Developing the MAR databases – Augmenting Genomic Versatility of Sequenced Marine Microbiota

Abstract

This thesis introduces the MAR databases as marine-specific resources in the genomic landscape. Paper 1 describes the curation effort and development leading to the MAR databases being created. It results in the highly valued reference database MarRef, the broader MarDB, and the marine gene catalog MarCat. Definition of a marine environment, the curation process, and the Marine Metagenomics Portal as a public web-service are described. It facilitates scientists to find marine sequence data for prokaryotes and to explore rich contextual information, secondary metabolites, updated taxonomy, and helps in evaluating genome quality. Many of these database advancements are covered in Paper 2. This includes new entries and development of specific databases on marine fungi (MarFun) and salmon related prokaryotes (SalDB). With the implementation of metagenome assembled and single amplified genomes it leads up to the database quality evaluation discussed in Paper 3. The lack of quality control in primary databases is here discussed based on estimated completeness and contamination in the genomes of the MAR databases. Paper 4 explores the microbiota of skin and gut mucosa of Atlantic salmon. By using a database dependent amplicon analysis, the full-length 16 rRNA gene proved accurate, but not a game-changer in taxonomic classification for this environmental niche. The proportion of dataset sequences lacking clear taxonomic classification suggests lack of diversity in current-day databases and inadequate phylogenetic resolution. Advancing phylogenetic resolution was the subject of Paper 5. Here the highly similar species of genus Aliivibrio became delineated using six genes in a multilocus sequence analysis. Five potentially novel species could in this way be delineated, which coincided with recent genome-wide taxonomy listings. Thus, Paper 4 and 5 parallel those of the MAR databases by providing insight into the inter-relational framework of bioinformatic analysis and marine database sources.