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| Status |
Public on Sep 24, 2024 |
| Title |
Comparative transcriptomic analyses reveal genetic factors underlying susceptibility of largemouth bass to transport stress |
| Organism |
Micropterus salmoides |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Live fish transport often results in mass mortality, but the underlying mechanisms are not well known. Largemouth bass (LMB, Micropterus salmoides) juveniles were subjected to 4-hour transportation followed by 5 days of recovery. Mortality (33.61 ± 10.58 %) of the transported fish mainly occurred between 2 and 3 days of recovery. Except for the dead fish, the survivors demonstrating abnormal symptoms were considered more sensitive to the transport stress than the normal ones. Liver of the abnormal fish had significantly (p < 0.05) lower glutathione (GSH) content and superoxide dismutase (SOD) activity, and irregular cellular morphology. The liver and spleen collected before transportation (T0), at the end of transportation (Te), after 1 day of recovery (R1d), and after 3, 4 and 5 days of recovery (R3d, R4d and R5d, from both the normal and abnormal fish) were subjected to RNA-sequencing. Time series gene expression data of the T0, Te, R1d, R3d-R5d (from the normal fish) samples were analyzed to explore transcriptional responses elicited by the transport stress. Transportation-activated transcriptional regulations could be classified as immediate response (Te), and early (R1d) and late recovery (R3d to R5d) phase in both tissues. High tissue specificity was found for functional enrichments of the up-regulated genes. The up-regulated genes of the liver are highly enriched in cholesterol, sterol and steroid biosynthesis, while those of the spleen are primarily associated with hemopoiesis and immune response. However, large numbers of functional enrichments were shared by the down-regulated genes of the liver and spleen, especially during the recovery phase. Representatives of the depressed processes included neurogenesis, angiogenesis and cell migration, etc. Moreover, large numbers of differentially expressed genes (DEGs) were identified between the normal and abnormal fish. Functional enrichment analyses for the DEGs revealed that failing to terminate the stress responses in the spleen and over depression of the physiological roles of the liver are critical for stress susceptibility of the abnormal fish. Furthermore, an array of core genes associated with stress susceptibility were identified. Our data provide novel insights into the genetic factors underlying susceptibility of LMB to the transport stress.
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| Overall design |
Sampling was performed before transportation (immediately after being netted from the pond, T0), at the end of transportation (Te), and after 1, 3, 4 and 5 d of recovery (R1d, R3d, R4d and R5d). At R3d, R4d and R5d, both normal (NO) and abnormal (AB) fish were sampled. The fish were dissected after being euthanized by immersion in 250 mg/L MS-222. After dissection, the liver (L) and spleen (S) tissues were collected individually. In total, 18 treatment groups and 68 samples were included in the study.
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| Contributor(s) |
Song G, Chen Y, Xiao J, Peng L, Qiao H, Liu S, Luo C, Long Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA1099702 |
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| Submission date |
Sep 20, 2024 |
| Last update date |
Sep 24, 2024 |
| Contact name |
Yong Long |
| E-mail(s) |
longyong@ihb.ac.cn
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| Organization name |
Institute of Hydrobiology, Chinese Academy of Sciences
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| Street address |
No. 7 Donghu South Rd.
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| City |
Wuhan |
| ZIP/Postal code |
430072 |
| Country |
China |
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| Platforms (1) |
| GPL34925 |
Illumina NovaSeq 6000 (Micropterus salmoides) |
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| Samples (68)
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| GSM8526797 |
Liver, before transportation, rep4 |
| GSM8526798 |
Spleen, before transportation, rep1 |
| GSM8526799 |
Spleen, before transportation, rep2 |
| GSM8526800 |
Spleen, before transportation, rep3 |
| GSM8526801 |
Spleen, before transportation, rep4 |
| GSM8526802 |
Liver, at the end of transportation, rep1 |
| GSM8526803 |
Liver, at the end of transportation, rep2 |
| GSM8526804 |
Liver, at the end of transportation, rep3 |
| GSM8526805 |
Liver, at the end of transportation, rep4 |
| GSM8526806 |
Spleen, at the end of transportation, rep1 |
| GSM8526807 |
Spleen, at the end of transportation, rep2 |
| GSM8526808 |
Spleen, at the end of transportation, rep3 |
| GSM8526809 |
Spleen, at the end of transportation, rep4 |
| GSM8526810 |
Liver, 1 day of recovery, rep1 |
| GSM8526811 |
Liver, 1 day of recovery, rep2 |
| GSM8526812 |
Liver, 1 day of recovery, rep3 |
| GSM8526813 |
Liver, 1 day of recovery, rep4 |
| GSM8526814 |
Spleen, 1 day of recovery, rep1 |
| GSM8526815 |
Spleen, 1 day of recovery, rep2 |
| GSM8526816 |
Spleen, 1 day of recovery, rep3 |
| GSM8526817 |
Spleen, 1 day of recovery, rep4 |
| GSM8526818 |
Liver from abnormal fish, 3 days of recovery, rep1 |
| GSM8526819 |
Liver from abnormal fish, 3 days of recovery, rep2 |
| GSM8526820 |
Liver from abnormal fish, 3 days of recovery, rep3 |
| GSM8526821 |
Spleen from abnormal fish, 3 days of recovery, rep1 |
| GSM8526822 |
Spleen from abnormal fish, 3 days of recovery, rep2 |
| GSM8526823 |
Spleen from abnormal fish, 3 days of recovery, rep3 |
| GSM8526824 |
Liver from normal fish, 3 days of recovery, rep1 |
| GSM8526825 |
Liver from normal fish, 3 days of recovery, rep2 |
| GSM8526826 |
Liver from normal fish, 3 days of recovery, rep3 |
| GSM8526827 |
Spleen from normal fish, 3 days of recovery, rep1 |
| GSM8526828 |
Spleen from normal fish, 3 days of recovery, rep2 |
| GSM8526829 |
Spleen from normal fish, 3 days of recovery, rep3 |
| GSM8526830 |
Liver from abnormal fish, 4 days of recovery, rep1 |
| GSM8526831 |
Liver from abnormal fish, 4 days of recovery, rep2 |
| GSM8526832 |
Liver from abnormal fish, 4 days of recovery, rep3 |
| GSM8526833 |
Liver from abnormal fish, 4 days of recovery, rep4 |
| GSM8526834 |
Spleen from abnormal fish, 4 days of recovery, rep1 |
| GSM8526835 |
Spleen from abnormal fish, 4 days of recovery, rep2 |
| GSM8526836 |
Spleen from abnormal fish, 4 days of recovery, rep3 |
| GSM8526837 |
Spleen from abnormal fish, 4 days of recovery, rep4 |
| GSM8526838 |
Liver from normal fish, 4 days of recovery, rep1 |
| GSM8526839 |
Liver from normal fish, 4 days of recovery, rep2 |
| GSM8526840 |
Liver from normal fish, 4 days of recovery, rep3 |
| GSM8526841 |
Liver from normal fish, 4 days of recovery, rep4 |
| GSM8526842 |
Spleen from normal fish, 4 days of recovery, rep1 |
| GSM8526843 |
Spleen from normal fish, 4 days of recovery, rep2 |
| GSM8526844 |
Spleen from normal fish, 4 days of recovery, rep3 |
| GSM8526845 |
Spleen from normal fish, 4 days of recovery, rep4 |
| GSM8526846 |
Liver from abnormal fish, 5 days of recovery, rep1 |
| GSM8526847 |
Liver from abnormal fish, 5 days of recovery, rep2 |
| GSM8526848 |
Liver from abnormal fish, 5 days of recovery, rep3 |
| GSM8526849 |
Liver from abnormal fish, 5 days of recovery, rep4 |
| GSM8526850 |
Spleen from abnormal fish, 5 days of recovery, rep1 |
| GSM8526851 |
Spleen from abnormal fish, 5 days of recovery, rep2 |
| GSM8526852 |
Spleen from abnormal fish, 5 days of recovery, rep3 |
| GSM8526853 |
Spleen from abnormal fish, 5 days of recovery, rep4 |
| GSM8526854 |
Liver from normal fish, 5 days of recovery, rep1 |
| GSM8526855 |
Liver from normal fish, 5 days of recovery, rep2 |
| GSM8526856 |
Liver from normal fish, 5 days of recovery, rep3 |
| GSM8526857 |
Liver from normal fish, 5 days of recovery, rep4 |
| GSM8526858 |
Spleen from normal fish, 5 days of recovery, rep1 |
| GSM8526859 |
Spleen from normal fish, 5 days of recovery, rep2 |
| GSM8526860 |
Spleen from normal fish, 5 days of recovery, rep3 |
| GSM8526861 |
Spleen from normal fish, 5 days of recovery, rep4 |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE277644_Abundance.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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