Date of Award

Spring 5-6-2014

Degree Type


Degree Name

MS Biology




Dr. Ziping Zhang

Committee Member

Dr. Jane Ko

Committee Member

Dr. Angela Klaus

Committee Member

Dr. Jessica Cottrell


Transcriptome, Sea Lamprey, Embryogenesis, Cytoscape, Bioinformatics, Genes


The sea lamprey (Petromyzon marinus) has survived throughout evolution for hundreds of millions of years. It is considered an invasive species to the Great Lakes that has caused dramatic changes in the ecosystem for fish communities resulting in the collapse of a fishing industry that was previously valued at billions of dollars. Successful management of the sea lamprey is essential to a sustainable fishing industry and biodiversity. Therefore sea lamprey embryos were studied at various stages of development by growing them in a simulated habitat. RNAs from adult female ovaries and embryos at different time points during embryogenesis were extracted and then subjected to Next Generation Sequencing (NGS). Approximately 14,000 transcripts in total were detected. Data from each stage was analyzed using log2 values to determine significant gene expression levels on FPKM values, which are fragments of transcripts derived from cDNA. Genes with greater than threefold changes from previous adjacent stages, were analyzed using Cytoscape, an open source network program to further verify their functional roles. Genes TGFBR1 (protein kinase), SMAD2 (signal transducer), TRAF6 (signal transducer), PCNA (DNA replication), SLX4 (endonuclease), and PXN (focal adhesion) were selected for their NGS expression levels, GO annotations, and biological function significance. Their NGS expression levels were verified using Real-Time PCR (qPCR). TGFBR1 was up-regulated in the Neurula/Egg and Gall Bladder/Eye Spot stage comparisons. PXN was up-regulated in the Neurula/Egg and Hatching/Head Protrusion comparisons. SMAD2 and TRAF6 were up-regulated in the Melanophore/Hatching, PCNA in the Completion/Gall Bladder, and SLX4 in the Eye Spot/Melanophore comparisons. This transcriptome analysis serves as a starting point for determining vital genes in sea lamprey embryogenesis and controlling the sea lamprey population.