A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog
Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to expl...
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PeerJ Inc.
2017-09-01
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| Online Access: | https://peerj.com/articles/3702.pdf |
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| author | Santiago Montero-Mendieta Manfred Grabherr Henrik Lantz Ignacio De la Riva Jennifer A. Leonard Matthew T. Webster Carles Vilà |
| author_facet | Santiago Montero-Mendieta Manfred Grabherr Henrik Lantz Ignacio De la Riva Jennifer A. Leonard Matthew T. Webster Carles Vilà |
| author_sort | Santiago Montero-Mendieta |
| collection | DOAJ |
| description | Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembled de-novo. We used RNA-seq to obtain the transcriptomic profile for Oreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome assemblies using readily available software and is freely available at: https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki. |
| first_indexed | 2024-03-09T07:53:36Z |
| format | Article |
| id | doaj.art-69f091f859f14e279ffe780a8c086970 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:53:36Z |
| publishDate | 2017-09-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-69f091f859f14e279ffe780a8c0869702023-12-03T01:19:40ZengPeerJ Inc.PeerJ2167-83592017-09-015e370210.7717/peerj.3702A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frogSantiago Montero-Mendieta0Manfred Grabherr1Henrik Lantz2Ignacio De la Riva3Jennifer A. Leonard4Matthew T. Webster5Carles Vilà6Conservation and Evolutionary Genetics Group, Department of Integrative Ecology, Doñana Biological Station (EBD-CSIC), Consejo Superior de Investigaciones Científicas, Seville, SpainDepartment of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (BILS), Uppsala Universitet, Uppsala, SwedenDepartment of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (BILS), Uppsala Universitet, Uppsala, SwedenDepartment of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, SpainConservation and Evolutionary Genetics Group, Department of Integrative Ecology, Doñana Biological Station (EBD-CSIC), Consejo Superior de Investigaciones Científicas, Seville, SpainDepartment of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala Universitet, Uppsala, SwedenConservation and Evolutionary Genetics Group, Department of Integrative Ecology, Doñana Biological Station (EBD-CSIC), Consejo Superior de Investigaciones Científicas, Seville, SpainWhole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembled de-novo. We used RNA-seq to obtain the transcriptomic profile for Oreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome assemblies using readily available software and is freely available at: https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.https://peerj.com/articles/3702.pdfGenomicsTranscriptomicsRNA-seqFrog transcriptomeTrinityGene ontology |
| spellingShingle | Santiago Montero-Mendieta Manfred Grabherr Henrik Lantz Ignacio De la Riva Jennifer A. Leonard Matthew T. Webster Carles Vilà A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog PeerJ Genomics Transcriptomics RNA-seq Frog transcriptome Trinity Gene ontology |
| title | A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog |
| title_full | A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog |
| title_fullStr | A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog |
| title_full_unstemmed | A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog |
| title_short | A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog |
| title_sort | practical guide to build de novo assemblies for single tissues of non model organisms the example of a neotropical frog |
| topic | Genomics Transcriptomics RNA-seq Frog transcriptome Trinity Gene ontology |
| url | https://peerj.com/articles/3702.pdf |
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