Module 14: Microbial Genomics

The genome sequence of an organism can provide information about the organism's __________.

genes, function, and evolutionary history

core genome

genes shared by all strains of the species

Vertical gene transfer

transfer of genes from an organism to its offspring

What is included in the genome?

coding regions of DNA, noncoding regions of DNA, and genes that encode RNAs

16s rRNA

common amplicon sequencing method used to identify and compare bacteria present within a give sample, used for studying phylogeny and taxonomy of samples from complex microbiomes

The field of study that can reveal how genes function, reveal how organisms interact with the environment, and show evolutionary relationships is __________.

comparative genomics

Comparing the different generations of DNA sequencing, which would be most appropriate for a 10 Mbp piece of DNA that could not be fragmented?

fourth generation

Gene duplication is thought to have had a significant influence on the evolution of microbes because __________.

the duplicated gene can be mutated, possibly leading to a useful new gene function or product, while the original copy can still perform its original (and possibly essential) genetic function

genome

All the genetic information in an organism; all of an organism's chromosomes.

DNA polymerase

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule

Horizontal gene transfer refers to the transfer of genes from one organism to another, as occurs during conjugation between bacteria. How does this differ from vertical gene transfer?

In horizontal gene transfer, genes are transferred from one mature adult organism to another. In vertical gene transfer, genes are transferred from adults to offspring.

Researchers discover a new species of bacterium that has an unusual metabolism. However, it has biochemical and morphological similarities to other species. What is the most comprehensive and effective approach to determine how to classify these bacteria?

The bacteria should be classified by using genomic analyses to construct phylogenies.

shotgun sequencing

a method used for sequencing long DNA strands, modified to allow whole genomes to be sequenced completely

template DNA

a strand of DNA that is used to synthesize a complementary strand of DNA or RNA

open reading frame

encodes a protein, a sequence of DNA or RNA that could be translated to give a polypeptide

RNA-Seq method

lets you quantify, discover and profile RNAs. can interrogate more than just differential gene expression. can find new genes for functional analysis.

what can genome sequences reveal about uncultured organisms?

metabolic pathways, energy production, nutrient requirements, and phylogenic relationships

whole genome sequences

process of determing the complete DNA sequence of an organism's genome at a single time

Sanger dideoxy sequencing

serves as an orthogonal method for confirmation sequence variants identified by NGS and provides a means to "patch" the coverage by NGS

metagenomics

the genomic analysis of pooled DNA or RNA from an environmental sample containing organisms that have not been isolated

sequence alignment

the insertion of gaps into a set of molecular sequences organized in rows so that homologous positions are organized in vertical columns

pathogenicity islands

chromosomal islands containing genes for virulence

features of a sequence used to detect an ORF

locate start and stop codons in the sequence, locating potential ribosome-binding sequences in addition to start and stop codons helps decide whether an ORF is functional and which start codon is actually used

If a researcher wanted to compare the enzymatic capacity to degrade compounds in a water column at various depths under a specific set of conditions, which would be the most useful approach?

metaproteomics

horizontal gene transfer

movement of genetic material from a donor organism to a recipient organism that is not its offspring

Sequencing an organism's genome often leads to identification of hypothetical proteins, which are characterized as __________.

proteins that likely exist though their function is unknown

pan genome

the totality of the genes present in the different strains of a species