Coral reefA coral reef is an underwater ecosystem characterized by reef-building corals. Reefs are formed of colonies of coral polyps held together by calcium carbonate. Most coral reefs are built from stony corals, whose polyps cluster in groups. Coral belongs to the class Anthozoa in the animal phylum Cnidaria, which includes sea anemones and jellyfish. Unlike sea anemones, corals secrete hard carbonate exoskeletons that support and protect the coral. Most reefs grow best in warm, shallow, clear, sunny and agitated water.
Coral bleachingCoral bleaching is the process when corals become white due to various stressors, such as changes in temperature, light, or nutrients. Bleaching occurs when coral polyps expel the zooxanthellae (dinoflagellates that are commonly referred to as algae) that live inside their tissue, causing the coral to turn white. The zooxanthellae are photosynthetic, and as the water temperature rises, they begin to produce reactive oxygen species. This is toxic to the coral, so the coral expels the zooxanthellae.
Black coralAntipatharians, also known as black corals or thorn corals, are an order of soft deep-water corals. These corals can be recognized by their jet-black or dark brown chitin skeletons, surrounded by the polyps (part of coral that is alive). Antipatharians are a cosmopolitan order, existing at nearly every location and depth, with the sole exception of brackish waters. However, they are most frequently found on continental slopes under deep. A black coral reproduces both sexually and asexually throughout its lifetime.
CoralCorals are marine invertebrates within the class Anthozoa of the phylum Cnidaria. They typically form compact colonies of many identical individual polyps. Coral species include the important reef builders that inhabit tropical oceans and secrete calcium carbonate to form a hard skeleton. A coral "group" is a colony of very many genetically identical polyps. Each polyp is a sac-like animal typically only a few millimeters in diameter and a few centimeters in height. A set of tentacles surround a central mouth opening.
DNA sequencingDNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. Knowledge of DNA sequences has become indispensable for basic biological research, DNA Genographic Projects and in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematics.
Third-generation sequencingThird-generation sequencing (also known as long-read sequencing) is a class of DNA sequencing methods currently under active development. Third generation sequencing technologies have the capability to produce substantially longer reads than second generation sequencing, also known as next-generation sequencing. Such an advantage has critical implications for both genome science and the study of biology in general. However, third generation sequencing data have much higher error rates than previous technologies, which can complicate downstream genome assembly and analysis of the resulting data.
Massive parallel sequencingMassive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation sequencing. Some of these technologies emerged between 1993 and 1998 and have been commercially available since 2005. These technologies use miniaturized and parallelized platforms for sequencing of 1 million to 43 billion short reads (50 to 400 bases each) per instrument run.
Sanger sequencingSanger sequencing is a method of DNA sequencing that involves electrophoresis and is based on the random incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication. After first being developed by Frederick Sanger and colleagues in 1977, it became the most widely used sequencing method for approximately 40 years. It was first commercialized by Applied Biosystems in 1986. More recently, higher volume Sanger sequencing has been replaced by next generation sequencing methods, especially for large-scale, automated genome analyses.
Whole genome sequencingWhole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast. Whole genome sequencing has largely been used as a research tool, but was being introduced to clinics in 2014.
Climate change adaptationClimate change adaptation is the process of adjusting to the effects of climate change. These can be both current or expected impacts. Adaptation aims to moderate or avoid harm for people. It also aims to exploit opportunities. Humans may also intervene to help adjustment for natural systems. There are many adaptation strategies or options.They can help manage impacts and risks to people and nature. We can classify adaptation actions in four ways. These are infrastructural and technological; institutional; behavioural and cultural; and nature-based options.
Exome sequencingExome sequencing, also known as whole exome sequencing (WES), is a genomic technique for sequencing all of the protein-coding regions of genes in a genome (known as the exome). It consists of two steps: the first step is to select only the subset of DNA that encodes proteins. These regions are known as exons—humans have about 180,000 exons, constituting about 1% of the human genome, or approximately 30 million base pairs. The second step is to sequence the exonic DNA using any high-throughput DNA sequencing technology.
Single-nucleotide polymorphismIn genetics and bioinformatics, a single-nucleotide polymorphism (SNP snɪp; plural SNPs snɪps) is a germline substitution of a single nucleotide at a specific position in the genome that is present in a sufficiently large fraction of considered population (generally regarded as 1% or more). For example, a G nucleotide present at a specific location in a reference genome may be replaced by an A in a minority of individuals. The two possible nucleotide variations of this SNP – G or A – are called alleles.
Clinical metagenomic sequencingClinical metagenomic next-generation sequencing (mNGS) is the comprehensive analysis of microbial and host genetic material (DNA or RNA) in clinical samples from patients by next-generation sequencing. It uses the techniques of metagenomics to identify and characterize the genome of bacteria, fungi, parasites, and viruses without the need for a prior knowledge of a specific pathogen directly from clinical specimens.
GeneIn biology, the word gene (from γένος, génos; meaning generation or birth or gender) can have several different meanings. The Mendelian gene is a basic unit of heredity and the molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and noncoding genes. During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function.
SequencingIn genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succinctly summarizes much of the atomic-level structure of the sequenced molecule. DNA sequencing DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. So far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger.
AdaptationIn biology, adaptation has three related meanings. Firstly, it is the dynamic evolutionary process of natural selection that fits organisms to their environment, enhancing their evolutionary fitness. Secondly, it is a state reached by the population during that process. Thirdly, it is a phenotypic trait or adaptive trait, with a functional role in each individual organism, that is maintained and has evolved through natural selection. Historically, adaptation has been described from the time of the ancient Greek philosophers such as Empedocles and Aristotle.
SpeciesIn biology, a species (: species) is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. It is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. Other ways of defining species include their karyotype, DNA sequence, morphology, behaviour, or ecological niche. In addition, paleontologists use the concept of the chronospecies since fossil reproduction cannot be examined.
Shotgun sequencingIn genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun. The chain-termination method of DNA sequencing ("Sanger sequencing") can only be used for short DNA strands of 100 to 1000 base pairs. Due to this size limit, longer sequences are subdivided into smaller fragments that can be sequenced separately, and these sequences are assembled to give the overall sequence.
Species complexIn biology, a species complex is a group of closely related organisms that are so similar in appearance and other features that the boundaries between them are often unclear. The taxa in the complex may be able to hybridize readily with each other, further blurring any distinctions. Terms that are sometimes used synonymously but have more precise meanings are cryptic species for two or more species hidden under one species name, sibling species for two (or more) species that are each other's closest relative, and species flock for a group of closely related species that live in the same habitat.
Invasive speciesAn invasive or alien species is an introduced species to an environment that becomes overpopulated and harms its new environment. Invasive species adversely affect habitats and bioregions, causing ecological, environmental, and/or economic damage. The term can also be used for native species that become harmful to their native environment after human alterations to its food web - for example, the purple sea urchin (Strongylocentrotus purpuratus) which has decimated kelp forests along the northern California coast due to overharvesting of its natural predator, the California sea otter (Enhydra lutris).
