Novel ‘omic Approaches for Identification and Evolution of Deep-Sea Corals

PROJECT DESCRIPTION:

Corals live in a variety of environments, from shallow tropical seas to the deep cold abyss. This project will help advance knowledge of the evolution and identification of corals in the deep sea. Using home computers/laptops, interns will use command line skills to mine existing data for ribosomal RNA genes and genes under positive selection within corals. This will involve genomic data mining, transcript/gene sequence alignments using bioinformatic programs, and gene annotation (i.e., BLAST) to facilitate target-capture bait design and genomic skimming efforts. This project will incorporate other methods including gene prediction analyses, orthologous sequence identification, SNP analysis, phylogenetic tree building efforts and tests for selection. Results gathered from this project will be used to create a target-enrichment bait set to test for directional selection across depth. In addition, new primers will be designed to identify corals from environmental DNA.

STUDENT PREREQUISITES & REQUIREMENTS:

The intern would preferably have some experience with command line skills and some exposure to bioinformatic programs and/or R software. A home/computer or laptop (OSx preferred) is necessary.

LEARNING OBJECTIVES:

The interns will learn how to use genomic-scale data to address questions in evolutionary biology of corals. They will also learn command line skills, and commonly-used tools in ‘omic fields. The interns will also learn general coral biology and taxonomy.

TIME REQUIREMENTS: 15-20 hours a week for 10 weeks.

AWARD: $3,000 Stipend

TENURE: Preferred start is October 2020.

HOW TO APPLY:

Please send CV and paragraph describing your interest in the internship to Andrea Quattrini quattrinia@si.edu and Danielle DeLeo deleod@si.edu

CONTACT INFORMATION

Name: Andrea Quattrini
Phone: 910-520-7264
E-mail: quattrinia@si.edu