Ophioplocus esmarki is one species within a family of brittle stars that includes an abbreviated mode of development with a non-feeding, vitellaria larva. This development contrasts with the ancestral mode that produces a feeding, ophiopluteus larva. This project aims to complete functional annotation of the O. esmarki transcriptome, to provide a comparison of gene classification in both the vitellaria and juvenile stages of development, and to identify developmental neural transcripts through ortholog searches, and verify their identify through phylogenetic analysis. During my undergraduate research, Illumina sequencing was performed at the University of Rochester Genomics Center. The samples underwent RNA isolation, quality checks and were then assembled through Trinity, FastQC, and Trimmomatic tools. Functional annotation was performed using Kyoto Encyclopedia of Genes and Genomes (KEGG), and EuKaryotic Orthologous Groups (KOG), and Gene Ontology (GO) tools. The graduate portion of the research then focused on identifying neural transcripts of interest. To begin, candidate transcripts from the model sea urchin, Strongylocentrotus purpuratus, were identified and run against the de novo transcriptome using a local tblastn search to find similar sequences in the O. esmarki juvenile sample. The transcript identities were then confirmed with the ortholog assignment tool in eggNOG-mapper. Through phylogenetic tree analysis, the identity of the transcripts was then validated by comparing the conserved domains within other species. The significance of this research will provide a greater understanding of O. esmarki through both stages of development, while also determining the key neural transcripts shared with other species.

Library of Congress Subject Headings


Publication Date


Document Type


Student Type


Degree Name

Bioinformatics (MS)

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)


Hyla Sweet

Advisor/Committee Member

Michael Osier

Advisor/Committee Member

Andre Hudson


RIT – Main Campus

Plan Codes