Characterization of a de novo assembled transcriptome of the Common Blackbird (Turdus merula)
Background In recent years, next generation high throughput sequencing technologies have proven to be useful tools for investigations concerning the genomics or transcriptomics also of non-model species. Consequently, ornithologists have adopted these technologies and the respective bioinformatics t...
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| Format: | Article |
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PeerJ Inc.
2017-12-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/4045.pdf |
| _version_ | 1797418389656829952 |
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| author | Sven Koglin Daronja Trense Michael Wink Hedwig Sauer-Gürth Dieter Thomas Tietze |
| author_facet | Sven Koglin Daronja Trense Michael Wink Hedwig Sauer-Gürth Dieter Thomas Tietze |
| author_sort | Sven Koglin |
| collection | DOAJ |
| description | Background In recent years, next generation high throughput sequencing technologies have proven to be useful tools for investigations concerning the genomics or transcriptomics also of non-model species. Consequently, ornithologists have adopted these technologies and the respective bioinformatics tools to survey the genomes and transcriptomes of a few avian non-model species. The Common Blackbird is one of the most common bird species living in European cities, which has successfully colonized urban areas and for which no reference genome or transcriptome is publicly available. However, to target questions like genome wide gene expression analysis, a reference genome or transcriptome is needed. Methods Therefore, in this study two Common Blackbirds were sacrificed, their mRNA was isolated and analyzed by RNA-Seq to de novo assemble a transcriptome and characterize it. Illumina reads (125 bp paired-end) and a Velvet/Oases pipeline led to 162,158 transcripts. For the annotation (using Blast+), an unfiltered protein database was used. SNPs were identified using SAMtools and BCFtools. Furthermore, mRNA from three single tissues (brain, heart and liver) of the same two Common Blackbirds were sequenced by Illumina (75 bp single-end reads). The draft transcriptome and the three single tissues were compared by their BLAST hits with the package VennDiagram in R. Results Following the annotation against protein databases, we found evidence for 15,580 genes in the transcriptome (all well characterized hits after annotation). On 18% of the assembled transcripts, 144,742 SNPs were identified which are, consequently, 0.09% of all nucleotides in the assembled transcriptome. In the transcriptome and in the single tissues (brain, heart and liver), 10,182 shared genes were found. Discussion Using a next-generation technology and bioinformatics tools, we made a first step towards the genomic investigation of the Common Blackbird. The de novo assembled transcriptome is usable for downstream analyses such as differential gene expression analysis and SNP identification. This study shows the importance of the approach to sequence single tissues to understand functions of tissues, proteins and the phenotype. |
| first_indexed | 2024-03-09T06:33:03Z |
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| language | English |
| last_indexed | 2024-03-09T06:33:03Z |
| publishDate | 2017-12-01 |
| publisher | PeerJ Inc. |
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| series | PeerJ |
| spelling | doaj.art-7c17e637ded4409e989cf61c34b956812023-12-03T11:03:14ZengPeerJ Inc.PeerJ2167-83592017-12-015e404510.7717/peerj.4045Characterization of a de novo assembled transcriptome of the Common Blackbird (Turdus merula)Sven Koglin0Daronja Trense1Michael Wink2Hedwig Sauer-Gürth3Dieter Thomas Tietze4Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, GermanyZoological Institute and Museum, University of Greifswald, Greifswald, GermanyInstitute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, GermanyInstitute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, GermanyInstitute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, GermanyBackground In recent years, next generation high throughput sequencing technologies have proven to be useful tools for investigations concerning the genomics or transcriptomics also of non-model species. Consequently, ornithologists have adopted these technologies and the respective bioinformatics tools to survey the genomes and transcriptomes of a few avian non-model species. The Common Blackbird is one of the most common bird species living in European cities, which has successfully colonized urban areas and for which no reference genome or transcriptome is publicly available. However, to target questions like genome wide gene expression analysis, a reference genome or transcriptome is needed. Methods Therefore, in this study two Common Blackbirds were sacrificed, their mRNA was isolated and analyzed by RNA-Seq to de novo assemble a transcriptome and characterize it. Illumina reads (125 bp paired-end) and a Velvet/Oases pipeline led to 162,158 transcripts. For the annotation (using Blast+), an unfiltered protein database was used. SNPs were identified using SAMtools and BCFtools. Furthermore, mRNA from three single tissues (brain, heart and liver) of the same two Common Blackbirds were sequenced by Illumina (75 bp single-end reads). The draft transcriptome and the three single tissues were compared by their BLAST hits with the package VennDiagram in R. Results Following the annotation against protein databases, we found evidence for 15,580 genes in the transcriptome (all well characterized hits after annotation). On 18% of the assembled transcripts, 144,742 SNPs were identified which are, consequently, 0.09% of all nucleotides in the assembled transcriptome. In the transcriptome and in the single tissues (brain, heart and liver), 10,182 shared genes were found. Discussion Using a next-generation technology and bioinformatics tools, we made a first step towards the genomic investigation of the Common Blackbird. The de novo assembled transcriptome is usable for downstream analyses such as differential gene expression analysis and SNP identification. This study shows the importance of the approach to sequence single tissues to understand functions of tissues, proteins and the phenotype.https://peerj.com/articles/4045.pdfRNAseqTranscriptomicsSNPCommon blackbirdOrnithology |
| spellingShingle | Sven Koglin Daronja Trense Michael Wink Hedwig Sauer-Gürth Dieter Thomas Tietze Characterization of a de novo assembled transcriptome of the Common Blackbird (Turdus merula) PeerJ RNAseq Transcriptomics SNP Common blackbird Ornithology |
| title | Characterization of a de novo assembled transcriptome of the Common Blackbird (Turdus merula) |
| title_full | Characterization of a de novo assembled transcriptome of the Common Blackbird (Turdus merula) |
| title_fullStr | Characterization of a de novo assembled transcriptome of the Common Blackbird (Turdus merula) |
| title_full_unstemmed | Characterization of a de novo assembled transcriptome of the Common Blackbird (Turdus merula) |
| title_short | Characterization of a de novo assembled transcriptome of the Common Blackbird (Turdus merula) |
| title_sort | characterization of a de novo assembled transcriptome of the common blackbird turdus merula |
| topic | RNAseq Transcriptomics SNP Common blackbird Ornithology |
| url | https://peerj.com/articles/4045.pdf |
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