A chloroplast is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in the energy-storage molecules ATP and NADPH while freeing oxygen from water in the cells. The ATP and NADPH is then used to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis, amino acid synthesis, and the immune response in plants. The number of chloroplasts per cell varies from one, in unicellular algae, up to 100 in plants like Arabidopsis and wheat.
Symbiogenesis is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possibly other organelles of eukaryotic cells are descended from formerly free-living prokaryotes taken one inside the other in endosymbiosis. Mitochondria appear to be phylogenetically related to Rickettsiales bacteria, while chloroplasts are thought to be related to cyanobacteria.
A plastid, pl. plastids, is a membrane-bound organelle found in the cells of plants, algae, and some other eukaryotic organisms;. They are considered to be intracellular endosymbiotic cyanobacteria.
Nucleomorphs are small, vestigial eukaryotic nuclei found between the inner and outer pairs of membranes in certain plastids. They are thought to be vestiges of primitive red and green algal nuclei that were engulfed by a larger eukaryote. Because the nucleomorph lies between two sets of membranes, nucleomorphs support the endosymbiotic theory and are evidence that the plastids containing them are complex plastids. Having two sets of membranes indicate that the plastid, a prokaryote, was engulfed by a eukaryote, an alga, which was then engulfed by another eukaryote, the host cell, making the plastid an example of secondary endosymbiosis.
The green algae are a group of chlorophyll-containing autotrophic eukaryotes consisting of the phylum Prasinodermophyta and its unnamed sister group that contains the Chlorophyta and Charophyta/Streptophyta. The land plants (Embryophytes) have emerged deep in the Charophyte alga as a sister of the Zygnematophyceae. Since the realization that the Embryophytes emerged within the green algae, some authors are starting to include them. The completed clade that includes both green algae and embryophytes is monophyletic and is referred to as the clade Viridiplantae and as the kingdom Plantae. The green algae include unicellular and colonial flagellates, most with two flagella per cell, as well as various colonial, coccoid and filamentous forms, and macroscopic, multicellular seaweeds. There are about 22,000 species of green algae, many of which live most of their lives as single cells, while other species form coenobia (colonies), long filaments, or highly differentiated macroscopic seaweeds.
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal gene transfer event (xenologs).
Viridiplantae constitute a clade of eukaryotic organisms that comprises approximately 450,000–500,000 species that play important roles in both terrestrial and aquatic ecosystems. They include the green algae, which are primarily aquatic, and the land plants (embryophytes), which emerged from within them. Green algae traditionally excludes the land plants, rendering them a paraphyletic group. However it is accurate to think of land plants as a kind of alga. Since the realization that the embryophytes emerged from within the green algae, some authors are starting to include them. They have cells with cellulose in their cell walls, and primary chloroplasts derived from endosymbiosis with cyanobacteria that contain chlorophylls a and b and lack phycobilins. Corroborating this, a basal phagotroph archaeplastida group has been found in the Rhodelphydia.
Hydnoroideae is a subfamily of parasitic flowering plants in the order Piperales. Traditionally, and as recently as the APG III system it given family rank under the name Hydnoraceae. It is now submerged in the Aristolochiaceae. It contains two genera, Hydnora and Prosopanche:
The Archaeplastida are a major group of eukaryotes, comprising the photoautotrophic red algae (Rhodophyta), green algae, land plants, and the minor group glaucophytes. It also includes the non-photosynthetic lineage Rhodelphidia, a predatorial (eukaryotrophic) flagellate that is sister to the Rhodophyta, and probably the microscopic picozoans. The Archaeplastida have chloroplasts that are surrounded by two membranes, suggesting that they were acquired directly through a single endosymbiosis event by phagocytosis of a cyanobacterium. All other groups which have chloroplasts, besides the amoeboid genus Paulinella, have chloroplasts surrounded by three or four membranes, suggesting they were acquired secondarily from red or green algae. Unlike red and green algae, glaucophytes have never been involved in secondary endosymbiosis events.
The Mesostigmatophyceae are a class of basal green algae found in freshwater. In a narrow circumscription, the class contains a single genus, Mesostigma. AlgaeBase then places the order within its circumscription of Charophyta. A clade containing Chlorokybus and Spirotaenia may either be added, or treated as a sister, with Chlorokybus placed in a separate class, Chlorokybophyceae. When broadly circumscribed, Mesostigmatophyceae may be placed as sister to all other green algae, or as sister to all Streptophyta.
Plant evolution is the subset of evolutionary phenomena that concern plants. Evolutionary phenomena are characteristics of populations that are described by averages, medians, distributions, and other statistical methods. This distinguishes plant evolution from plant development, a branch of developmental biology which concerns the changes that individuals go through in their lives. The study of plant evolution attempts to explain how the present diversity of plants arose over geologic time. It includes the study of genetic change and the consequent variation that often results in speciation, one of the most important types of radiation into taxonomic groups called clades. A description of radiation is called a phylogeny and is often represented by type of diagram called a phylogenetic tree.
Red algae, or Rhodophyta, are one of the oldest groups of eukaryotic algae. The Rhodophyta comprises one of the largest phyla of algae, containing over 7,000 currently recognized species with taxonomic revisions ongoing. The majority of species (6,793) are found in the Florideophyceae (class), and mostly consist of multicellular, marine algae, including many notable seaweeds. Red algae are abundant in marine habitats but relatively rare in freshwaters. Approximately 5% of red algae species occur in freshwater environments, with greater concentrations found in warmer areas. Except for two coastal cave dwelling species in the asexual class Cyanidiophyceae, there are no terrestrial species, which may be due to an evolutionary bottleneck in which the last common ancestor lost about 25% of its core genes and much of its evolutionary plasticity.
Guillardia is a genus of marine biflagellate cryptomonad algae with a plastid obtained through secondary endosymbiosis of a red alga.
The UTC clade is a grouping of green algae.
Chloroplast DNA (cpDNA) is the DNA located in chloroplasts, which are photosynthetic organelles located within the cells of some eukaryotic organisms. Chloroplasts, like other types of plastid, contain a genome separate from that in the cell nucleus. The existence of chloroplast DNA was identified biochemically in 1959, and confirmed by electron microscopy in 1962. The discoveries that the chloroplast contains ribosomes and performs protein synthesis revealed that the chloroplast is genetically semi-autonomous. The first complete chloroplast genome sequences were published in 1986, Nicotiana tabacum (tobacco) by Sugiura and colleagues and Marchantia polymorpha (liverwort) by Ozeki et al. Since then, a great number of chloroplast DNAs from various species have been sequenced.
A putative gene is a segment of DNA that is believed to be a gene. Putative genes can share sequence similarities to already characterized genes and thus can be inferred to share a similar function, yet the exact function of putative genes remains unknown. Newly identified sequences are considered putative gene candidates when homologs of those sequences are found to be associated with the phenotype of interest.
Jeffrey Donald Palmer is a Distinguished Professor of Biology at Indiana University Bloomington.
Genome skimming is a sequencing approach that uses low-pass, shallow sequencing of a genome, to generate fragments of DNA, known as genome skims. These genome skims contain information about the high-copy fraction of the genome. The high-copy fraction of the genome consists of the ribosomal DNA, plastid genome (plastome), mitochondrial genome (mitogenome), and nuclear repeats such as microsatellites and transposable elements. It employs high-throughput, next generation sequencing technology to generate these skims. Although these skims are merely 'the tip of the genomic iceberg', phylogenomic analysis of them can still provide insights on evolutionary history and biodiversity at a lower cost and larger scale than traditional methods. Due to the small amount of DNA required for genome skimming, its methodology can be applied in other fields other than genomics. Tasks like this include determining the traceability of products in the food industry, enforcing international regulations regarding biodiversity and biological resources, and forensics.
