Bioproject ID: PRJNA647859

bioproject id PRJNA647859      to NCBI
key word low oxygen;air-breathing, mRNA-seq, tra catfish, terrestrial adaptation, low-oxygen tolerance
experiment type low oxygen
publication Ma X et al., "Comparative Transcriptome Analysis During the Seven Developmental Stages of Channel Catfish (Ictalurus punctatus) and Tra Catfish (Pangasianodon hypophthalmus) Provides Novel Insights for Terrestrial Adaptation.", Front Genet, 2020;11:608325
description Channel catfish (Ictalurus punctatus) and tra catfish (Pangasianodon hypophthalmus) both belong to the order Siluriformes. Channel catfish does not possess an air-breathing organ (ABO), and thus cannot breathe in the air, while tra catfish is a facultative air-breather and use the swim bladder as its air-breathing organ, which provides for aerial breathing in low oxygen conditions. Tra and channel catfish serve as a great comparative model for studying the transition of life from water to terrestrial living, as well as for understanding genes that are crucial for development of the swim bladder and the function of air-breathing in tra catfish. We selected seven developmental stages in tra catfish for RNA-Seq analysis based on their transition to a stage that could live at 0 ppm oxygen. More than 587 million sequencing clean reads were generated in tra catfish, and a total of 21, 448 unique genes were detected. A comparative genomic analysis was conducted between channel catfish and tra catfish. Gene expression analysis was performed for these tra catfish specific genes. Hypoxia challenge and microtomy experiments collectively suggested that there are critical timepoints for the development of the air-breathing function and swim bladder development stages in tra catfish. Key genes were identified to be the best candidates of genes related to the air-breathing ability in tra catfish. This study provides a large data resource for functional genomic studies in air-breathing function in tra catfish, and sheds light on the adaption of aquatic organisms to the terrestrial environment. Overall design: Profile of transcriptome-wide gene expression levels in seven early development stages of Pangasianodon hypophthalmus
abstract Tra catfish (Pangasianodon hypophthalmus), also known as striped catfish, is a facultative air-breather that uses its swim bladder as an air-breathing organ (ABO). A related species in the same order (Siluriformes), channel catfish (Ictalurus punctatus), does not possess an ABO and thus cannot breathe in the air. Tra and channel catfish serve as great comparative models for investigating possible genetic underpinnings of aquatic to land transitions, as well as for understanding genes that are crucial for the development of the swim bladder and the function of air-breathing in tra catfish. In this study, hypoxia challenge and microtomy experiments collectively revealed critical time points for the development of the air-breathing function and swim bladder in tra catfish. Seven developmental stages in tra catfish were selected for RNA-seq analysis based on their transition to a stage that could live at 0 ppm oxygen. More than 587 million sequencing clean reads were generated, and a total of 21,448 unique genes were detected. A comparative genomic analysis between channel catfish and tra catfish revealed 76 genes that were present in tra catfish, but absent from channel catfish. In order to further narrow down the list of these candidate genes, gene expression analysis was performed for these tra catfish-specific genes. Fourteen genes were inferred to be important for air-breathing. Of these, HRG, GRP, and CX3CL1 were identified to be the most likely genes related to air-breathing ability in tra catfish. This study provides a foundational data resource for functional genomic studies in air-breathing function in tra catfish and sheds light on the adaptation of aquatic organisms to the terrestrial environment.

Sample Information

sample id sample name tissue strain treatment description
1. SRR12287823 GSM4682421 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 2dpf_rep1
2. SRR12287824 GSM4682422 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 2dpf_rep2
3. SRR12287825 GSM4682423 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 4dpf_rep1
4. SRR12287826 GSM4682424 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 4dpf_rep2
5. SRR12287827 GSM4682425 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 6dpf_rep1
6. SRR12287828 GSM4682426 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 6dpf_rep2
7. SRR12287829 GSM4682427 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 8dpf_rep1
8. SRR12287830 GSM4682428 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 8dpf_rep2
9. SRR12287831 GSM4682429 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 9dpf_rep1
10. SRR12287832 GSM4682430 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 9dpf_rep2
11. SRR12287833 GSM4682431 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 10dpf_rep1
12. SRR12287834 GSM4682432 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 10dpf_rep2
13. SRR12287835 GSM4682433 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 11dpf_rep1
14. SRR12287836 GSM4682434 whole-body nan Low-Oxygen (Anoxia) Challenge Pangasianodon hypophthalmus 11dpf_rep2