Abstract
Motivation: Siberian sturgeon is a long lived and late maturing fish farmed for caviar production in 50 countries. Functional genomics enable to find genes of interest for fish farming. In the absence of a reference genome, a reference transcriptome is very useful for sequencing based functional studies. Results: We present here a high-quality transcriptome assembly database built using RNA-seq reads coming from brain, pituitary, gonadal, liver, stomach, kidney, anterior kidney, heart, embryonic and pre-larval tissues. It will facilitate crucial research on topics such as puberty, reproduction, growth, food intake and immunology. This database represents a major contribution to the publicly available sturgeon transcriptome reference datasets. Availability: The database is publicly available at http://siberiansturgeontissuedb.sigenae.org Supplementary information: Supplementary data are available at Database online.
Highlights
The Siberian sturgeon, Acipenser baerii, is a non-teleost ray-finned fish (Actinopterygii) species of the order Acipenseriformes, which includes sturgeons and paddlefishes [1] and faces critical conservation problems [2, 3]
We have the same pattern for the BUSCO metrics with 89.5% of reconstructed genes for Meta_Oases and 89.3% for Meta_trinity, which is much higher than the 84.4% of All_Oases and the 80.3% of All_trinity
The All_Oases and in a lesser manner the All_trinity have a very high percentage of genes falling in BUSCO duplicated category, indicating that these genes are in multi-copy in the contig sets
Summary
The Siberian sturgeon, Acipenser baerii, is a non-teleost ray-finned fish (Actinopterygii) species of the order Acipenseriformes, which includes sturgeons and paddlefishes [1] and faces critical conservation problems [2, 3]. Siberian sturgeons from the easternmost of the three great Siberian rivers have been cultured in Europe since the early 1980s and this culture is performed in 50 countries in the Northern and Southern Hemispheres [4]. Its production remains on the craft scale with worldwide production of only 27 500 tons per year [4], as compared to industrial levels of salmonid and tilapia production at 3 281 100 and 5 977 000 tons per year, respectively [5]. Knowledge of sturgeon physiology and genetics is less advanced than for other aquaculture species. Salmonids and African ciclids benefit from over 100 years of biological research, with genome assemblies published for Atlantic salmon [6], trout [7] and tilapia [8].
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