Chloroplast genomes: diversity, evolution, and applications in genetic engineering
Daniell, H., Lin, C., Yu, M., & Chang, W. (2016). Chloroplast genomes: diversity, evolution, 
and applications in genetic engineering. Genome Biology, 17(1). 
https://doi.org/10.1186/s13059-016-1004-2
Summary:
The review article Chloroplast genomes: diversity, evolution, and applications in genetic 
engineering, by Dr. Henry Daneil et all covers the impact of intracellular gene transfer, 
conservation, diversity, trans genes, and the domestication of plants. The article begins by explaining that the first chloroplast to be sequenced was that of a tobacco plant in 1986. Since then, over 800 chloroplast genomes have been sequenced. The article explains that there are two systems used for chloroplast sequencing, Illumina (PCR) or single-molecule real-time sequencing (SMRT). The Illumina is a faster system, but “has a 90.59%” accuracy, and the SMRT system “has a 99.99% accuracy” but is slower. For sequencing, the goal is speed and not always accuracy. This is important for any chloroplast genome because they are large, and the genome has “120-130 genes.” However, there is still diversity in these chloroplasts. By sequencing the genomes, there is evidence of the evolutionary relationships of all plants. For example, the flowers of odontoglossum and odontocdium are derived from the same female plant, odontoglossum bictoniense.
The article also discusses the advances and impacts in chloroplast genome engineering. 
The main advancement that is discussed is about transgenes in the chloroplasts. These are genes that are “bombarded” into plant cells by a gene gun. However, repetitive sequencing reduces the efficiency of integration of the transgene when heterologous flanking sequences are being used. 
Lastly, the article talks about the future of genome engineering; there are positives and negatives to focus on. For example, there is concern that insects will gain resistance against biopesticides. However, understanding the genome of chloroplasts will help us study extinct plants to keep more plants from going extinct. 

 

Reflection: 
The whole idea of how transgenes enter the genome was really interesting to read 
about because both the process of actually inserting the transgene and the effect it has on 
the plant demonstrated the importance of the chloroplast genome in the function of the 
plant cell. Specifically, how they’re inserted into the genome of the plant cell. Everything 
about the process, from the gold particles being the vectors for the genes to the gene gun 
required, is like nothing I have ever heard of. If I were to research this further, I would 
want to deep dive into how the transgenes actually benefit the plant's survival, or the 
specific detriments that this review article skipped over. This article relates to what we 
have learned in class because we did cover a large variety of plants and chloroplasts. 
We did begin to scrape the surface of the complexity of chloroplasts, but this article was 
a much deeper dive than we realistically have time for. By reading this article, my 
understanding of the specific functions of chloroplasts was reinforced. More specifically, 
the mechanisms and evolutionary changes that took place to get the chloroplasts that exist 
in the plants we study today.