How Many Genes Are in the Plant Plastid Genome?

Plastid genomic landscapes reveal critical insights into plant molecular biology. Researchers investigate the gene repertoire within these genomic structures, exploring their composition, structural variability, and evolutionary implications across diverse botanical species. But how many genes are typically found in the plant plastid genome? This article dives into the fascinating details of plastid genome structure, gene composition, and its variability across plant species while highlighting its evolutionary significance and practical applications.

Overview of Plastid Genome Structure

Genetic material within plant cellular organelles, the chloroplast genome, exhibits a remarkably stable architectural configuration. Characterized by a distinctive quadripartite organization, this genomic structure encompasses two symmetrical inverted repeat segments, complemented by distinct single-copy domains—one expansive and one compact. This organizational arrangement facilitates the formation of a circular DNA molecule, with genomic dimensions typically spanning approximately 100 to 220 kilobase pairs.

Typical structure of the chloroplast genome

Inverted repeat sequences (IRs): Two IRs in the chloroplast genome are highly conserved and are usually between 20,000 and 25,000 kb in length. These regions contain many important genes, such as ribosomal RNA genes, transfer RNA genes, and some genes that encode photosynthesis related proteins.

Large single copy region (LSC): Located between two IRs, it is the largest part of the genome and usually accounts for about 80% of the entire genome. The LSC region contains many genes involved in photosynthesis, translation and transcription.

Small single copy region (SSC): Located between LSC and IRs, it is the smallest part of the genome and usually accounts for about 20% of the entire genome. The SSC region also contains some key genes, such as photosynthesis related genes and transfer RNA genes.

Figure 1. Structural organization of organelle genomes.(Mahapatra,et.al ,2021)

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Gene Composition in Plastid Genomes

The plant chloroplast genome is a circular DNA molecule in plant cells. Its genetic composition and function are crucial for photosynthesis, energy production, and the normal operation of chloroplasts.

Protein-coding genes: About 66 to 82 genes, mainly involved in photosynthesis, including photosystem I (PSI), photosystem II (PSII), antenna complex (LHC) and electron transport chain-related proteins.

For example, psaA and rbcL are key genes for photosystem I.

Transfer RNA (tRNA) genes: About 29 to 36 genes responsible for aminoacyl-tRNA synthesis during translation.

Ribosomal RNA (rRNA) gene: There are usually 4 genes responsible for the assembly and function of the ribosome.

Together, these genes ensure efficient energy production and gene expression within plastids. For more on plant-microorganism interactions and their genetic insights, visit our resource on sequencing plant-microorganism interactions.

Variability Across Plant Species

While the core structure and gene composition are conserved, plastid genomes show notable variability across different plant groups:

Seed Plants

The chloroplast genome of seed plants contains an average of 101-118 genes, with genome sizes ranging from 100-220 kb, most of which are related to photosynthesis. These genomic structures are relatively conservative and usually have two IRs, dividing the genome into two SSCs and a LSC. This structure is very common in photosynthetic plants.

Parasitic Plants

The chloroplast genome of parasitic plants has shrunk significantly, with an average of only 12-28 genes, and the genome size is usually less than 30 kb. This is because parasitic plants rely on their hosts for energy and lose their ability to synthesize. As a result, a large number of photosynthesis-related genes in their chloroplast genomes have been lost or degraded into pseudogenes. For example, the chloroplast genomes of some parasitic plants have even completely lost their photosynthesis function, retaining only a small number of genes related to transcription and translation.

Angiosperms

The chloroplast genome of angiosperms contains an average of 110-130 genes, with genome sizes ranging from 115-165 kb. Although the number of genes varies slightly between different species, genomic structure and function are highly conserved in most angiosperms. This conservation allows angiosperms to adapt to a variety of environmental conditions and spread rapidly over the course of evolution.

Gymnosperms

The chloroplast genome size of gymnosperms varies significantly, ranging from 120 to 150 kb. The chloroplast genomes of some gymnosperms have undergone extensive genomic rearrangements, including events such as inversion, insertions and deletions. These rearrangements may be related to the evolutionary history of gymnosperms, such as adapting to different ecological environments or coping with specific survival pressures.

These differences are mainly caused by the following factors:

Lifestyle: Because parasitic plants rely on their hosts for energy, their chloroplast genomes have significantly shrunk and their photosynthesis function has been lost.

Evolutionary pressure: Due to its extensive distribution and diversity, the chloroplast genome of angiosperms has maintained a high degree of conservation during evolution.

Genome rearrangement: The chloroplast genome of gymnosperms has experienced more genomic rearrangement events, which may be a result of its adaptation to different ecological environments.

Evolutionary Significance of Plastid Genes

The importance of the chloroplast genome in plant evolution is reflected in many aspects, including gene loss, horizontal gene transfer (HGT), and the impact of these processes on plant diversity and phylogenetic relationships.

Gene loss: The adaptive evolution of parasitic plants

Parasitic plants gradually lose their photosynthesis function due to their dependence on their hosts to provide organic carbon sources, which leads to significant gene loss in their chloroplast genomes. For example, only a few key genes, such as ribosomal protein, tRNA and rRNA genes, remain in the chloroplast genomes of many parasitic plants, while a large number of genes related to photosynthesis are lost or degraded into pseudogenes. This phenomenon suggests that the parasitic lifestyle has fundamentally changed the selective pressure on the chloroplast genome, thus promoting the simplification and functional reorganization of the chloroplast genome.

Studies have shown that the chloroplast genomes of parasitic plants are usually accompanied by structural rearrangements, such as the increase of inversions and repetitive sequences, and these changes further promote the adaptive evolution of the chloroplast genomes.

Figure 2.Repeat DNA in Plastomes of Orobanchaceae.(Wicke,et.al ,2013)

Horizontal gene transfer: promoting unique adaptations of the genome

Horizontal gene transfer is another key factor in the evolution of the chloroplast genome. Studies have shown that despite relatively few horizontal gene transfer events in the chloroplast genome, significant HGT phenomena still exist in some cases. For example, in red algae plants, studies have found that there are genes from other organisms (such as cyanobacteria) in the chloroplast genome. These genes are integrated into the chloroplast genome through HGT and participate in the maintenance of chloroplast functions.

Horizontal gene transfer not only increases the diversity of the chloroplast genome, but may also provide new biological functions for plants. For example, certain cyanobacant-derived PPO (proline oxidase) genes are integrated into chloroplasts, which may provide additional antioxidant capabilities for plants. In addition, some studies have pointed out that HGT may be one of the important drivers of chloroplast evolution, especially during the transition of plants from aquatic to terrestrial environments.

Phylogeny and diversity of chloroplast genomes

Chloroplast genomes have become an important tool for studying plant phylogeny due to their high conservation and low mutation rate. Still, due to significant simplification or rearrangement of chloroplast genomes in some plants, this may conflict with phylogenetic relationships. For example, the chloroplast genomes of certain parasitic plants are inconsistent with their traditional taxonomic status, suggesting that chloroplast data may reveal evolutionary relationships that are not fully reflected in traditional phylogenetic trees.

In recent years, with the development of high-throughput sequencing technology, scientists have been able to more comprehensively analyze the structural and functional changes of the chloroplast genome.

Conclusion

Plastid genomes represent pivotal molecular structures in botanical research, encoding approximately 101-130 genes across a 100-220 kb genomic landscape. Their conserved architecture reveals intricate insights into photosynthetic mechanisms, evolutionary adaptations, and genetic diversity. Protein-coding, tRNA, and rRNA genes collectively orchestrate critical cellular functions, with notable variations observed in parasitic plants and gymnosperm lineages.

Genomic variability emerges through complex processes like horizontal gene transfer and structural rearrangements, reflecting ecological pressures and evolutionary dynamics. Significant gene losses in parasitic species and extensive genomic modifications in gymnosperms underscore the plastid genome’s adaptive potential.

Ongoing research leverages these genomic structures to elucidate phylogenetic relationships, plant adaptations, and biotechnological opportunities, cementing their significance in scientific exploration.

References

1. Mahapatra, K., Banerjee, S., De, S., Mitra, M., Roy, P., & Roy, S. (2021). An Insight Into the Mechanism of Plant Organelle Genome Maintenance and Implications of Organelle Genome in Crop Improvement: An Update. Frontiers in cell and developmental biology, 9, 671698. https://doi.org/10.3389/fcell.2021.671698
2. Wicke, S., Müller, K. F., de Pamphilis, C. W., et.al. (2013). Mechanisms of functional and physical genome reduction in photosynthetic and nonphotosynthetic parasitic plants of the broomrape family. The Plant cell, 25(10), 3711–3725. https://doi.org/10.1105/tpc.113.113373