# Multi-tissue Siberian sturgeon RNA sequencing data

Christophe Köpp, Cédric Cabau, André Lasalle, Santiago Di Landro, Gonzalo Greif, Denise Vizziano-Cantonnet

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Christophe Köpp, Cédric Cabau, André Lasalle, Santiago Di Landro, Gonzalo Greif, et al. Multi-tissue Siberian sturgeon RNA sequencing data. Data in Brief, 2020, 31, 10.1016/j.dib.2020.105820. hal-03157670

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Data Article

Multi-tissue Siberian sturgeon RNA
sequencing data

<figure><img src="image_3.png" /></figure>

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updates

Christophe Klopp<sup>a</sup>, Cédric Cabau<sup>c</sup>, André Lasalle<sup>b</sup>, Santiago Di Landro<sup>b</sup>, Gonzalo Greif<sup>c</sup>, Denise Vizziano-Cantonnet<sup>b,*</sup>

ARTICLE INFO

Article history:
Received 17 February 2020
Revised 14 May 2020
Accepted 2 June 2020
Available online 7 June 2020

**Keywords:**
Siberian sturgeon
Transcriptomics
Brain-pituitary-gonad axis
Anterior-kidney
Kidney
Stomach
Liver
Embryos

A B S T R A C T

Siberian sturgeon, Acipenser baerii, is a commercially valu-
able fish for flesh and caviar production and a threatened
species. We produced transcriptomic data for ten tissues
with relevance to puberty, reproduction, early development,
growth and food intake. The data includes RNA-Seq read
sets of brain, pituitary, anterior-kidney, kidney, stomach, liver,
heart, embryonic, pre-larval, and immature gonad sequences.
Tissues were collected from sex differentiated fish (17 to 42
months of age, 66 to 85 cm) RNA was extracted and se-
quenced. Our purpose is to facilitate fundamental studies
of sturgeon physiology to wild and aquaculture populations
management.

© 2020 The Author(s). Published by Elsevier Inc.
This is an open access article under the CC BY license.
(http://creativecommons.org/licenses/by/4.0/)

Article history:
Received 17 February 2020
Revised 14 May 2020
Accepted 2 June 2020
Available online 7 June 2020

**Keywords:**
Siberian sturgeon
Transcriptomics
Brain-pituitary-gonad axis
Anterior-kidney
Kidney
Stomach
Liver
Embryos

<footnote><sup>a</sup> INRAE, SIGENAE, MIAT UR875, F-31326, Castanet Tolosan, France, 'SIGENAE, GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France</footnote>

<footnote><sup>b</sup> Laboratorio de Fisiología de la Reproducción y Ecología de Peces, Instituto de Biología, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Iguá 4225, Montevideo, 11400, Uruguay</footnote>

<footnote><sup>c</sup> Laboratorio de Interacción Hospedero-Patógeno/Unidad de Biología Molecular, Instituto Pasteur de Montevideo, Uruguay</footnote>

<footnote>* Corresponding author.</footnote>

<footnote>E-mail address: vizziano@fcien.edu.uy (D. Vizziano-Cantonnet).</footnote>
**Specifications Table**

<table><tr><td>Subject</td><td>Biology</td></tr><tr><td>Specific subject area</td><td>Transcriptomics, physiology and aquaculture</td></tr><tr><td>Type of data</td><td>Raw RNA-Seq data and assembled reference transcriptome assembly</td></tr><tr><td>How data were acquired</td><td>Illumina MiSeq Illumina HiSeq 2500</td></tr><tr><td>Data format</td><td>Raw data and assembly information</td></tr><tr><td>Parameters for data collection</td><td>Tissues collected from immature fish: pituitary, anterior-kidney, kidney, stomach, liver, gonads<br>Tissues collected from gametogenetic fish: brain Tissues collected from sex undifferentiated fish: embryonic, pre-larval</td></tr><tr><td>Description of data collection</td><td>Tissues sequenced in a pool: pituitary, testis, ovary, anterior kidney, kidney, heart, stomach, liver. Tissues sequenced individually: brain, pituitary, anterior kidney, kidney, heart, stomach, liver.</td></tr><tr><td>Data source location</td><td>Laboratorio de Fisiología de la Reproducción y Ecología de Peces, Facultad de Ciencias, Universidad de la República Oriental del Uruguay. Country: Uruguay<br>Site of collection: Estuario del Plata sturgeon farm, San Gregorio de Polanco, Tacuarembó, Uruguay</td></tr><tr><td>Data accessibility</td><td>Raw data of RNA Seq analysis are available on Sequence Read Archive (SRA) database and connected with BioProject PRJNA589958, https://www.ncbi.nlm.nih.gov/bioproject/PRJNA589958 Reference transcriptome assembly is available at the NCBI in TSA GICB00000000 https://dataview.ncbi.nlm.nih.gov/object/PRJNA589958?reviewer=ik54sg8njqstt0j9psepieaona</td></tr></table>

**Value of Data**

* The dataset will facilitate research on topics of interest in Siberian sturgeon aquaculture such as puberty, reproduction, growth, food intake, and immunology. Insights into these processes will improve management of both wild and aquaculture populations.

* This data benefits the community of scientists working on fish biology and aquaculture. It also can be used for fish evolution studies.

* This data includes different tissues enabling to better understand different functions. For example, the data on the brain-pituitary axis will be helpful for studies on puberty, growth and food intake control.

* This is the first Siberian sturgeon RNA-seq multi-tissue data set.

**1. Data Description**

The Siberian sturgeon, Acipenser baerii, is a non-teleost ray-finned fish (Actinopterygii) which face critical conservation problems [1,2] due to overfishing, incidental fishing, river pollution, dam construction, other environmental disruptions, and poor fishery management [1-4]. There has been sharp decline in commercial Siberian sturgeon catches [5] and has now spread to 49 countries worldwide [6]. Knowledge of sturgeon physiology and genetics is less advanced than for other industrial species such as salmonids.

Here, we present a novel Siberian sturgeon multi-tissue data set including brain, pituitary, gonadal, liver, stomach, kidney, anterior kidney, heart, embryonic, and pre-larval transcriptomes, with the goal of facilitating crucial research on topics of interest in sturgeon physiology, such as puberty, reproduction, growth, food intake, and in immunology. Insights into these processes will improve management of both wild and aquaculture populations.

Samples of brain, pituitary, gonads, liver, stomach, kidney, anterior kidney were taken from males and females aged 15-42 months (Table 1). Samples were also collected from embryos one day prior to hatching and pre-larvae on the day of hatching.

In a first experiment a pool of tissues was sequenced using Illumina MiSeq (Table 2) and in a second experiment tissues were sequenced individually (Table 2). Raw data correspond to Fastq for RNA-Seq reads and fasta for assembled contigs.
<caption>**Table 1**</caption>

Characteristics of fish used to obtain tissue samples for individual and pool sequencing.

<table><thead><tr><th>Fish Id</th><th>Age</th><th>Sex</th><th>Stage</th><th>Tissue samples</th><th>Total length/cm</th><th>Total weight/kg</th><th>Individual (I) and/or Pool (P)</th></tr></thead><tbody><tr><td>259</td><td>17</td><td>Male</td><td>Immature</td><td>Testis</td><td>77.5</td><td>1.8</td><td>P</td></tr><tr><td>262</td><td>17</td><td>Female</td><td>Immature</td><td>Ovary</td><td>75.5</td><td>1.6</td><td>P</td></tr><tr><td>380</td><td>15</td><td>Male</td><td>Non-reproductive</td><td>Brain</td><td>66.8</td><td>0.879</td><td>I</td></tr><tr><td>381</td><td>15</td><td>Female</td><td>Non-reproductive</td><td>Anterior-kidney</td><td>66.1</td><td>0.851</td><td>I, P</td></tr><tr><td>381</td><td>15</td><td>Female</td><td>Non-reproductive</td><td>Kidney</td><td>66.1</td><td>0.851</td><td>I, P</td></tr><tr><td>381</td><td>15</td><td>Female</td><td>Non-reproductive</td><td>Heart</td><td>66.1</td><td>0.851</td><td>I, P</td></tr><tr><td>382</td><td>15</td><td>Male</td><td>Non-reproductive</td><td>Stomach</td><td>64.1</td><td>0.842</td><td>I, P</td></tr><tr><td>384</td><td>20</td><td>Male</td><td>Non-reproductive</td><td>Liver</td><td>76.5</td><td>1.85</td><td>I, P</td></tr><tr><td>630</td><td>42</td><td>Male</td><td>Non-reproductive</td><td>Pituitary</td><td>85.5</td><td>2.44</td><td>I, P</td></tr></tbody></table>
<table><caption>**Table 2**
Sample identification (Id), library name, SRA and SAMN, sequencer and quality of sequences produced.</caption><thead><tr><th>Fish Id</th><th>Tissue samples</th><th>Library name</th><th>SRA files</th><th>SAMN files</th><th>Sequencer</th><th>Nb reads <sup>(1)</sup></th><th>Alignment rate <sup>(2)</sup></th><th>Q20 ratio <sup>(3)</sup></th></tr></thead><tbody><tr><td>380</td><td>Brain</td><td>380C</td><td>SRR10466940</td><td>SAMN13295011</td><td>Illumina HiSeq 2500</td><td>92,338,008</td><td>95.10</td><td>99.28</td></tr><tr><td>381</td><td>Anterior-kidney</td><td>381Int</td><td>SRR10466939</td><td>SAMN13295012</td><td>Illumina HiSeq 2500</td><td>71,233,652</td><td>97.11</td><td>99.36</td></tr><tr><td>381</td><td>Kidney</td><td>381Rein</td><td>SRR10466938</td><td>SAMN13295013</td><td>Illumina HiSeq 2500</td><td>62,440,734</td><td>96.56</td><td>99.39</td></tr><tr><td>381</td><td>Heart</td><td>381Coeur</td><td>SRR10466937</td><td>SAMN13295014</td><td>Illumina HiSeq 2500</td><td>69,179,714</td><td>97.30</td><td>99.37</td></tr><tr><td>382</td><td>Stomach</td><td>382Est</td><td>SRR10466936</td><td>SAMN13295015</td><td>Illumina HiSeq 2500</td><td>66,452,854</td><td>98.67</td><td>99.33</td></tr><tr><td>384</td><td>Liver</td><td>384Foie</td><td>SRR10466935</td><td>SAMN13295016</td><td>Illumina HiSeq 2500</td><td>70,511,690</td><td>98.67</td><td>99.41</td></tr><tr><td>630</td><td>Pituitary</td><td>630Hyp</td><td>SRR10466934</td><td>SAMN13295017</td><td>Illumina HiSeq 2500</td><td>69,219,726</td><td>94.81</td><td>99.4</td></tr><tr><td>Nd</td><td>Embryos.One day prior hatching</td><td>Sexsturg-E1-E2</td><td>SRR10466932</td><td>SAMN13295019</td><td>Illumina HiSeq 2500</td><td>80,075,510</td><td>97.04</td><td>97.43</td></tr><tr><td>Nd</td><td>Pre-larvaeDay of hatching</td><td>Sexsturg-L1-L5</td><td>SRR10466931</td><td>SAMN13295020</td><td>Illumina HiSeq 2500</td><td>85,793,960</td><td>96.78</td><td>97.12</td></tr><tr><td>259, 262, 381, 382, 384, 630</td><td>Pool of tissues, testis, ovary, anterior kidney, kidney, heart, stomach, liver, pituitary</td><td>poolTejidosEsturion</td><td>SRR10466933</td><td>SAMN13295018</td><td>Illumina MiSeq</td><td>17,594,907</td><td>99.08</td><td>97.16</td></tr></tbody></table>

<footnote>(1) Number of reads</footnote>

<footnote>(2) Alignment rate: is the number of sequences aligned on the de novo transcriptome reference divided by the total number of sequences of the sample expressed in percent</footnote>

<footnote>(3) Q20 ratio is the number of raw read base pairs having a quality score equal or over 20 divided by the total number of read base pairs of the sample expressed in percent.</footnote>
## 2. Experimental design, materials, and methods

### 2.1. Ethics statement

Research procedures involving animal experimentation complied with international principles on the use and care of laboratory animals and Uruguayan regulations on animal welfare. The protocol was approved by the Comisión de Etica en el Uso de Animales of the Comisión Honoraria de Experimentación Animal CHEA of Uruguay (Authorization Number 240,011-002,227-16).

### 2.2. Experimental animals and rearing procedures

Siberian sturgeon individuals were obtained from a fish farm (Estuario del Plata, Uruguay) and reared at natural conditions [7]. Using a batch of embryos arrived from Poland to Uruguay and cultured at the Estuario del Plata farm (San Gregorio de Polanco, Tacuarembó), we collected (embryos one day prior to hatching and pre-larvae on the day of hatching). For fish aged from 15 to 42 months, we also used fish cultured at Estuario del Plata that came at embryo stage from Poland. They were sacrificed by spinal transection to obtain brain, pituitary, gonads, liver, stomach, kidney, anterior kidney (Table 1).

### 2.3. RNA extraction, cDNA library construction, and illumina sequencing

RNA from various tissues (pituitary, testicular, ovarian, liver, stomach, kidney, anterior kidney, heart, Table 1) was extracted using the Illumina RNAspin Mini RNA Isolation Kit (GE Healthcare) according to manufacturer instructions, and quality was assessed using the Agilent 2100 Bioanalyzer. cDNA synthesis was carried out on 4 µg of total RNA. The RNA samples conformed to the required purity criteria (A260/A230 and A260/A280 > 1.8) and quality levels (RIN > 8) for cDNA library preparations for sequencing. 0.5 µg of RNA of each tissue were mixed to create the pool. Sequencing was performed using the Epicenter kit (ScriptSeq™ v2 RNA-Seq Library Preparation Kit) on an Illumina MiSeq system with paired-end read length of 2 × 75 base pairs at the Universidad de Biología Molecular of Institut Pasteur in Montevideo, Uruguay.

Individual samples of brain, pituitary, liver, stomach, kidney, anterior kidney, embryonic, and pre-larval tissues were sequenced to provide deeper coverage. For the individual samples, total RNA was extracted and libraries constructed on a Tecan EVO200 liquid handler using the Illumina TruSeq Stranded mRNA sample prep kit. Libraries quality were checked on an Agilent High Sensitivity DNA Kit and quantified with the KAPA Library Quantification Kit to ensure accuracy and performed on an Illumina HiSeq 2500 system (high-throughput mode) using a paired-end read length of 2 × 100 base pairs with the Illumina TruSeq SBS Kit, v3. Individual tissue samples were sequenced at the Plateforme Génomique (INRA Auzeville in Castanet-Tolosan, France). Assembly and annotation were performed using both the pooled and individual tissue data. The number of reads per set ranged between 17,594,907 and 92,338,008. The read quality was assessed by calculating a Q20 ratio corresponding to the fraction of nucleotides having a quality score over 20 for all the reads of each sample (Table 2). The Q20 ratio ranged from 97.12 to 99.41%.

### 2.4. Transcriptome assembly

The transcriptome was assembled in two steps using the de novo RNA-Seq Assembly Pipeline (DRAP) 1.9 [8]. First, 10 tissue assemblies were performed with runDrap using 20 million reads for each sample but the pool for which all the reads where used. Second the resulting contigs were merged with runMeta to produce the final reference file.
The transcriptome quality was checked using BUSCO (version 3.0.0) [9] using the Actinopterygii reference protein set (actinopterygii_odb9). Over 90% (4147/4584) of the BUSCO expected proteins were found in unique or duplicated copies in the set. The read quality was also reassessed using the read versus contig alignment rate (Table 2) ranging from 94.81 to 99.08%. The alignment was performed with bwa [https://doi.org/10.1093/bioinformatics/btp324] version 0.7.12-r1039 with default parameters and the alignment rate was calculated on the bam file produced with samtools view and flagstat [https://doi.org/10.1093/bioinformatics/btp352] version 1.3.1 using default parameters.

## Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

## Acknowledgements

Many thanks are due to the chief executive officer of Estuario del Plata Facundo Márquez, to Dr. Vet. Andres Ryncowski, Mr. Eduardo Oliver, and all of the Estuario del Plata (Uruguay) staff for their ample support and kindness during the development of this work.

This work was supported by the Comisión Sectorial de Investigación Científica (CSIC), Universidad de la República Oriental del Uruguay, Grant C225-348-Uruguay; Agencia Nacional de Investigación e Innovación-Dirección Nacional de Recursos Acuáticos ANII-DINARA – FPA 9975-Uruguay; and Agencia Nacional de Investigación e Innovación - FMV_1_2017_1_135908.

## Author contributions

C.K. and D.V.C. conceived and designed the experiments; D.V.C directed the research project, acquired the funding and administrate the projects; A.L., G.G., and S.D.L. performed the experiments; C.K., C.C., and D.V.C. analyzed the data and organized the datasets; the manuscript was written by C.K., C.C., and D.V.C.

## Supplementary materials

Supplementary material associated with this article can be found, in the online version, at doi:10.1016/j.dib.2020.105820.

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