Abstract
The Snowtrout, Schizothorax richardsonii, is a vulnerable fish species found in different rivers and rivulets of the Himalayan region. The species is also a suitable poikilotherm to study the low-temperature tolerance as it dwells well at a temperature range of 5–20 °C. The solute carrier (SLC) group of membrane transport proteins play an integral role in cellular acclimation response. The present RNA sequencing was done to identify solute carrier transporter which are the major gene cascades responsible for transport of sugars, amino acids, oligonucleotides, ions, drugs, etc. to and from the cell organelles. A reference transcriptome database was created from liver tissue of Schizothorax richardsonii through RNA sequencing on Illumina HiSeq 2000 platform. The sequences were annotated and characterized under various solute carrier families in the species. So far, 113 transcripts were identified as solute carrier transporter genes categorized under 13 different families. This data will be useful for many researchers working on gene cloning and differential expression of solute carriers.
Keywords: RNA-Seq, Molecular characterization, Cellular transporters
Specifications table
| Subject area | Biology |
| More specific subject area | Transcriptome |
| Type of data | Transcriptome sequences |
| How data was acquired | RNA sequencing using Illumina HiSeq 2000 platform |
| Data format | Raw .fasta sequence in text file and table |
| Experimental factors | Liver samples of both control and heat shocked individuals |
| Experimental features | De novo assembly, GO annotation, Gene identification using Blastx tool |
| Data source location | Bhubaneswar, India |
| Data accessibility | Data is being provided with this article |
| Related research article | Barat A., Sahoo P.K., Kumar R., Goel C., Singh A.K. (2016) Transcriptional response to heat shock in liver of snow trout (Schizothorax richardsonii)—a vulnerable Himalayan Cyprinid fish, Funct. Integr. Genomics. 16 203–213.https://doi.org/10.1007/s10142-016-0477-0 |
Value of the data
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1. Data
The raw RNA-Seq data is available on NCBI GENBANK (SRA acc. No. SRX643306). The present dataset is extracted (annotated and characterized as solute carrier transporter) from the de novo assembly of transcriptome data of Schizothorax richardsonii. Nucleotide sequences of all solute carrier genes identified in the transcriptome of S. richardsonii is provided in ‘.txt’ file format.
2. Experimental design, materials and methods
The details of sample collection, experimental design, RNA isolation, and sequencing were reported earlier [1]. RNA sequence data of Schizothorax richardsonii (Bio-project accession no PRJNA253239) were retrieved from NCBI GenBank (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA253239). The raw reads were subjected to quality check using Fast QC v.0.11.8 followed by trimming using Fastx toolkit V.0.0.13. The trimmed and cleaned reads of both (SRR1503433 and SRR1552917) were pooled for de novo assembly using CLC Genomics Workbench (QIAGEN Bioinformatics, USA). The contigs so obtained were further assembled into transcripts using CAP3 [2]. The coding sequences of assembled transcripts were identified using TransDecoder v.5.5.0 (https://github.com/TransDecoder/TransDecoder/releases) on default parameters. The CDS generated through TransDecoder were matched for functional annotations using nonredundant BLASTx tool of NCBI GenBank (https://blast.ncbi.nlm.nih.gov). The gene identified as solute carrier transporters were extracted from complete transcriptome assembly using in-house pearl script (Table 1).
Table 1.
Details of solute carrier families observed in the liver transcriptome of Schizothorax richardsonii.
| Contig ID | SLC | Gene ID | Gene name | GeneBank | BLASTx e value |
|---|---|---|---|---|---|
| Inorganic anion/cation transport | |||||
| 1062810 | slc4 | slc4a1a | band 3 anion transport protein | NP_938152.1 | 0.0 |
| 1066568 | Slc4a2a | anion exchange protein 2 | NP_001032314.1 | 0.0 | |
| 1068006 | Slc4a2b | anion exchanger | NP_001107912.1 | 0.0 | |
| 1072522 | Slc4a7 | Predicted: Sodium bicarbonate cotransporter 3 | XP_009290880.1 | 0.0 | |
| 1036206 | Slc9 | Slc9a3r1 | Na (+)/H (+) exchange regulatory cofactor NHE-RF1 | NP_997872.2 | 2e-135 |
| 1069006 | Slc12 | Slc12a2 | potassium/chloride transporters | NP_001002080.1 | 0.0 |
| 1070924 | Slc12a4 | Predicted: potassium/chloride transporters | XP_691291.2 | 0.0 | |
| 1046148 | Slc12a6 | potassium/chloride transporters | XP_020792176.1 | 6e-69 | |
| 1068568 | Slc12a8 | potassium/chloride transporters | NP_001121749.1 | 0.0 | |
| 1017415 | Slc12a9 | potassium/chloride transporters | NP_001122020.1 | 3e-91 | |
| 1069036 | Slc20 | Slc20a1a | sodium-dependent phosphate transporter | NP_998344.1 | 0.0 |
| 1059836 | Slc20a1b | sodium-dependent phosphate transporter 1-B | NP_997753.1 | 2e-162 | |
| 1063094 | Slc26 | Slc26a1 | sulphate anion transporter 1 | NP_001074136.1 | 0.0 |
| 1054148 | Slc26a2 | Predicted: sulfate transporter | XP_020359215.1 | 4e-178 | |
| 1068556 | Slc26a5 | prestin | NP_958881.1 | 0.0 | |
| 1059638 | Slc26a11 | sodium-independent sulfate anion transporter | NP_956061.1 | 0.0 | |
| Amino acid and oligopeptide transport | |||||
| 1061674 | Slc1 | Slc1a3a | excitatory amino acid transporter 1 | NP_997805.1 | 0.0 |
| 1035372 | Slc3 | Slc3a2b | amino acid transporter heavy chain | NP_958922.2 | 4e-108 |
| 1057762 | Slc7 | Slc7a1 | PREDICTED: high affinity cationic amino acid transporter 1 isoform | XP_683623.4 | 0.0 |
| 1068818 | Slc7a3 | cationic amino acid transporter, y + system | NP_001007330.2 | 0.0 | |
| 1063888 | Slc7a6 | Y + L amino acid transporter 2 | NP_001018310.1 | 0.0 | |
| 1018741 | Slc7a9 | PREDICTED: B (0,+)-type amino acid transporter 1 | XP_005169080.1 | 3e-77 | |
| 1061224 | Slc17 | Slc17a5 | Sialin [Danio rerio] anion/sugar transporter |
NP_001070195.1 | 0.0 |
| 1062834 | Slc17a9b | anion/sugar transporter | NP_001002635.1 | 0.0 | |
| 1069738 | Slc36 | Slc36a1 | proton-coupled amino acid transporter 1 | XP_687732.4 | 0.0 |
| 1069074 | Slc38 | Slc38a2 | sodium-coupled neutral amino acid transporter 2 | NP_001038569.1 | 0.0 |
| 1070630 | Slc38a3 | sodium-coupled neutral amino acid transporter 5 | NP_001002648.1 | 0.0 | |
| 1067430 | Slc38a4 | sodium-coupled neutral amino acid transporter 4 | NP_001005944.2 | 0.0 | |
| 1034094 | Slc38a6 | probable sodium-coupled neutral amino acid transporter 6 | NP_001018308.1 | 6e-144 | |
| 1067684 | Slc38a7 | putative sodium-coupled neutral amino acid transporter 7 | NP_001003648.1 | 0.0 | |
| 1022612 | Slc43 | Slc43a1a | amino acid system L transporter | NP_001314915.1 | 2e-132 |
| 1002903 | Slc43a1b | large neutral amino acids transporter small subunit 3 | NP_001076469.1 | 2e-87 | |
| 1013829 | Slc43a2a | large neutral amino acids transporter small subunit 4 |
NP_956545.1 | 2e-61 | |
| 972610 | Slc43a2b | large neutral amino acids transporter small subunit 4 | NP_001008585.1 | 4e-82 | |
| 1059342 | Slc43a3b | solute carrier family 43 member 3 | NP_001035011.1 | 0.0 | |
| Transport of glucose and other sugars | |||||
| 1066294 | Slc2 | Slc2a1 | solute carrier family 2, facilitated glucose transporter member 1-like | XP_020346873.1 | 0.0 |
| 1009559 | Slc2a2 | glucose transporter 2 | KC513421.2 | 1e-106 | |
| 1068576 | Slc2a8 | solute carrier family 2, facilitated glucose transporter member 6 | NP_997963.1 | 0.0 | |
| 1062118 | Slc2a12 | solute carrier family 2, facilitated glucose transporter member 12 | NP_956832.1 | 0.0 | |
| 1039720 | Slc5 | Slc5a2 | sodium/glucose cotransporter 2 | NP_998091.1 | 9e-88 |
| 1044578 | Slc50 | Slc50a1 | sugar transporter SWEET1 |
NP_001012515.1 | 2e-115 |
| Transport of bile salts and organic anions | |||||
| 1045170 | Slc10 | Slc10a3 | SLC10A3-like protein, partial | KJ777502.1 | 5e-105 |
| 1067754 | Slc13 | Slc13a5 | Di- and tricarboxylate transporter [Carbohydrate transport and metabolism] | NP_001136038.1 | 0.0 |
| Monocarboxylate transporter | |||||
| 1065692 | Slc16 | Slc16a2 | thyroid hormone transporter | NP_001245159.1 | 0.0 |
| 1056880 | Slc16a3 | monocarboxylate transporter 4 | NP_997873.1 | 0.0 | |
| 1071962 | Slc16a4 | monocarboxylate transporter 5 | NP_001074068.2 | 0.0 | |
| 1061320 | Slc16a7 | monocarboxylate transporter 2 like | XP_004070979.1 | 0.0 | |
| 1016957 | Slc16a8 | Uncharacterized protein | NP_997797.1 | 1e-53 | |
| 1067292 | Slc16a9a | solute carrier family 16, member 9a | NP_956704.1 | 0.0 | |
| 1021626 | Slc47 | Slc47a2 | multidrug and toxin extrusion protein 1 | NP_001073648.1 | 8e-94 |
| Metalion transport | |||||
| 1048352 | Slc30 | Slc30a1a | zinc transporter 1 | NP_957173.1 | 0.0 |
| 1069498 | Slc30a5 | zinc transporter 5 | NP_001002322.1 | 0.0 | |
| 1040510 | Slc30a7 | Co/Zn/Cd efflux system component | AB987984.1 | 0.0 | |
| 1003631 | Slc39 | Slc39a1 | zinc transporter ZIP1 | XP_020353560.1 | 1e-14 |
| 1039056 | Slc39a4 | zinc transporter ZIP4 | NP_001124249.1 | 1e-28 | |
| 1044232 | Slc39a6 | zinc transporter ZIP6 | NP_001001591.1 | 6e-76 | |
| 1043306 | Slc39a9 | zinc transporter ZIP9 | NP_001013558.1 | 0.0 | |
| 1067228 | Slc39a10 | ZIP Zinc transporter | AB988007.1 | 0.0 | |
| 1059932 | Slc39a13 | zinc transporter ZIP13 | NP_001005306.3 | 0.0 | |
| 1045216 | Slc41 | Slc41a1 | Divalent cation transporter | FQ310506.3 | 0.0 |
| Transport of urea, neurotransmitters and biogenic amines, ammonium and choline | |||||
| 1069812 | Slc6 | Slc6a13 | neurotransmitter transporter | NP_001004533.1 | 0.0 |
| 987653 | Slc18 | Slc18b1 | MFS-type transporter | NP_001017841.1 | 7e-44 |
| 1051398 | Slc22 | Slc22a2 | organic cation transporter | NP_998315.1 | 0.0 |
| 1031164 | Slc22 | Slc22a18 | organic cation transporter | NP_001032462.1 | 3e-102 |
| 1051684 | Slc44 | Slc44a4 | choline transporter-like protein 4 | NP_956707.1 | 0.0 |
| Transport of vitamins and cofactors | |||||
| 1035792 | Slc23 | Slc23a1 | nucleobase transporters | NP_001166970.1 | 4e-174 |
| 1064658 | Slc33 | Slc33a1 | acetyl-coenzyme A transporter 1 | NP_957402.1 | 2e-136 |
| 1062610 | Slc46 | Slc46a1 | proton-coupled folate transporter | NP_956579.1 | 0.0 |
| 997095 | Slc52 | Slc52a2 | riboflavin transporter 1 | NP_955950.1 | 8e-87 |
| Nucleoside/nucleotide transport | |||||
| 1065114 | Slc29 | Slc29a1a | Equilibrative nucleoside transporter 1 | NP_001025348.1 | 0.0 |
| 1031960 | Slc35 | Slc35b1 | solute carrier family 35 member B1 | NP_001004583.1 | 4e-57 |
| 1063694 | Slc35b2 | adenosine 3′-phospho 5′-phosphosulfate transporter 1 precursor | NP_991198.1 | 0.0 | |
| 1055528 | Slc35b3 | adenosine 3′-phospho 5′-phosphosulfate transporter 2 |
NP_001035084.1 | 0.0 | |
| 1047578 | Slc35b4 | UDP-xylose and UDP-N-acetylglucosamine Transporter |
NP_997817.2 | 0.0 | |
| 1045786 | Slc35c1 | GDP-fucose transporter 1 | NP_001008590.1 | 0.0 | |
| 1027680 | Slc35c2 | ovarian cancer overexpressed 1: Triose-phosphate Transporter family | NP_997808.1 | 2e-123 | |
| 1055762 | Slc35e1 | solute carrier family 35 member E1 | NP_998239.1 | 1e-179 | |
| 1013693 | Slc35e2 | solute carrier family 35 member E2-like | XP_020362107.1 | 5e-98 | |
| 1049536 | Slc35e4 | solute carrier family 35 member E4 | NP_001017857.1 | 8e-171 | |
| 1064524 | Slc35f2 | solute carrier family 35, member F2 | NP_001070024.1 | 0.0 | |
| Transport of fatty acids, prostaglandins and steroid sulphates | |||||
| 1053548 | Slc27 | Slc27a1a | long-chain fatty acid transport protein 1 | NP_001013555.1 | 0.0 |
| 994313 | Slc27a1b | long-chain-acyl-CoA synthetase | NP_001070716.1 | 1e-84 | |
| 1020140 | Slc27a2 | long-chain-acyl-CoA synthetase | NP_001020470.1 | 5e-44 | |
| 1053812 | Slc27a4 | long-chain fatty acid transport protein 4 | NP_001017737.1 | 0.0 | |
| 1055764 | Slc27a6 | long-chain fatty acid transport protein 6 precursor | NP_001070854.1 | 0.0 | |
| Transport of fatty acids, prostaglandins and steroid sulphates, thyroid sulphates | |||||
| nil | |||||
| Heme transport | |||||
| 1054106 | Slc48 | Slc48a16 | heme transporter hrg1-A | NP_956300.1 | 7e-85 |
| Transport across mitochondrial membranes | |||||
| 907636 | Slc25 | Slc25a3b | mitochondrial carrier; phosphate carrier | BC067565.1 | 7e-21 |
| 1044412 | Slc25a5 | ADP/ATP transporter on adenylate translocase | NP_775354.1 | 0.0 | |
| 1054268 | Slc25a6 | adenine nucleotide translocator), ADP/ATP translocase 3 | NP_989562.2 | 0.0 | |
| 1025440 | Slc25a10 | dicarboxylate transporter, | NP_957466.1 | 2e-98 | |
| 1072488 | Slc25a12 | mitochondrial carrier, Aralar 1 | NP_997947.1 | 0.0 | |
| 1048712 | Slc25a14 | brain mitochondrial carrier protein 1 | NP_956458.1 | 0.0 | |
| 1047404 | Slc25a16 | mitochondrial carrier protein/graves disease carrier protein | NP_991112.1 | 0.0 | |
| 1035454 | Slc25a20 | carnitine/acylcarnitine translocase | NP_957153.1 | 4e-173 | |
| 1063614 | Slc25a21 | mitochondrial oxodicarboxylate carrier | NP_001070100.1 | 0.0 | |
| 1062104 | Slc25a22 | mitochondrial glutamate carrier | NP_998573.1 | 3e-169 | |
| 1037430 | Slc25a25 | calcium-binding mitochondrial carrier proteinSCaMC-2-A | NP_998422.1 | 4e-144 | |
| 987757 | Slc25a26 | adenosylmethionine mitochondrial carrier protein | NP_001025314.1 | 2e-99 | |
| 979606 | Slc25a27 | mitochondrial uncoupling protein 4 | NP_956635.1 | 3e-54 | |
| 1067474 | Slc25a28 | mitoferrin-2 | NP_998284.2 | 3e-119 | |
| 1065884 | Slc25a29 | mitochondrial carnitine/acylcarnitine carrier protein CACL | NP_001025408.1 | 2e-155 | |
| 1006145 | Slc25a32a | mitochondrial folate transporter/carrier | NP_956550.1 | 3e-113 | |
| 1061138 | Slc25a32b | mitochondrial folate transporter/carrier | NP_001013354.1 | 0.0 | |
| 1041964 | Slc25a33 | solute carrier family 25 member 33 | NP_998322.1 | 4e-151 | |
| 1022370 | Slc25a36a | solute carrier family 25 member 36-A | NP_001002667.1 | 2e-129 | |
| 1045510 | Slc25a37 | mitoferrin-1 | NP_001035060.1 | 4e-101 | |
| 888952 | Slc25a38a | solute carrier family 25 member 38A | NP_001070070.1 | 1e-27 | |
| 1026578 | Slc25a39 | solute carrier family 25 member 39 | NP_956780.1 | 2e-159 | |
| 1058676 | Slc25a40 | solute carrier family 25 member 40 | NP_001002360.1 | 0.0 | |
| 1046498 | Slc25a42 | mitochondrial coenzyme A transporter SLC25A42 | NP_001038918.1 | 0.0 | |
| 1064802 | Slc25a43 | solute carrier family 25 member 43 | NP_001004497.2 | 0.0 | |
| 1058484 | Slc25a44a | solute carrier family 25, member 44 a | NP_001007351.1 | 0.0 | |
| 1019095 | Slc25a47b | hepatocellular carcinoma down-regulated mitochondrial carrier homolog B | NP_001083050.1 | 1e-91 | |
Footnotes
Transparency document associated with this article can be found in the online version at https://doi.org/10.1016/j.dib.2019.103712.
Nucleotide sequences of solute carrier genes identified in the transcriptome of S. richardsonii.
Supplementary data to this article can be found online at https://doi.org/10.1016/j.dib.2019.103712.
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Appendix A. Supplementary data
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References
- 1.Barat A., Sahoo P.K., Kumar R., Goel C., Singh A.K. Transcriptional response to heat shock in liver of snow trout (Schizothorax richardsonii)—a vulnerable Himalayan Cyprinid fish. Funct. Integr. Genomic. 2016;16:203–213. doi: 10.1007/s10142-016-0477-0. [DOI] [PubMed] [Google Scholar]
- 2.Huang X., Madan A. CAP3: a DNA sequence assembly program. Genome Res. 1999;9:868–877. doi: 10.1101/gr.9.9.868. [DOI] [PMC free article] [PubMed] [Google Scholar]
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