Graduate Career

In Dr. Zhanjiang (John) Liu’s lab at Auburn University, my research focused on utilizing genomics and bioinformatics to answer ecological and evolutionary questions in catfish. My dissertation involved analyses of walking catfish (Clarias batrachus) genome and transcriptome sequences to reveal genetic basis of its adaptation to transition from water to land. Whole genome sequences of C. batrachus were assembled for comparison with non-air-breathing fishes to identify its specific genomic architecture. In the meantime, transcriptomes of air-breathing organ and water-breathing organ (gill) were sequenced and compared to demonstrate the functional differences between them. Furthermore, I wrote a book chapter summarizing next-generation sequencing and assembly of whole genome sequences, and introducing the usage of several assembly programs. In addition, I worked on QTL analysis of performance traits in catfish, including disease resistance, hypoxia tolerance and fast growth. Especially for fast growth, I identified several QTL and candidate genes through genome-wide association studies (GWAS) and also validated the results using bulk segregant RNA sequencing (BSR-seq). Those candidate genes would provide a useful tool for marker-assisted selection or gene-assisted selectin in catfish industry. Finally, I worked on identification and characterization of olfactory receptors, taste receptors and pheromone receptors in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus) to understand their possible roles in reproductive isolation between these two catfishes.

a. Liu Z, Liu S, Yao J, Bao L, Zhang J, Li Y, Jiang C, Sun L, Zhang Y, Zhou T, Zeng Q, Fu Q, Gao S, Li N, et al. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts[J]. Nature communications, 2016, 7.

b. Wang X, Liu S, Jiang C, Geng X, Zhou T, Li N, Bao L, Li Y, Yao J, Yang Y, Zhong X, Jin Y, Dunham R, Liu Z. Multiple across-strain and within-strain QTLs suggest highly complex genetic architecture for hypoxia tolerance in channel catfish. Molecular genetics and genomics, 2016, 1-14.

c. Gao S, Liu S, Yao J, Li N, Yuan Z, Zhou T, Li Q, Liu Z. Genomic organization and evolution of olfactory receptors and trace amine-associated receptors in channel catfish, Ictalurus punctatus[J]. Biochimica et Biophysica Acta (BBA)-General Subjects, 2016.

d. Gao S, Liu S, Yao J, Zhao T, Li N, Li Q, Dunham R, Liu Z. Taste receptors and gustatory associated G proteins in channel catfish, Ictalurus punctatus[J]. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 2017, 21: 1-9.

e. Gao S, Yuan Z, Li N, Zhang J, Liu Z. Determining Sequence Identities: BLAST, Phylogenetic Analysis, and Syntenic Analyses[J]. Bioinformatics in Aquaculture, 2017.

f. Li N, Wang X, Liu Z. Next-Generation Sequencing Technologies and the Assembly of Short Reads into Reference Genome Sequences[J]. Bioinformatics in Aquaculture, 2017.

g. Zhou T, Li N, Liu S, Jin Y, Fu Q, Gao S, Liu Y, Liu Z. The NCK and ABI adaptor genes in catfish and their involvement in ESC disease response[J]. Developmental & Comparative Immunology, 2017, 73: 119-123.

h. Li N, Zhou T, Geng X, Jin Y, Wang X, Liu S, et al. Identification of novel genes significantly affecting growth in catfish through GWAS analysis[J]. Molecular Genetics and Genomics, 2017: 1-13.

i. Jin Y, Zhou T, Li N, Liu S, Xu X, Pan Y, et al. JAK and STAT members in channel catfish: Identification, phylogenetic analysis and expression profiling after Edwardsiella ictaluri infection[J]. Developmental & Comparative Immunology, 2017.

j. GWAS analysis revealed the association of genes for muscle and bone development with growth in catfish. Conference poster, International Plant & Animal Genome XXV at San Diego, CA, USA, 2017.