Dataset Information

Data on the de novo transcriptome assembly for the migratory bird, the Common quail (Coturnix coturnix).

ABSTRACT: The Common or European quail (Coturnix coturnix) is a Galliform bird of ecological importance for research in the field of animal migration. The Common quail is also a game bird, thus, of great interest for recreational activities and conservation management. Here, we generated a high quality de novo transcriptome for the Common quail for which no reference genome is to date publicly available. The transcriptome was obtained from a population of Common quail originated from captive founders raised under laboratory conditions. Paired-end RNA-Sequencing reads were obtained from extracted total RNA of brain tissue punches (preoptic-hypothalamic region) of 23 quails, which yielded to 5.5-11.2 million reads per individual bird for a total of 236 million reads. After assembly optimization, we used a stringent filtering analysis pipeline to remove redundant and low confidence transcripts. The final transcriptome consisted of 22,293 transcripts of which 21,551 (97%) were provided with annotation data. Our data offers a high quality pipeline for compiling transcriptomes of complex non-genomic species. Our data also provide a robust reference for gene expression studies in this species or other related Galliform species, including the Japanese quail.

SUBMITTER: Marasco V

PROVIDER: S-EPMC7394769 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Data on the de novo transcriptome assembly for the migratory bird, the Common quail (Coturnix coturnix).

Marasco Valeria V Fusani Leonida L Pola Gianni G Smith Steve S

Data in brief 20200720

The Common or European quail (Coturnix coturnix) is a Galliform bird of ecological importance for research in the field of animal migration. The Common quail is also a game bird, thus, of great interest for recreational activities and conservation management. Here, we generated a high quality de novo transcriptome for the Common quail for which no reference genome is to date publicly available. The transcriptome was obtained from a population of Common quail originated from captive ...[more]

PMID: 32775561

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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

Data on the de novo transcriptome assembly for the migratory bird, the Common quail (Coturnix coturnix).

Publications

Data on the <i>de novo</i> transcriptome assembly for the migratory bird, the Common quail (<i>Coturnix coturnix</i>).

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OmicsDI is part of the ELIXIR infrastructure

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Dataset Information

Data on the de novo transcriptome assembly for the migratory bird, the Common quail (Coturnix coturnix).

Publications

Data on the &lt;i&gt;de novo&lt;/i&gt; transcriptome assembly for the migratory bird, the Common quail (&lt;i&gt;Coturnix coturnix&lt;/i&gt;).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Data on the <i>de novo</i> transcriptome assembly for the migratory bird, the Common quail (<i>Coturnix coturnix</i>).