Comparative Transcriptome Analysis of Female and Male Fine-Patterned Puffer: Identification of Candidate Genes Associated with Growth and Sex Differentiation
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Sample Collection
2.3. RNA Extraction, cDNA Library Building, and Transcriptome Sequencing
2.4. Assembly and Annotation
2.5. Analysis of Potential Candidate Genes
2.6. Simple Sequence Repeat (SSR) Loci Detection
2.7. Quantitative Real-Time PCR Validation
3. Results
3.1. Sequencing and Assembly
3.2. Annotation of T. poecilonotus Transcriptome
3.3. Potential Candidate Genes and Pathways
3.4. Discovery of Molecular Markers
3.5. Transcriptome Data Validation
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
References
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Sample | Raw Reads (M) | Clean Reads (M) | Clean Bases (Gb) | Clean Reads Q30 (%) | Clean Reads Ratio (%) |
---|---|---|---|---|---|
Female-1 | 52.59 | 48.33 | 7.25 | 87.49 | 91.90 |
Female-2 | 44.04 | 40.55 | 6.08 | 86.17 | 92.06 |
Female-3 | 47.33 | 44.00 | 6.60 | 86.04 | 92.98 |
Male-1 | 47.33 | 43.93 | 6.59 | 86.37 | 92.81 |
Male-2 | 47.33 | 43.63 | 6.54 | 86.48 | 92.19 |
Male-3 | 47.33 | 43.58 | 6.54 | 86.18 | 92.09 |
Sample | Total Number | Total Length | Mean Length | N50 | GC (%) |
---|---|---|---|---|---|
Female-1 | 81,249 | 145,145,039 | 1786 | 3128 | 48.91 |
Female-2 | 72,625 | 118,111,439 | 1626 | 2823 | 49.00 |
Female-3 | 72,194 | 120,065,634 | 1663 | 2836 | 49.06 |
Male-1 | 93,484 | 144,668,988 | 1547 | 2725 | 48.62 |
Male-2 | 95,350 | 142,802,517 | 1497 | 2627 | 48.55 |
Male-3 | 84,292 | 131,779,534 | 1563 | 2735 | 48.81 |
All-Unigene | 149,814 | 309,566,984 | 2066 | 3538 | 48.64 |
Database | Number of Unigenes | Percentage (%) |
---|---|---|
Total | 122,719 | 81.91% |
NT | 70,243 | 46.89% |
NR | 63,250 | 42.22% |
SwissProt | 67,197 | 44.85% |
KEGG | 100,035 | 66.77% |
KOG | 90,961 | 60.72% |
GO | 63,518 | 42.40% |
Gene | Unigene | Annotation | Log2(♂/♀) | Q-Value |
---|---|---|---|---|
Dmtr1 | Unigene1322 | doublesex and mab-3-related transcription factor 1 | 6.66 | 2.34 × 10−07 |
Sox3 | Unigene1791 | SRY-box containing transcription factor 3 | 5.72 | 8.44 × 10−04 |
Dnali1 | Unigene12399 | axonemal dynein light intermediate polypeptide 1 | 7.63 | 3.40 × 10−07 |
Ropn1l | CL4645.Contig3 | ropporin-1-like protein | 9.37 | 1.32 × 10−18 |
Cyp19a | CL5324.Contig8 | cytochrome P450 aromatase | −7.54 | 2.15 × 10−07 |
Zp1 | CL6076.Contig3 | zona pellucida sperm-binding protein 1 | −12.66 | 1.43 × 10−110 |
Zp2 | CL8003.Contig1 | zona pellucida sperm-binding protein 2 | −7.70 | 1.84 × 10−20 |
Zp3 | CL7875.Contig2 | zona pellucida sperm-binding protein 3 | −7.93 | 4.04 × 10−16 |
Start-7 | CL3580.Contig10 | stAR-related lipid transfer protein 7 | 7.57 | 2.66 × 10−06 |
Gdf3 | CL9083.Contig1 | growth differentiation factor 3 | −8.90 | 3.99 × 10−14 |
Gdf9 | CL6347.Contig1 | growth differentiation factor 9 | −9.23 | 1.61 × 10−12 |
Gtf3a | Unigene10317 | Transcription factor IIIA-like | −2.42 | 2.11 × 10−08 |
42sp43 | Unigene8014 | P43 5S RNA-binding protein-like | −7.38 | 6.57 × 10−24 |
Mnd1 | Unigene817 | meiotic nuclear division protein 1 homolog | 3.25 | 8.39 × 10−03 |
Star | Unigene31813 | steroidogenic acute regulatory protein | −2.49 | 3.42 × 10−04 |
Wee1 | CL12054.Contig1 | wee1-like protein kinase | 2.05 | 6.42 × 10−03 |
Spaca6 | CL4045.Contig1 | sperm acrosome membrane-associated protein 6 | 5.97 | 4.05 × 10−04 |
Spaca4 | CL12530.Contig2 | sperm acrosome membrane-associated protein 4 | 3.53 | 2.18 × 10−15 |
Spata5 | CL8799.Contig2 | spermatogenesis-associated protein5 | 6.47 | 7.85 × 10−05 |
Spata7 | CL4586.Contig1 | spermatogenesis-associated protein 7 | 2.93 | 1.40 × 10−03 |
Spata17 | CL4320.Contig15 | spermatogenesis-associated protein 17 | 8.17 | 2.09 × 10−08 |
Spata32 | Unigene13081 | spermatogenesis-associated protein 32 | 4.78 | 1.72 × 10−06 |
Gene | Unigene | Annotation | Log2(♂/♀) | Q-Value |
---|---|---|---|---|
Igfbp1 | CL6482.Contig4 | insulin-like growth factor-binding protein 1 | −8.52 | 2.51 × 10−09 |
Igfbp3 | Unigene7287 | Insulin-like growth factor-binding protein 3 | −3.36 | 9.25 × 10−06 |
Igf1r | Unigene24558 | Insulin-like growth factor 1 receptor | −1.06 | 1.75 × 10−02 |
Ghr | CL9297.Contig1 | Growth hormone receptor | −4.79 | 3.10 × 10−03 |
Sstr2 | Unigene6248 | Somatostatin receptor 2 | 7.45 | 5.93 × 10−07 |
Fabp1 | CL7463.Contig1 | fatty acid-binding protein 1 | 3.85 | 8.11 × 10−12 |
Fabp4 | CL10654.Contig1 | fatty acid-binding protein 4 | −8.28 | 6.17 × 10−56 |
Fabp6 | CL6561.Contig1 | fatty acid-binding protein 6 | 6.70 | 2.41 × 10−04 |
Fabp7 | Unigene40265 | fatty acid-binding protein 7 | 5.45 | 2.86 × 10−05 |
Grb1 | CL5906.Contig1 | Growth factor receptor-bound proteins 1 | 2.16 | 6.38 × 10−03 |
Grb7 | Unigene6338 | Growth factor receptor-bound proteins 7 | −2.98 | 8.15 × 10−03 |
Grb10 | CL11116.Contig1 | Growth factor receptor-bound proteins 10 | 3.07 | 1.43 × 10−04 |
Htr1 | Unigene31616 | 5-hydroxytryptamine receptor 1D-like | 4.59 | 1.31 × 10−04 |
Htr2 | Unigene28993 | 5-hydroxytryptamine receptor 2C-like | 5.27 | 3.86 × 10−03 |
Htr3 | CL1712.Contig2 | 5-hydroxytryptamine receptor 3 | 5.61 | 1.44 × 10−03 |
Htr6 | Unigene18275_ | 5-hydroxytryptamine receptor 6 | 4.33 | 7.54 × 10−03 |
Prlr | CL1256.Contig1 | Prolactin receptor | −8.19 | 3.29 × 10−11 |
Prl | CL12326.Contig4 | Prolactin | −5.65 | 4.17 × 10−06 |
Myhc | Unigene12897 | myosin heavy chain | 6.29 | 5.15 × 10−05 |
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Shan, B.; Liu, Y.; Yang, C.; Li, Y.; Wang, L.; Sun, D. Comparative Transcriptome Analysis of Female and Male Fine-Patterned Puffer: Identification of Candidate Genes Associated with Growth and Sex Differentiation. Fishes 2021, 6, 79. https://doi.org/10.3390/fishes6040079
Shan B, Liu Y, Yang C, Li Y, Wang L, Sun D. Comparative Transcriptome Analysis of Female and Male Fine-Patterned Puffer: Identification of Candidate Genes Associated with Growth and Sex Differentiation. Fishes. 2021; 6(4):79. https://doi.org/10.3390/fishes6040079
Chicago/Turabian StyleShan, Binbin, Yan Liu, Changping Yang, Yuan Li, Liangming Wang, and Dianrong Sun. 2021. "Comparative Transcriptome Analysis of Female and Male Fine-Patterned Puffer: Identification of Candidate Genes Associated with Growth and Sex Differentiation" Fishes 6, no. 4: 79. https://doi.org/10.3390/fishes6040079