Exploring Coral Reefs Using the Tools of Molecular Genetics

Abstract

The tools of molecular genetics have been transformed over the last decades and have in turn transformed our understanding of coral reefs. Initially limited to information on single genes, we are now capable of analyzing entire genomes. These developments make it possible to do many things that were either impossible or extremely difficult before: identify cryptic species, microbes, larvae and gut contents; determine relationships among populations and species; characterize reproductive and dispersal patterns; infer mechanisms of speciation; and soon perhaps embark on genetic engineering. Notably, many aspects of coral reef conservation can and will increasingly benefit from insights derived from the application of molecular genetic tools.

Glossary

Some terms and concepts useful for understanding molecular genetic studies.

Barcode

is a standard short stretch of DNA that is unique to each species and therefore used to delineate species or identify unknown specimens. In animals, the most common barcode is a 658 bp segment of the mitochondrial cytochrome c oxidase subunit I gene.

Barcode of Life Data Systems (BOLD)

is an online platform for the storage, analysis and publication of DNA barcode records.

Coalescent theory

uses a mathematical model to reconstruct the genealogy of genes back to their common ancestor.

DNA microarray

analyses are most commonly used to measure the expression levels of a large number of target genes simultaneously. Microarray chips contain thousands of microscopic spots where specific DNA probes are inserted. The relative abundance of target genes is quantified via fluorescence when target DNA hybridizes to probes.

Environmental DNA

is the sum total of DNA in an environmental sample. It comprises not only the DNA from intact organisms in the sample, but also other sources of cellular or extracellular DNA released by an organism into the environment (e.g. in mucus, gametes, feces).

Expressed Sequence Tags (ESTs)

are portions of complementary DNA (cDNA) that are constructed from messenger RNA. These fragments of expressed coding genes are used for gene discovery, mapping, gene prediction, gene expression and polymorphism analysis.

GenBank

is a publicly available collection of DNA sequences hosted by the National Institute of Health (NIH).

Genome

is the entirety of the genetic information contained in an organism.

Genomic library

is the collection of DNA fragments representing the genome of an organism stored as short fragments within many individual bacteria or yeast cells. Such collections facilitated early efforts at genome sequencing .

Genomics

is the quantitative analysis of the genome.

High-throughput sequencing

technologies (i.e. pyrosequencing, semiconductor sequencing ) produce millions of sequences concurrently within a few hours. These technologies have drastically lowered the cost of studies that require large amounts of sequence data .

Metabarcoding

uses DNA-based species identification and high-throughput sequencing as a cost - and time-effective way to infer the species composition of environmental samples (e.g. plankton, sediments).

Metagenomics

is the study of the genetic material collected from the environment. It provides a profile of diversity , including many small organisms that cannot be cultured, and a detailed characterization of the metabolic genes present in an environmental sample.

MicroRNA (miRNA)

are short non-coding RNA molecules (approximately 22 nucleotides in length) found in the genomes of plants, animals and some viruses that play a key role in the regulation of gene expression.

Microsatellites

are short repeating DNA sequences (two to ten base pairs in length) found across the genome of a species. Because they evolve rapidly, they are especially useful for population studies and individual fingerprinting.

Molecular clock

is a mathematical approach that uses the fossil record and rates of DNA sequence evolution to estimate the time since two species or a group of species diverged.

Molecular cloning

is a technique that uses a host organism (easy-to-grow bacteria) to replicate a single DNA molecule into multiple identical copies.

Nuclear DNA/organelle DNA/ribosomal DNA

are different types of DNA found in the nucleus and organelles (such as the mitochondria, mtDNA) of eukaryotic organisms. Ribosomal DNA (rDNA) refers to the genes that code the RNA that makes up the ribosomes.

Operational Taxonomic Units (OTUs)

are low-level taxa often equivalent to species that are defined genetically rather than being identified to species using traditional morphological methods.

Phylogeography

is the study of historical processes (i.e. vicariance, population expansion) that explain the present day distribution of populations or species using mitochondrial/nuclear gene genealogies.

Polymerase Chain Reaction (PCR)

is used to replicate a single copy of a DNA fragment into millions of copies of the same DNA fragment within a few hours, allowing the DNA to be sequenced.

Primers

are strands of nucleic acids used as a starting point for DNA replication during the polymerase chain reaction.

Protein electrophoresis

is a laboratory technique used to separate individual proteins from complex mixtures using differences in size and electric charge. This was one of the first molecular genetic tools to be used in coral reef studies.

Proteomics

is the study of the composition, structure and function of the whole set of proteins produced by the coding genes of an organism.

Restriction-site Associated DNA (or RAD)

sequencing is a method used to sample thousands of random parts of the genome of many individuals simultaneously using high-throughput sequencing. Because it analyzes a small fraction of the entire genome, it allows affordable study of many markers across the genome for population genetic studies in non-model species.

Restriction Fragment Length Polymorphism (RFLP)

analysis is a DNA profiling technique that uses restriction enzymes to cut stretches of DNA at specific genetic sequences within a gene, followed by analysis of variation in the lengths of the fragments.

Sanger Capillary Sequencing

is an automated DNA sequencing technology developed in 1977 by Fred Sanger. It uses a laser to read the position and identity of dye-labeled nucleotides on DNA fragments previously amplified via PCR.

Shotgun Sequencing

is a method used to read the sequence of very long stretches of DNA (i.e. genomes). The process involves shearing the long DNA stretch into smaller fragments (<1000 bp) that can be sequenced individually and later reassembled bioinformatically using overlapping regions.

Single Nucleotide Polymorphism (SNP)

is a genetic variant at one position in a DNA sequence shared by multiple individuals in a population. The frequency of different SNP alleles can be analyzed with respect to such factors as environment or geographic locale.

Transcriptomics

is the study of sets of genes expressed in the genome of a given organism under specific conditions.