Genom glossary

• A factor that is produced by a pathogen and required for it to cause disease. It should be noted that defining this term precisely is difficult.

• An organism that can cause disease in another organism.

• A cluster of genes acquired by horizontal gene transfer that encodes products that contribute to virulence.

• The simplest type of transposable element in bacteria. It contains only the genes required for its own transposition.

• Any process in which an organism transfers genetic material to another cell that is not its offspring. This process is in contrast to vertical gene transfer, which is much more common and occurs when genetic material is passed from parent to offspring or, more generally, from ancestor to descendent.

• Specific genes to single strains

• Genes present in two or more strains, but not in all

• The total of gene sets of all strains in a clade. • Includes the core genome, dispensable genome and unique genes (singletons).

• High-throughput sequencing method that parallelizes the sequencing process to produce millions of sequences at once.

• Sanger sequencing aka Chain termination sequencing

• Method for closing gaps in genomes using Sanger sequencing. Slow progress through repetitive cycles of sequencing and primer design

• Amount of “free space” on the genome.

• Coding sequence, i.e. a region on the genome that is translated into a protein.

• The collective DNA sequences of an organism.

• Study of metagenomes, genetic material recovered directly from environmental samples.

• Study of the collection of all metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes.

• Study of the entire complement of proteins, including the modifications made to a particular set of proteins, produced by an organism or system.

• Study of the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells under a given condition.

• Study of the set of all DNA molecules in one or a population of cells.

• Field of science in which biology, computer science, and information technology merge to form a single discipline. The ultimate goal of the field is to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned.• Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software engineering, data mining, image processing, modeling and simulation, signal processing, discrete mathematics, control and system theory, circuit theory, and statistics, for generating new knowledge of biology and medicine, and improving & discovering new models of computation (e.g. DNA computing, neural computing, evolutionary computing, immuno-computing, swarm-computing, cellular-computing).

• Various measurements of the environment where the metagenomic sample was collected.

• branch of science that encompasses the description, identification, nomenclature, and classification of organisms

• Direct sequencing of environmental DNA• Study of two aspects: taxonomic content (who is there?) and functional content (what can they do??)

• Also called targeted sequencing of marker genes• Study of selected marker gene(s) after PCR amplification from environmental DNA.

• Study of total (microbial) RNA from environmental samples.

• Also called community genomics• Study of metagenomes, genetic material recovered directly from environmental samples.• Seeks to understand microbial ecosystems by studying the genomic content of the constituent microbes in their natural community setting.

• Separated by a gene duplication event: if a gene in an organism is duplicated to occupy two different positions in the same genome, then the two copies are paralogous.• Provides insight into “evolutionary innovation”(adapting a pre-existing gene product for a new function).

• Sequences are direct descendants of a sequence in a common ancestor.• Separated by a speciation event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous.• Most likely have similar domain structure, three-dimensional structure, and biological function.

• Shared ancestry between protein or DNA sequences.• Genes are or are not homologous (not measured in degrees)

• Quantitative measure of relatedness between nucleotide or amino acid sequences (% sequence identity).• Allows quantifying changes that occur as two sequences diverge (e.g. substitutions, insertions, deletions).• Identification of residues crucial for maintaining a protein’s structure or function.• High degrees of sequence similarity might imply a common evolutionary history and possible commonality in biological function.

• Structured system of controlled vocabularies.

• A measure that reflects bias for guanine bases on the leading strand of DNA and cytosine bases on the lagging strand.

• Genes present in all strains

• Percentage of guanine and cytosine residues within a genome.

• A variation between two genomes that involves a single base pair.

• A genome that went through the finishing stage, and is a complete representation of all DNA sequences in the sequenced organism.

• The final phase in a genome-sequencing project, in which all gaps between contigs are closed and all ambiguities are resolved. This is much more labor-intensive than the shotgun phase, so the sequencing of many genomes is now left unfinished.

• A genome that has been assembled into a number of contigs. Gaps can represent variable amounts of missing information.

• A set of contigs ordered by linking information.