Ribosomal DNA in the context of "Rhizaria"

Marine fungi are species of fungi that live in marine or estuarine environments. They are not a taxonomic group, but share a common habitat. Obligate marine fungi grow exclusively in the marine habitat while wholly or sporadically submerged in sea water. Facultative marine fungi normally occupy terrestrial or freshwater habitats, but are capable of living or even sporulating in a marine habitat.

Marine fungi account for about 5% of the total ocean biomass. About 2,149 species of marine fungi have been described, within eleven phyla and 856 genera, although only about 64 species have been fully genetically sequenced. Many species of marine fungi are known only from spores and it is likely a large number of species have yet to be discovered. It has been estimated that less than 1% of all marine fungal species have been described, due to difficulty in targeting marine fungal DNA and difficulties that arise in attempting to grow cultures of marine fungi. It is impracticable to culture many of these fungi, but their nature can be investigated by examining seawater samples and undertaking rDNA analysis of the fungal material found.

Foraminifera (/fəˌræməˈnɪfərə/ fə-RAM-ə-NIH-fə-rə; Latin for "hole bearers"; informally called "forams") are single-celled organisms, members of a phylum or class of Rhizarian protists characterized by streaming granular ectoplasm for catching food and other uses; and commonly an external shell called a test of diverse forms and materials. Tests of chitin (found in some simple genera, and Textularia in particular) are believed to be the most primitive type. Most foraminifera are marine, the majority of which live on or within the seafloor sediment (i.e., are benthic, with different sized species playing a role within the macrobenthos, meiobenthos, and microbenthos), while a smaller number float in the water column at various depths (i.e., are planktonic), which belong to the suborder Globigerinina. Fewer are known from freshwater or brackish conditions, and some very few (nonaquatic) soil species have been identified through molecular analysis of small subunit ribosomal DNA.

Foraminifera typically produce a foraminifera test, or shell, which can have either one or multiple chambers, some becoming quite elaborate in structure. These shells are commonly made of calcium carbonate (CaCO
₃) or agglutinated sediment particles. Over 50,000 species are recognized, both living (6,700–10,000) and fossil (40,000). They are usually less than 1 mm in size, but some are much larger, the largest species reaching up to 20 cm.

Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits. rRNA is the physical and mechanical factor of the ribosome that forces transfer RNA (tRNA) and messenger RNA (mRNA) to process and translate the latter into proteins. Ribosomal RNA is the predominant form of RNA found in most cells; it makes up about 80% of cellular RNA despite never being translated into proteins itself. Ribosomes are composed of approximately 60% rRNA and 40% ribosomal proteins, though this ratio differs between prokaryotes and eukaryotes.

Nannochloropsis is a genus of algae comprising six known species. The genus in the current taxonomic classification was first termed by Hibberd (1981). The species have mostly been known from the marine environment but also occur in fresh and brackish water. All of the species are small, nonmotile spheres which do not express any distinct morphological features that can be distinguished by either light or electron microscopy. The characterisation is mostly done by rbcL gene and 18S rRNA sequence analysis.

The algae of the genus Nannochloropsis differ from other related microalgae in that they have chlorophyll a and completely lack chlorophyll b and chlorophyll c. In addition they are able to build up a high concentrations of a range of pigments such as astaxanthin, zeaxanthin and canthaxanthin. They have a diameter of about 2 to 3 micrometers and a very simple ultrastructure with reduced structural elements compared to neighbouring taxa.

Spacer DNA is a region of non-coding DNA between genes. The terms intergenic spacer (IGS) or non-transcribed spacer (NTS) are used particularly for the spacer DNA between the many tandemly repeated copies of the ribosomal RNA genes.

In bacteria, spacer DNA sequences are only a few nucleotides long. In eukaryotes, they can be extensive and include repetitive DNA, comprising the majority of the DNA of the genome. In ribosomal DNA, there are spacers within and between gene clusters, called internal transcribed spacer (ITS) and external transcribed spacers (ETS), respectively. In animals, the mitochondrial DNA genes generally have very short spacers. In fungi, mitochondrial DNA spacers are common and variable in length, and they may also be mobile.