Chloroplasts are the membrane-bound compartments inside plant and algal cells that capture sunlight and convert it into chemical energy through photosynthesis. They are found in every green leaf, blade of grass, and strand of seaweed, but the full roster of organisms carrying chloroplasts (or closely related structures called plastids) stretches far beyond the plant kingdom. Algae of wildly different lineages, single-celled protists, and even a handful of animals harbor functional chloroplasts, each having acquired them through different evolutionary paths.
How Chloroplasts Got Their Start
Chloroplasts trace back to an ancient event in which a single-celled organism engulfed a photosynthetic cyanobacterium and, rather than digesting it, kept it alive inside. Over hundreds of millions of years, that captive cyanobacterium lost its independence and became an organelle. This idea, known as endosymbiotic theory, is supported by the fact that chloroplasts still carry their own small genome and are surrounded by a double membrane, echoing the original engulfment. Proteins shared between modern cyanobacteria and chloroplasts, especially those involved in oxygen-producing photosynthesis, provide the strongest molecular evidence for this origin.1PubMed Central. Are Cyanobacteria an Ancestor of Chloroplasts or Just One of the Gene Donors for Plants and Algae? That single primary endosymbiosis event gave rise to the chloroplasts in three major groups: green algae and land plants, red algae, and a small, lesser-known group called glaucophytes.2PubMed. From cyanobacteria and cyanophages to chloroplasts: the fate of the genomes of oxyphototrophs and the genes encoding photosystem II proteins
The Classic Green Chloroplast
When most people picture a chloroplast, they are thinking of the type found in land plants and green algae. These chloroplasts contain the pigment chlorophyll, which gives leaves their green color, and they have an internal system of stacked membrane discs. These stacks physically separate two photosystems that operate at different speeds, an arrangement that helps the chloroplast run photosynthesis efficiently.3PubMed. Why do thylakoid membranes from higher plants form grana stacks? Every tree, fern, moss, grass, and flowering plant on Earth uses this basic design. Green algae, from the single-celled species floating in a pond to the large seaweeds waving in coastal waters, share it too.
But a chloroplast is not always green, and it is not always devoted to photosynthesis. Within a single plant, chloroplasts can transform into other types of plastids depending on what the tissue needs. In a ripe tomato, chloroplasts convert into chromoplasts packed with red and orange pigments. In a potato tuber underground, they become amyloplasts that store starch. In the white inner petals of a flower, they exist as colorless leucoplasts. All of these forms share a common lineage and can, in some cases, convert back into photosynthetic chloroplasts if the right signals appear.4PubMed. Diversity and Plasticity of Plastids in Land Plants
Red Algae and Glaucophytes
Red algae are the organisms behind nori sheets, the seaweed wrapping on sushi, and the coralline crusts that help cement coral reefs. Their chloroplasts descend from the same original cyanobacterial ancestor as those in green plants, but they took a different evolutionary path. Red algal chloroplasts retain a light-harvesting antenna called the phycobilisome, which is the same structure cyanobacteria use to collect light. Green algae and land plants lost phycobilisomes entirely, replacing them with different antenna pigments.5PubMed Central. What Happened to the Phycobilisome? Phycobilisomes let red algae absorb wavelengths of light that penetrate deeper water, which is part of why red algae can thrive in dim underwater environments where green algae struggle.
Glaucophytes are a tiny, obscure group of freshwater algae that most people have never heard of, but they are fascinating because their chloroplasts are the most cyanobacteria-like of any living organism. The chloroplasts of glaucophytes still retain a thin layer of peptidoglycan, the rigid bacterial cell-wall material, sandwiched between their two envelope membranes.6DNA Research. Analysis of an improved Cyanophora paradoxa genome assembly – Section: Peptidoglycan No other chloroplasts have kept this feature. Glaucophytes also retain phycobilisomes, just like red algae. Together, green plants, red algae, and glaucophytes represent the three lineages that inherited chloroplasts directly from that original cyanobacterial capture event.
Chloroplasts Acquired Secondhand
The story does not end with those three groups. In several independent events, non-photosynthetic organisms swallowed an alga that already had chloroplasts and kept the chloroplast for themselves. This is called secondary endosymbiosis, and it spread photosynthesis to a surprisingly wide range of life forms.
Green algal chloroplasts were picked up by euglenids (the graceful, flagellated pond-water organisms often shown in biology textbooks) and by a group called chlorarachniophytes. Red algal chloroplasts were captured in what appears to have been a single event, eventually giving rise to the plastids in an enormous and ecologically dominant group that includes brown algae, diatoms, and several other lineages.7PubMed Central. The endosymbiotic origin, diversification and fate of plastids Diatoms alone are responsible for a staggering share of the planet’s photosynthesis, contributing close to half of all carbon fixation in the ocean.8Current Biology. V-type H+-ATPase around diatom chloroplasts enhances photosynthetic carbon fixation
Because these chloroplasts came wrapped inside another organism, they ended up enclosed by extra membranes. Diatoms and related algae have chloroplasts surrounded by four membranes rather than the usual two, a telltale sign of that Russian-nesting-doll history.9PubMed. Protein import pathways in ‘complex’ chloroplasts derived from secondary endosymbiosis involving a red algal ancestor Euglenids have three-membrane chloroplasts, and they can even survive if their chloroplasts are experimentally destroyed, switching to a purely food-eating lifestyle.10PubMed Central. Euglena Central Metabolic Pathways and Their Subcellular Locations
Some dinoflagellates have taken this process even further, engaging in what is called tertiary endosymbiosis. Certain dinoflagellate species replaced their original red-algae-derived chloroplast by engulfing another alga that itself had a secondary chloroplast. The genus Karenia, notorious for producing harmful algal blooms (red tides), carries a chloroplast originally stolen from a haptophyte alga.11PubMed. Tertiary endosymbiosis driven genome evolution in dinoflagellate algae Other dinoflagellates called “dinotoms” carry functional diatom chloroplasts inside them.12PubMed Central. Evidence for the Retention of Two Evolutionary Distinct Plastids in Dinoflagellates with Diatom Endosymbionts The result is a biological layer cake with membranes and genomes nested several levels deep.
Animals That Steal Chloroplasts
A handful of animals have figured out how to run chloroplasts without inheriting them. Certain sacoglossan sea slugs feed on algae by puncturing cell walls and sucking out the contents, but instead of digesting the chloroplasts, they incorporate them into cells lining their digestive tract. The stolen chloroplasts, called kleptoplasts, can keep photosynthesizing inside the slug for weeks or even months, providing the animal with sugars made from sunlight.13PubMed Central. Food shaped photosynthesis: Photophysiology of the sea slug Elysia viridis fed with two alternative chloroplast donors
The slug Elysia crispata has been raised in the lab on different algal diets, and the species of alga it eats determines its body color, the size of its kleptoplasts, and even its pigment profile. Slugs fed on one alga species had kleptoplasts averaging about 28 square micrometers, while those switched to a different alga ended up with kleptoplasts around 9 square micrometers. Within just ten days of the diet switch, no trace of the original alga’s signature pigments could be found.14PubMed Central. Laboratory Rearing of the Photosynthetic Sea Slug Elysia crispata (Gastropoda, Sacoglossa) The slugs are essentially wearing the color of whatever they last ate.
Kleptoplasty is not limited to sea slugs. The marine ciliate Mesodinium rubrum, a single-celled organism, gets over 95% of its carbon from photosynthesis using chloroplasts it steals from cryptophyte algae.15PubMed Central. Retention of blue-green cryptophyte organelles by Mesodinium rubrum and their effects on photophysiology and growth Mesodinium blooms can turn patches of ocean a striking red and are closely linked to marine food webs.16Scientific Reports. Unveiling the hidden genetic diversity and chloroplast type of marine benthic ciliate Mesodinium species Unlike the permanent chloroplasts in plants, kleptoplasts eventually degrade and must be replenished by eating more algae, which is why this process falls short of true endosymbiosis.
Organisms That Have Chloroplasts but Do Not Photosynthesize
Not all plastids are used for photosynthesis. Some organisms have retained a chloroplast-derived organelle long after abandoning sunlight as an energy source. The most medically significant example is the apicoplast, a vestigial plastid found in Plasmodium parasites, the organisms that cause malaria. The apicoplast cannot photosynthesize, but it carries out essential metabolic tasks like synthesizing fatty acids and other molecules the parasite needs to survive. Because humans have no plastids of any kind, the apicoplast has become an attractive drug target. Some existing antimalarial drugs already hit apicoplast pathways, causing a distinctive “delayed death” effect in which the parasite appears fine at first but dies during its next replication cycle.17PubMed. Targeting the apicoplast in malaria
Parasitic plants offer another striking case. Dodder (Cuscuta) species are rootless, leafless vines that wrap around host plants and drain nutrients directly from them. Their chloroplast genomes have shrunk dramatically, with the smallest species retaining only about 60 kilobases compared to the roughly 120-kilobase genomes of their closest photosynthetic relatives. Photosynthesis genes are the most heavily deleted.18PubMed Central. Elucidating the evolutionary dynamics of parasitism in Cuscuta: in-depth phylogenetic reconstruction and extensive plastomes reduction Rafflesia, the genus famous for producing the world’s largest flowers, may have gone even further. Researchers searching for a chloroplast genome in Rafflesia lagascae found only tiny, degraded fragments with no intact genes, suggesting this plant may have lost its chloroplast genome almost entirely.19PubMed Central. Possible Loss of the Chloroplast Genome in the Parasitic Flowering Plant Rafflesia lagascae (Rafflesiaceae)
The Chloroplast Genome and Why Most of It Moved
A typical plant chloroplast genome contains around 113 unique genes, encoding ribosomal proteins, transfer RNAs, and components of the photosynthetic machinery.20PubMed Central. Inverted repeats dynamics shape Asclepiadoideae (Apocynaceae) Chloroplast genomes That sounds like a lot until you consider that the cyanobacterial ancestor likely had thousands of genes. The vast majority migrated to the host cell’s nucleus over evolutionary time, meaning that most of the proteins a chloroplast needs are actually produced outside the chloroplast and then imported back in. This import relies on specialized protein channels in the chloroplast’s outer and inner membranes, which work together to pull proteins through.21PubMed Central. Chloroplast protein import machinery and quality control
For a long time, chloroplast genomes were thought to be boringly stable in structure. Recent large-scale sequencing has overturned that assumption, revealing pervasive rearrangements including inversions, gene losses, horizontal gene transfers from other organisms, and shifts in the repeated DNA segments that are a hallmark of these genomes.22PubMed Central. Beyond conservation: the landscape of chloroplast genome rearrangements in angiosperms Parasitic lineages like dodder and Rafflesia sit at one extreme of this variation, but even fully photosynthetic plants show more structural shuffling than textbooks once suggested.
How Chloroplasts Divide and Get Passed On
Chloroplasts cannot be made from scratch. New ones arise only when existing chloroplasts divide, much like bacteria splitting in two. The division machinery is a hybrid: part of it descends from the bacterial protein FtsZ, which cyanobacteria still use to divide, and part of it is a eukaryotic addition involving the motor protein dynamin.23PubMed Central. Mechanisms of organelle division and inheritance and their implications regarding the origin of eukaryotic cells In most flowering plants, chloroplasts are inherited only from the mother, because the egg cell contributes essentially all the cytoplasm (and thus all the chloroplasts) to the embryo, while the pollen contributes little or none. This maternal inheritance pattern is one reason chloroplast DNA is so useful in tracing plant lineage, and it has practical implications for genetic engineering, as we will see below.
Chloroplast Biotechnology
The fact that chloroplasts have their own genome, and that they are maternally inherited, makes them an appealing target for genetic engineering. Inserting foreign genes into the chloroplast genome rather than the nuclear genome offers several advantages. Each plant cell contains many chloroplasts, and each chloroplast carries many copies of its genome, so a successfully inserted gene gets amplified to high copy numbers, which translates into high levels of the desired protein. More than 40 different foreign genes have been stably inserted into tobacco chloroplast genomes, producing everything from insect-resistance proteins to vaccine antigens and industrial enzymes.24PubMed Central. Breakthrough in chloroplast genetic engineering of agronomically important crops
Maternal inheritance also acts as a biological containment system. Because chloroplast DNA generally does not spread through pollen, the risk of engineered genes escaping into wild relatives is much lower than with conventional nuclear-genome engineering. This addresses one of the longstanding concerns about genetically modified crops. Researchers continue to expand the toolkit for chloroplast transformation, working to move beyond tobacco into staple crops and exploring the use of plants as cheap bioreactors for pharmaceutical production.25PubMed. Genetic engineering of the chloroplast: novel tools and new applications
The Chloroplast’s Role in Global Carbon
It is easy to think of chloroplasts primarily as a feature of forests and farmland, but oceanic chloroplasts do an outsized share of the planet’s photosynthetic work. Phytoplankton, the microscopic algae drifting in the sunlit layer of every ocean, make up only about one to two percent of global plant carbon by mass. Yet they fix somewhere between 30 and 50 billion metric tons of carbon per year, roughly 40% of the global total.26PubMed. The role of phytoplankton photosynthesis in global biogeochemical cycles Diatoms, with their complex four-membrane chloroplasts derived from red algae, are among the most productive of these oceanic photosynthesizers. The oxygen you breathe owes nearly as much to algal chloroplasts floating in seawater as it does to tropical rainforests.
A New Organelle on the Block
In 2024, researchers confirmed something that blurs the line between endosymbiont and organelle in a completely new way. A nitrogen-fixing cyanobacterium called UCYN-A, which lives inside a marine haptophyte alga called Braarudosphaera bigelowii, has crossed the threshold from symbiont to organelle. UCYN-A is tightly integrated into the alga’s cell architecture, divides in synchrony with its host, and imports proteins encoded by the algal nucleus, all hallmarks of a true organelle.27PubMed. Nitrogen-fixing organelle in a marine alga Researchers have dubbed it the “nitroplast,” and it represents the first known nitrogen-fixing organelle. UCYN-A is of cyanobacterial origin, just like chloroplasts, but instead of providing photosynthesis it provides the ability to convert atmospheric nitrogen into a usable form.28ISME Communications. Metagenomics reveals the genetic diversity between sublineages of UCYN-A and their algal host plastids
The nitroplast discovery matters because it shows that the kind of evolutionary integration that produced chloroplasts over a billion years ago is not a one-off event locked in deep time. It can happen again, with a different metabolic gift. It also suggests scientists should be looking more carefully at close symbioses in the ocean for other organelles in the making.
Chloroplasts and Photoprotection
Chloroplasts do not simply absorb all the light that hits them. Too much light energy can damage the photosynthetic machinery, so chloroplasts have built-in safety valves. One of the best studied is the xanthophyll cycle, in which pigment molecules inside the chloroplast are chemically converted between forms that pass energy along for photosynthesis and forms that safely release excess energy as heat. Different algal lineages use different versions of this cycle. Vascular plants, green algae, and brown algae use one variant, while diatoms, haptophytes, and dinoflagellates use another.29PubMed. Regulation and function of xanthophyll cycle-dependent photoprotection in algae The fact that separate lineages evolved distinct photoprotective pigment cycles underscores how independently chloroplasts have been fine-tuned in different hosts, even when their deep ancestry is shared.