Transcriptome Sequencing Reveals the Traits of Spermatogenesis and Testicular Development in Large Yellow Croaker (Larimichthys crocea)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Sample Collection, Histological Identification, RNA Isolation, and cDNA Library Preparation
2.3. Sequencing and Mapping to the Reference Genome
2.4. Differential Expression Analysis
2.5. Functional Annotation and Pathway Enrichment Analysis
2.6. Quantitative Real-Time PCR (qPCR) Validation
3. Results
3.1. Identification of Testes in Developmental Stage IV
3.2. Overview of the Transcriptome Profiles
3.3. Differentially Expressed Genes (DEGs) of the Two Libraries
3.4. DEGs Annotation and Pathway Analysis
3.5. Validation of RNA-Seq Data by qPCR
4. Discussion
4.1. Neuroactive Ligand–Receptor Interaction Pathway
4.2. GnRH and MAPK Signaling Pathway
4.3. Cell Cycle Pathway
4.4. Genes Encoding Microtubule-Based Motor Proteins
4.5. Actin Cytoskeleton and Myosins
4.6. Heat Shock Protein Genes (HSPs)
4.7. Synaptonemal Complex Protein 2 Gene (Sycp2)
4.8. Doublesex- and Mab-3-Related Transcription Factor 1 (Dmrt1)
4.9. Spermatogenesis-Associated Genes (Spatas)
4.10. DEAD-Box Helicases (Ddxs)
4.11. Tudor Domain-Containing Protein Genes (Tdrds) and Piwis
5. Conclusions
6. Data Accessibility
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Item | Description |
---|---|
Investigation type | Eukaryote |
Project name | Transcriptome for L. crocea |
Collection date | May 2016 |
Lat_lon | 29°86′ N, 121°56′ E |
Geo loc name | Ningbo, China |
Environment | Marine water |
Biotic_relationship | Free-living |
Trophic level | Heterotroph |
Temp | 21 °C |
Salinity | 24 PSU |
Estimated size | 16.35 Gb |
Sequencing meth | Illumina HiSeqTM 2500 |
Mapping software | TopHat2 |
Annotation source | Nr/Nt/Swiss-Prot/KEGG/COG/GO |
BioProject ID of raw reads | PRJNA471154 for TES/PRJNA471574 for PMT |
Accession number of raw reads | SRP148410 for TES/SRP148493 for PMT |
Gene ID | Annotation | Primer | Sequence (5′→3′) |
---|---|---|---|
gene15399 | tex9 | F | GCTGTAGACGACTCGGCTGACTT |
R | TGAGCATCTGAAACGCCTGATCCT | ||
gene14348 | tex36 | F | GCAAGGAGTTGTCACACTGGCATC |
R | TCCATCGTGGCACAGGCAGAAG | ||
gene2626 | tex11 | F | TCGGTGAAGTCTCTGCTCTGGAAG |
R | GGACGCCCTCTGTTGGATTCTCA | ||
gene21265 | tcte1 | F | TGATCGGAGACAGAGGAGCCAGAG |
R | CGGTTGAGACGCAGGTTGAGTGA | ||
gene20395 | stpg2 | F | GCAGTCTCCAGAACCGCTCCAA |
R | CAGTGTGTCCTCCTCGTAGCCAAA | ||
gene3104 | spata7 | F | CTGAGGATGAGTCCAACGGCACAT |
R | AGATTTCCCGCCTTCTGGTGAGAC | ||
gene26146 | spata20 | F | GTTCCTGGACGACTACGCCTTCAT |
R | TGGACGCCGACACTGAGTTAGC | ||
gene26767 | spag5 | F | GGACATCCAGCAAGCCAATGACAG |
R | CCTCGCCAACTCGTTCTCCATCT | ||
gene26247 | spag17 | F | CCAGACGAGGAGGAGGACAGAGAA |
R | TTCAGGATGGTGATGCCGAACTCA | ||
gene16701 | pabp1l | F | AGTCCGCTAATGGAGGCTCTGTC |
R | AGTGGTGGTCCTTGTGGTTGATGT | ||
gene10808 | nme5h | F | TCCACGGCAGCGAGTCATTTCAT |
R | TCAGCCAGTCAGCAAGCCAGATAC | ||
gene21216 | meig1 | F | ACAACTCCAAGCCGAAGTCCATGA |
R | TTGACATCACGGTCCAGGCACTC | ||
gene13149 | lhcgrl | F | TGGCATCAAGGAGGTGGCAAGT |
R | TGGTAGGCGGACTCTGCGATCA | ||
gene1213 | hsp40a1 | F | AGGTCGTGGGAGTCGGAAAGGA |
R | TGTGGACACTTGCTGGACCATACC | ||
gene17675 | ggn | F | GCTGAAGTGCCACCTGAGTCACA |
R | GCCGCTGTTGTATTGCTGCTCTG | ||
XM_019257255.1 | β-actin | F | CTGTCCCTGTATGCCTCTGGTC |
R | CTTGATGTCACGCACGATTTCC |
Samples | TES | PMT |
---|---|---|
Clean reads | 26,201,689 | 28,786,700 |
Clean bases (Gb) | 7.8 | 8.5 |
GC percentage | 50.73% | 50.16% |
% ≥ Q20 | 93.38% | 93.64% |
% ≥ Q30 | 85.81% | 86.27% |
Total mapped | 33,390,310 (63.72%) | 38,470,859 (66.82%) |
Uniquely mapped | 30,802,638 (58.78%) | 35,380,000 (61.45%) |
GO.ID | The Third-Level Functional Categories | All Gene Number | DEG Number | KSa |
---|---|---|---|---|
GO:0001539 | cilium or flagellum-dependent cell motility | 18 | 12 | 4.60E-06 |
GO:0007018 | microtubule-based movement | 61 | 31 | 7.90E-05 |
GO:0007283 | spermatogenesis | 20 | 11 | 0.00017 |
GO:0003006 | developmental process involved in reproduction | 70 | 23 | 0.0035 |
GO:0048515 | spermatid differentiation | 10 | 5 | 0.00452 |
GO:0007126 | meiotic nuclear division | 22 | 10 | 0.00474 |
GO:0044702 | single organism reproductive process | 89 | 30 | 0.00857 |
GO:0071695 | anatomical structure maturation | 6 | 1 | 0.00991 |
GO:0007286 | spermatid development | 9 | 4 | 0.01166 |
GO:0046903 | secretion | 64 | 8 | 0.01212 |
GO:0090068 | positive regulation of cell cycle process | 12 | 2 | 0.01577 |
GO:0033143 | regulation of intracellular steroid hormone receptor signaling pathway | 6 | 1 | 0.01586 |
GO:0007281 | germ cell development | 29 | 11 | 0.01627 |
GO:0035265 | organ growth | 11 | 4 | 0.01688 |
GO:0000910 | cytokinesis | 25 | 7 | 0.018 |
GO:0051495 | positive regulation of cytoskeleton organization | 23 | 4 | 0.01847 |
GO:0048729 | tissue morphogenesis | 289 | 50 | 0.01997 |
GO:0002009 | morphogenesis of an epithelium | 236 | 38 | 0.02012 |
GO:0051653 | spindle localization | 12 | 1 | 0.02114 |
GO:0048608 | reproductive structure development | 38 | 9 | 0.02247 |
GO:0061458 | reproductive system development | 38 | 9 | 0.02247 |
GO:0007010 | cytoskeleton organization | 223 | 50 | 0.02305 |
GO:0045010 | actin nucleation | 14 | 4 | 0.02346 |
GO:0007548 | sex differentiation | 33 | 9 | 0.02645 |
GO:0060070 | canonical Wnt signaling pathway | 77 | 12 | 0.03034 |
GO:0008406 | gonad development | 28 | 8 | 0.03043 |
GO:0060029 | convergent extension involved in organogenesis | 12 | 1 | 0.03087 |
GO:0051493 | regulation of cytoskeleton organization | 63 | 11 | 0.03124 |
GO:0007017 | microtubule-based process | 170 | 58 | 0.03224 |
GO:0030029 | actin filament-based process | 132 | 30 | 0.0363 |
GO:0046330 | positive regulation of JNK cascade | 11 | 1 | 0.04252 |
GO:0030036 | actin cytoskeleton organization | 130 | 30 | 0.04805 |
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Luo, S.; Gao, X.; Ding, J.; Liu, C.; Du, C.; Hou, C.; Zhu, J.; Lou, B. Transcriptome Sequencing Reveals the Traits of Spermatogenesis and Testicular Development in Large Yellow Croaker (Larimichthys crocea). Genes 2019, 10, 958. https://doi.org/10.3390/genes10120958
Luo S, Gao X, Ding J, Liu C, Du C, Hou C, Zhu J, Lou B. Transcriptome Sequencing Reveals the Traits of Spermatogenesis and Testicular Development in Large Yellow Croaker (Larimichthys crocea). Genes. 2019; 10(12):958. https://doi.org/10.3390/genes10120958
Chicago/Turabian StyleLuo, Shengyu, Xinming Gao, Jie Ding, Cheng Liu, Chen Du, Congcong Hou, Junquan Zhu, and Bao Lou. 2019. "Transcriptome Sequencing Reveals the Traits of Spermatogenesis and Testicular Development in Large Yellow Croaker (Larimichthys crocea)" Genes 10, no. 12: 958. https://doi.org/10.3390/genes10120958
APA StyleLuo, S., Gao, X., Ding, J., Liu, C., Du, C., Hou, C., Zhu, J., & Lou, B. (2019). Transcriptome Sequencing Reveals the Traits of Spermatogenesis and Testicular Development in Large Yellow Croaker (Larimichthys crocea). Genes, 10(12), 958. https://doi.org/10.3390/genes10120958