, using its transcriptome as reference, to determine micro-variations in sole larvae exposed to different salinities. Therefore, the workflow seems to produce robust and reliable micro-variations in coding genes based on RNA-seq, irrespective of the nature of the reference sequence. We think that this paves the way to correlate micro-variations and differentially expressed genes in non-model organisms with the aim of foster breeding plans.

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Literatur
1.
Zurück zum Zitat APROMAR: Asociación Empresarial de Acuicultura de España: La Acuicultura en España 2018. Technical report, Ministerio de Agricultura y Pesca, Alimentación y Medioambiente (2018) APROMAR: Asociación Empresarial de Acuicultura de España: La Acuicultura en España 2018. Technical report, Ministerio de Agricultura y Pesca, Alimentación y Medioambiente (2018)
2.
Zurück zum Zitat Arroyo, M., Bautista, R., Larrosa, R., Cobo, M.Á., Claros, M.G.: Biomarker potential of repetitive-element transcriptome in lung cancer. PeerJ 7, e8277 (2019)CrossRef Arroyo, M., Bautista, R., Larrosa, R., Cobo, M.Á., Claros, M.G.: Biomarker potential of repetitive-element transcriptome in lung cancer. PeerJ 7, e8277 (2019)CrossRef
4.
Zurück zum Zitat Benzekri, H., et al.: De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a database and design of a microarray. BMC Genomics 15, 952 (2014)CrossRef Benzekri, H., et al.: De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a database and design of a microarray. BMC Genomics 15, 952 (2014)CrossRef
5.
Zurück zum Zitat Brouard, J.S., Schenkel, F., Marete, A., Bissonnette, N.: The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments. J. Anim. Sci. Biotechnol. 10, 44 (2019)CrossRef Brouard, J.S., Schenkel, F., Marete, A., Bissonnette, N.: The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments. J. Anim. Sci. Biotechnol. 10, 44 (2019)CrossRef
6.
Zurück zum Zitat Córdoba-Caballero, J., Seoane-Zonjic, P., Manchado, M., Gonzalo Claros, M.: De novo Transcriptome Assembly of Solea senegalensis v5.0 Using TransFlow. In: Rojas, I., Valenzuela, O., Rojas, F., Ortuño, F. (eds.) IWBBIO 2019. LNCS, vol. 11465, pp. 48–59. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-17938-0_5CrossRef Córdoba-Caballero, J., Seoane-Zonjic, P., Manchado, M., Gonzalo Claros, M.: De novo Transcriptome Assembly of Solea senegalensis v5.0 Using TransFlow. In: Rojas, I., Valenzuela, O., Rojas, F., Ortuño, F. (eds.) IWBBIO 2019. LNCS, vol. 11465, pp. 48–59. Springer, Cham (2019). https://​doi.​org/​10.​1007/​978-3-030-17938-0_​5CrossRef
7.
Zurück zum Zitat DePristo, M.A., et al.: A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43(5), 491–8 (2011)CrossRef DePristo, M.A., et al.: A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43(5), 491–8 (2011)CrossRef
8.
Zurück zum Zitat Dobin, A., et al.: STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1), 15–21 (2013)CrossRef Dobin, A., et al.: STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1), 15–21 (2013)CrossRef
9.
Zurück zum Zitat Falgueras, J., Lara, A.J., Fernández-Pozo, N., Cantón, F.R., Pérez-Trabado, G., Claros, M.G.: SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read. BMC Bioinf. 11, 38 (2010)CrossRef Falgueras, J., Lara, A.J., Fernández-Pozo, N., Cantón, F.R., Pérez-Trabado, G., Claros, M.G.: SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read. BMC Bioinf. 11, 38 (2010)CrossRef
10.
Zurück zum Zitat González Gayte, I., Bautista Moreno, R., Seoane Zonjic, P., Claros, M.G.: DEgenes Hunter - A Flexible R Pipeline for Automated RNA-seq Studies in Organisms without Reference Genome. Genomics Comput. Biol. 3(3), e31 (2017)CrossRef González Gayte, I., Bautista Moreno, R., Seoane Zonjic, P., Claros, M.G.: DEgenes Hunter - A Flexible R Pipeline for Automated RNA-seq Studies in Organisms without Reference Genome. Genomics Comput. Biol. 3(3), e31 (2017)CrossRef
11.
Zurück zum Zitat Koboldt, D.C., et al.: Varscan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22(3), 568–76 (2012)CrossRef Koboldt, D.C., et al.: Varscan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22(3), 568–76 (2012)CrossRef
12.
Zurück zum Zitat Manchado, M., Planas, J.V., Cousin, X., Rebordinos, L., Claros, M.G.: Genetic and genomic characterization of soles. In: Muñoz-Cueto, J.A., Mañanós-Sánchez, E.L., Sánchez-Vázquez, F.J. (eds.) The Biology of Sole. Number B6.1, pp. 361–379. CRC Press (2019) Manchado, M., Planas, J.V., Cousin, X., Rebordinos, L., Claros, M.G.: Genetic and genomic characterization of soles. In: Muñoz-Cueto, J.A., Mañanós-Sánchez, E.L., Sánchez-Vázquez, F.J. (eds.) The Biology of Sole. Number B6.1, pp. 361–379. CRC Press (2019)
13.
Zurück zum Zitat McLaren, W., et al.: The ensembl variant effect predictor. Genome Biol. 17(1), 122 (2016)CrossRef McLaren, W., et al.: The ensembl variant effect predictor. Genome Biol. 17(1), 122 (2016)CrossRef
14.
Zurück zum Zitat Mi, H., Muruganujan, A., Thomas, P.D.: Panther in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 41((Database issue)), D377–D386 (2013)PubMed Mi, H., Muruganujan, A., Thomas, P.D.: Panther in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 41((Database issue)), D377–D386 (2013)PubMed
15.
Zurück zum Zitat Rudin, C.M., et al.: Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer. Nature Gen. 44(10), 1111–1116 (2012)CrossRef Rudin, C.M., et al.: Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer. Nature Gen. 44(10), 1111–1116 (2012)CrossRef
16.
Zurück zum Zitat Stein, S., Bahrami-Samani, E., Xing, Y.: Using RNA-Seq to Discover genetic polymorphisms that produce hidden splice variants. Methods Mol. Biol. 1648, 129–142 (2017)CrossRef Stein, S., Bahrami-Samani, E., Xing, Y.: Using RNA-Seq to Discover genetic polymorphisms that produce hidden splice variants. Methods Mol. Biol. 1648, 129–142 (2017)CrossRef
17.
Zurück zum Zitat Wang, W., et al.: Genetic structure of six cattle populations revealed by transcriptome-wide SNPs and gene expression. Genes Genomics 40(7), 715–724 (2018)CrossRef Wang, W., et al.: Genetic structure of six cattle populations revealed by transcriptome-wide SNPs and gene expression. Genes Genomics 40(7), 715–724 (2018)CrossRef
19.
Zurück zum Zitat Yuan, Y., et al.: Genome-wide association and differential expression analysis of salt tolerance in gossypium hirsutum l at the germination stage. BMC Plant Biol. 19(1), 394 (2019)CrossRef Yuan, Y., et al.: Genome-wide association and differential expression analysis of salt tolerance in gossypium hirsutum l at the germination stage. BMC Plant Biol. 19(1), 394 (2019)CrossRef
Metadaten
Titel
Micro-Variations from RNA-seq Experiments for Non-model Organisms
verfasst von
Elena Espinosa
Macarena Arroyo
Rafael Larrosa
Manuel Manchado
M. Gonzalo Claros
Rocí­o Bautista
Copyright-Jahr
2020
DOI
https://doi.org/10.1007/978-3-030-45385-5_48