Transcriptomic Responses of Blue Bat Star Patiria pectinifera to Sediment Burial
Abstract
1. Introduction
2. Results
2.1. Survival and Physicochemical Variations at Different Depths of Sediment Burial
2.2. Transcriptomic Sequence Assembly and Functional Annotations
2.3. Annotations of DEGs
2.4. Comparison of DEGs with Other Echinoderms
3. Discussion
3.1. Hypoxic Stress as a Major Physicochemical Determinant in the Sediment Burial
3.2. Metabolic Responses to Hypoxic Stress
3.3. Immune Responses to Hypoxic Stress
3.4. Signaling Pathway Responses to Hypoxic Stress
4. Materials and Methods
4.1. Preparison of Deep-Sea Sediments and Rearing of Patiria pectinifera
4.2. Sediment Burial
4.3. RNA Extraction, Library Preparation and Illumina Hiseq Sequencing
4.4. De Novo Assembly and Functional Annotations
4.5. Differential Expression Analysis and Functional Enrichment Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
BP | Biological process |
CC | Cellular component |
CDSs | Coding sequences |
COG | Clusters of Orthologous Genes |
CP | Cellular processes |
DEGs | Differentially expressed genes |
DO | Dissolved oxygen |
EIP | Environmental information processing |
FDR | False discovery rate |
GIP | Genetic information processing |
GO | Gene Ontology |
ISA | International Seabed Authority |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
logFC | Log fold change |
M | Metabolism |
MF | Molecular function |
OS | Organismal systems |
PPAR | Peroxisome proliferator-activated receptor |
RPKM | Reads per kilobase of exon per million mapped reads |
RIG-I-like | Retinoic acid-inducible gene-I-like |
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Sediment Grain Size (μm) | Burial Depth (cm) | Survival Rates (%) |
---|---|---|
<63 | 2 | 95.2 |
5 | 81.0 | |
63 to 250 | 2 | 100.0 |
5 | 100.0 |
Sample | Raw Reads | Raw Bases(bp) | Clean Reads | Clean Bases(bp) | Valid Bases(%) | GC Content(%) |
---|---|---|---|---|---|---|
Experimental group 1 | 4,7078,864 | 7,061,829,600 | 44,362,144 | 6,577,106,998 | 93.1 | 45.1 |
Experimental group 2 | 48,983,870 | 7,347,580,500 | 46,163,352 | 6,844,046,669 | 93.1 | 45.1 |
Experimental group 3 | 44,980,718 | 6,747,107,700 | 42,781,734 | 6,357,259,233 | 94.2 | 45.2 |
Control group 1 | 43,523,738 | 6,528,560,700 | 40,288,662 | 5,897,539,644 | 90.3 | 46.0 |
Control group 2 | 43,174,760 | 6,476,214,000 | 39,964,578 | 5,850,154,113 | 90.3 | 46.0 |
Control group 3 | 44,645,024 | 6,696,753,600 | 41,962,408 | 6,177,159,182 | 92.2 | 46.3 |
Class | Species | Accession Number | Size (Mbp) | GC Content (%) | Transcripts | CDSs |
---|---|---|---|---|---|---|
Asteroidea | Acanthaster planci | GCF_001949145.1 | 383.8 | 41.5 | 36,221 | 33,201 |
Asterias amurensis | GCF_032118995.1 | 491.5 | 39.0 | 30,608 | 26,569 | |
Asterias rubens | GCF_902459465.1 | 417.6 | 39.0 | 28,238 | 24,049 | |
Patiria miniata | GCF_015706575.1 | 608.3 | 40.5 | 40,283 | 35,403 | |
Crinoidea | Anneissia japonica | GCF_011630105.1 | 589.6 | 34.5 | 38,110 | 32,774 |
Antedon mediterranea | GCF_964355755.1 | 354.5 | 33.5 | 33,480 | 25,416 | |
Echinoidea | Diadema antillarum | GCF_040938485.1 | 1800.0 | 38.5 | 39,579 | 36,155 |
Lytechinus pictus | GCF_037042905.1 | 811.7 | 36.5 | 37,286 | 29,875 | |
Lytechinus variegatus | GCF_018143015.1 | 869.6 | 36.5 | 38,196 | 33,669 | |
Strongylocentrotus purpuratus | GCF_000002235.5 | 921.8 | 37.5 | 45,168 | 38,439 | |
Holothuroidea | Apostichopus japonicus | GCF_037975245.1 | 671.6 | 37.5 | 57,784 | 45,056 |
Ophiuroidea | Amphiura filiformis | GCF_039555335.1 | 1600.0 | 36.5 | 46,206 | 39,055 |
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Dong, H.; Wan, L.; Wang, C.; Sun, C.; Wang, X.; Xu, L. Transcriptomic Responses of Blue Bat Star Patiria pectinifera to Sediment Burial. Int. J. Mol. Sci. 2025, 26, 5208. https://doi.org/10.3390/ijms26115208
Dong H, Wan L, Wang C, Sun C, Wang X, Xu L. Transcriptomic Responses of Blue Bat Star Patiria pectinifera to Sediment Burial. International Journal of Molecular Sciences. 2025; 26(11):5208. https://doi.org/10.3390/ijms26115208
Chicago/Turabian StyleDong, Han, Linli Wan, Chunsheng Wang, Cong Sun, Xiaogu Wang, and Lin Xu. 2025. "Transcriptomic Responses of Blue Bat Star Patiria pectinifera to Sediment Burial" International Journal of Molecular Sciences 26, no. 11: 5208. https://doi.org/10.3390/ijms26115208
APA StyleDong, H., Wan, L., Wang, C., Sun, C., Wang, X., & Xu, L. (2025). Transcriptomic Responses of Blue Bat Star Patiria pectinifera to Sediment Burial. International Journal of Molecular Sciences, 26(11), 5208. https://doi.org/10.3390/ijms26115208