Dataset Information

Characterization of a de novo assembled transcriptome of the Common Blackbird (Turdus merula).

ABSTRACT: 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.

SUBMITTER: Koglin S

PROVIDER: S-EPMC5732540 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Characterization of a <i>de novo</i> assembled transcriptome of the Common Blackbird (<i>Turdus merula</i>).

Koglin Sven S Trense Daronja D Wink Michael M Sauer-Gürth Hedwig H Tietze Dieter Thomas DT

PeerJ 20171213

<h4>Background</h4>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 co ...[more]

PMID: 29255646

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Project description:Necropsy of two free-ranging common blackbirds (Turdus merula) found dead in central Italy revealed the presence of a high number of cyclocoelid flukes in the coelomatic cavity. Cyclocoelid flukes primarily infect avian respiratory system. Histologically, air sac walls were covered with a fibrinous exudate containing degenerate heterophils, many trematodes and some colonies of Gram-positive cocci. The superficial bronchi and parabronchi were markedly distended, and the adjacent pulmonary parenchyma was congested and collapsed. Trematodes, surrounded by a mild suppurative to pyogranulomatous inflammatory reaction, were also observed on the pericardial, intestinal, kidney and hepatic serosal surfaces. The death of the two examined birds was likely due to the high parasite load and associated severe lesions. At parasitological examination, flukes showed a tongue-shaped elongate body, tapered anteriorly and rounded posteriorly, of 2,088-2,314 μm in width and 8,268-11,830 μm in length. The mouth was slightly oval and sub-terminal, with a small oral sucker. The oval pharynx measured 250-309 μm, and the two caeca joined posteriorly. Two large (550-702 μm × 450-520 μm) globular testes were situated obliquely to each other, whereas an oval (250 × 300 μm in mean) or round (about 334 μm in diameter) intertesticular ovary was placed in a longitudinal straight line with the testes. The ootype was about 110 μm in diameter, while the brown-yellow eggs measured 131.5 × 73.9 μm in mean. The genital pore was post-pharyngeal, while the symmetrically arranged vitelline glands were not confluent posteriorly. Morphoflogical diagnosis led to the identification of Morishitium polonicum, a cyclocoelid fluke species that typically inhabits the air sacs of blackbirds. The morphological diagnosis was corroborated by molecular phylogenetic analysis of the mitochondrial (CO1, ND1) DNA loci. The present study provides the first report of pathological lesions and death caused by M. polonicum in birds.

Project description:BACKGROUND: Common carp (Cyprinus carpio) is one of the most important aquaculture species of Cyprinidae with an annual global production of 3.4 million tons, accounting for nearly 14% of the freshwater aquaculture production in the world. Due to the economical and ecological importance of common carp, genomic data are eagerly needed for genetic improvement purpose. However, there is still no sufficient transcriptome data available. The objective of the project is to sequence transcriptome deeply and provide well-assembled transcriptome sequences to common carp research community. RESULT: Transcriptome sequencing of common carp was performed using Roche 454 platform. A total of 1,418,591 clean ESTs were collected and assembled into 36,811 cDNA contigs, with average length of 888 bp and N50 length of 1,002 bp. Annotation was performed and a total of 19,165 unique proteins were identified from assembled contigs. Gene ontology and KEGG analysis were performed and classified all contigs into functional categories for understanding gene functions and regulation pathways. Open Reading Frames (ORFs) were detected from 29,869 (81.1%) contigs with an average ORF length of 763 bp. From these contigs, 9,625 full-length cDNAs were identified with sequence length from 201 bp to 9,956 bp. Comparative analysis revealed that 27,693(75.2%) contigs have significant similarity to zebrafish Refseq proteins, and 24,371(66.2%), 24,501(66.5%) and 25,025(70.0%) to teraodon, medaka and three-spined stickleback refseq proteins. A total of 2,064 microsatellites were initially identified from 1,730 contigs, and 1,639 unique sequences had sufficient flanking sequences on both sides for primer design. CONCLUSION: The transcriptome of common carp had been deep sequenced, de novo assembled and characterized, providing the valuable resource for better understanding of common carp genome. The transcriptome data will facilitate future functional studies on common carp genome, and gradually apply in breeding programs of common carp, as well as closely related other Cyprinids.

Dataset Information

Characterization of a de novo assembled transcriptome of the Common Blackbird (Turdus merula).

Publications

Characterization of a <i>de novo</i> assembled transcriptome of the Common Blackbird (<i>Turdus merula</i>).

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