Award: OCE-1046371

DIMENSIONS: Collaborative Research, ­Uncovering the novel diversity of the copepod microbiome and its effect on habitat invasions by the copepod host Project # 1046371 Project PI: Joana C. Silva This proposal was part of a Collaborative Research on Dimensions of Biodiversity. The current project took place at the Institute for Genome Sciences, University of Maryland School of Medicine. The collaborative proposal, with Project # 1046372, was led by Dr. Carol E. Lee, at the University of Wisconsin. PROJECT OUTCOMES REPORT DATA GENERATED Genomics or transcriptomics data were generated for the four studies listed below. 1. The adult transcritome, and sex-related differential gene expression in the common copepod, Eurytemora affinis. As part of this study, transcriptomics data in the form of RNAseq (total of 2.2x109 Illumina sequence reads) were generated for an inbred line of laboratory-reared E. affinis. Replicates were done for males, females and mixed adults. Data stored under BioProject ID PRJNA278152. 2. Exploring regulatory mechanisms underlying evolutionary shifts in gene expression during saline to freshwater invasions by the copepod E. affinis. As part of this study, transcriptomics data in the form of RNAseq (2.7x109 Illumina sequence reads) were generated for several fresh and salt water populations. Replicates included single-sex, outbred, parental individuals and F1 hybrids. Data stored under BioProject ID PRJNA278152. 3. The microbiome of the common copepod, Eurytemora affinis, and that of the surrounding water, in freshwater and saltwater environments. As part of this study, 16S rDNA sequence data (8.8x109 Illumina sequence reads) were generated for paired samples of E. affinis and surrounding water from several fresh and salt water copepod populations, from the Gulf of Mexico to the St. Lawrence River system. For each location replicates for both copepod and water were generated. Data stored under BioProject ID 309119. 4. Impact of library construction protocol, number of libraries and sequencing platform on the quality of metagenome assemblies. For total DNA collected from a single sample of water, several genomic libraries were generated for sequencing with the following platforms Illumina HiSeq and MiSeq, 454 Pyrosequencing and Pacific Biosciences. Metagenomics data (62.5x1010 bp from a combination of all sequencing platforms) was stored under BioProject ID 309119. TRAINING Pre-doctoral Six pre-doctoral trainees, from high-school, community college and four-year college programs, were trained in a variety of topics related to high-throughput sequencing, genomics and transcriptomics, including molecular biology techniques, genome structural annotation and transcriptomics data analysis. Current position of trainees includes a graduate from an Ivy League school, a Physician?s Assistant with the U.S. Army, a medical school student and two software engineers. Doctoral Three University of Wisconsin, Madison, doctoral students attended genomics/transcriptomics workshops and/or were trained on the analysis of genomics/transcriptomics data. They have all graduated. Post-doctoral One post-doctoral fellow at the Institute for Genome Sciences, University of Maryland School of Medicine (UMSOM), was trained in genomics and bioinformatics, transcriptomics, focusing on olfactory receptors and differential gene expression analysis. He is currently a Bioinformatics Analyst. Another post-doctoral fellow, from the Center for Biotechnology, University of Nebraska–Lincoln, used transcriptomics data generated by this project in his project on the evolution of olfaction. MANUSCRIPTS The students, fellows and the PI supported directly through this award participated, so far, 10 manuscripts published, submitted or in preparation. Last Modified: 06/17/2019 Submitted by: Joana C Carneiro Da Silva