An organized nucleus is absent in both Cyanophyta and Prochlorophyta, where DNA molecules are free in the cytoplasm. The central region of those algae features the naked (without histone proteins) circular DNA genome, which is not contained within a double membrane, and consists of a single unbranched molecule. Transcription and translation processes are accomplished by the assistance of abundant 70S ribosomes located in the centroplasm. These ribosomes are smaller than their counterparts in the eukaryotic cytoplasm, but are typical of all prokaryotes, mitocondria, and chloroplasts. Cyanobacteria can only reproduce asexually, but appear to have some forms of genetic recombination possible, which are divided into two categories: transformation and conjugation. Transformation occurs when DNA is shed by one cell into the environment and is taken up by another cell and incorporated into its genome replacing homologous sections of DNA. The ability to be transformed by external DNA is specie-specific and typically requires special environmental conditions. Conjugation is a “parasexual” process in which one of the partners develops a conjugation tube that connects to the recipient cell. Typically a plasmid (a small circle of DNA) from the donor cell passes through the conjugation tube. It is thought that genes for gas vacuolation, antibiotic resistance, and toxin production are carried on plasmids in cyanobacteria.

In eukaryotic algae genetic information in the form of DNA, together with the controlling services for its selective expression, occurs in plastids (plastome), mitochondria (chondrome), and in the cell nucleus (genome). In the previous section, we have described organization and behavior of chloroplast DNA, which are similar to those of mitochondria. It is worthwhile to recall that plastid and mithocondrial genes and the way in which they are expressed have much in common with the system of gene expression of prokaryotes, and there are many plastid genes with extended introns that are very rare in prokaryotes (genes are mosaics of introns and exons. Introns are the DNA sequences of unknown function that are removed in the primary mRNA transcript. Exons are the DNA sequences that code for amino acids). In the nucleus of eukaryotic algae, long, linear, and unbranched molecules of DNA are associated with proteins and small amount of RNA. Two types of proteins are found: the relatively uniform histones (about 20), involved in the structural organization of the DNA, and the very variable proteins involved in gene activity regulation, such as DNA and RNA polymerases.

The DNA– protein complex, made up of repeating units termed nucleosomes, is known as chromatin, which is usually highly dispersed in the interphase nucleus. During mitosis and meiosis metaphases the DNA–protein complexes are more helically condensed around the nucleosome and form the chromosomes, each chromosome consisting of a single DNA molecule.

The nucleus is surrounded by a two-membrane envelope continuous with the endoplasmic reticulum. Between the two membranes there is a narrow perinuclear space about 20 nm wide. The nuclear envelope is perforated by numerous pores 60–100 nm in diameter. Nuclear pores have a complicated superstructure; they are not simply free openings, but are gateways in nuclear envelope through which the controlled transport of macromolecules (RNA, proteins) takes place. Pores can be arranged in straight lines as in Bumilleria (Xanthophyceae, Heterokontophyta), in closely hexagonal groups as in Prorocentrum (Dinophyta), or can be randomly distributed as in Glenodinium (Dinophyta).

All algal nuclei possess nucleoli that vary in shape, size, and number in the different algal divisions. Nucleoli are dense concentrations of ribonucleoprotein-rich material, which are intimately associated with the specific region of the chromosomal DNA coding for ribosomal RNA. Nucleoli can be single and central as in Cryptomonas (Cryptophyta) or be more than 20 scattered in the nucleus as in Euglena acus (Euglenophyta).

In eukaryotic algae, the features of the interphase nucleus, DNA replication, and processes of transcription and translation in the expression of genetic information and cytokinesis are comparable with those of all the other eukaryotes. Exceptions to this rule will be described.

Rhodophyta
The basic features of mitosis and cytokinesis are the same throughout the division, though some variation may occur. Unlike other groups of eukaryotic algae, where the mitotic spindle is formed between two pairs of centrioles, one at each spindle pole, in red algae the poles of the spindle are marked by ring-shaped structures named polar rings. The absence of centrioles reflects the complete absence of flagella in the red algae. The chromosomal and interzonal microtubules do not converge towards the polar rings, so that the spindle poles are very broad. The nuclear envelope does not break down, though it is perforated by large holes, hence the mitosis is closed. The spindle persists for some time at early telophase, holding daughter nuclei apart; it collapses only at late telophase, when daughter nuclei are kept separated by a vacuole. Cytokinesis is by furrowing, but is typically incomplete; the furrow impinges upon the vacuole but leaves open a cytoplasmic connection between sibling cells. This connection is then filled and blocked by a proteinaceous stopper, named pit plug. The simplest type of pit plug consists only of a proteinaceous core; two- or one-layered caps partly composed of polysaccharides can border the core of both sides with different thickness. Acap membrane can be present between the two layers of the cap or bounding the plug core.

Cryptophyta
These algae possess a peculiar organelle termed nucleomorph located in the space between the chloroplast endoplasmic reticulum and the chloroplast envelope. This organelle has a double membrane around it, pierced by pores and contains both DNA and a nucleolus-like structure where rRNA genes are transcribed. The DNA is organized in three small chromosomes encoding genes for its own maintenance. It possesses the ability to self-replicate, without forming a spindle during mitosis. It is considered a vestigial nucleus belonging to a photosynthetic eukaryotic symbiont.

Dinophyta
The dinoflagellate nucleus, known as dinokaryon, is bounded in the usual eukaryotic fashion by a nuclear envelope penetrated by pores. However, it possesses a number of unusual features, including high amounts of DNA per cell (five to ten times the most common eukaryotic levels, up to a maximum of 200 pg in Gonyaulax polyedra). It is relatively large, often occupying about one half of the volume of the cell. Nuclear shapes are variable, ranging from spheroid to U-, V-, or Y- shaped configurations. In most dinoflagellates the chromosomes remain continuously condensed and visible, by both light and electron microscopy, during interphase and mitosis. Chromosome counts range from 12 to around 400, but may be variable within a species. A prominent nucleolus is also persistent. Each chromosome consists of a tightly super-coiled structure of DNA double helix. The permanent condensed chromosome shows a swirled, fibrillar appearance due to the naked DNA double helices (i.e., no histones are present). The 3–6 nm fibrils are packed in a highly ordered state, up to six level of coiling. A small amount of basic protein is present in a few species, such as Oxyrrhis marina, but none of it corresponds in amino acid content to the histones normally present in eukaryotic chromosomes. A further peculiarity of dinoflagellate chromosomes is the high amount of calcium and other divalent metals, such as iron, nickel, or copper, which may play a role in chromosomal organization. In some dinoflagellate, such as Noctiluca and Blastodinium, the chromosomes undergo an expanded, decondensed change during interphase and are termed noctikaryotic.

Dinoflagellate mitosis is also unusual. At the time of division, chromosomes divide longitudinally, the split starting at one end of the chromosome and moving along the entire length. The nucleus is invaded by cytoplasmic channels that pass from one pole to the other. Microtubules are present in these channels. The nuclear envelope and the nucleolus are persistent throughout nuclear division. The chromosomes upon dividing assume a V- or Y-configuration, and the apices of such chromosomes are closely associated with the nuclear envelope surrounding a cytoplasmic channel. This association suggests that the cytoplasmic channels serve as mechanism for the movement of chromosomes.

The nuclear envelope persists during mitosis (closed mitosis), as it does in other algae, for example, Euglenophyta and Raphidophyceae. However, with the exception of O. marina, where mitotic spindle is intranuclear, the chromosomes do not appear fibrillar, and the mitosis strongly resembles that of Euglena, the mitotic spindle is always extranuclear. The spindle microtubules pass through furrows and tunnels that form in the nucleus at prophase. No obvious spindle pole bodies other than concentric aggregation of Golgi bodies are present. Some microtubules contact the nuclear envelope, lining the tunnels at points where the chromosomes also contact. The chromosomes have differentiated dense regions inserted into the envelope.

Dinoflagellate cells undergo binary fission, and each daughter cell can retain half the parent cell wall, which splits along a predetermined fission line. This mode of reproduction is called “desmoschisis,” and examples are Ceratium and many Gonyaulax species. In other dinoflagellates, daughter cells do not share the parent cell wall; this mode of division is called “eleutheroschisis.” Binary fission may take place either inside the mother cell (many freshwater Peridinium species), or the protoplast may leave the mother cell wall before division through a hole or slit. In thecate species (many marine Protoperidinium species) the protoplast escapes, after special thecal plates are dislocated, through a hole. In several species the protoplast has no flagella and deforms its cell wall during the escape from the mother theca; however, this is not a typical ameboid stage. After cell division, each daughter cell produces a new cell wall, or a new theca in thecate cells.