Comparative Analysis of Chloroplast Genomes

The chloroplast genome contains important genetic information. The coding and non-coding regions of the chloroplast genome have significant differences in the rate of molecular evolution, and these differences are suitable for different classes of systematic studies. In addition, the nucleotide substitution rate of chloroplast DNA is moderate, and the size of the chloroplast genome is not very large, which is convenient for sequencing. Studies have found that the chloroplast genomes of various species have good collinearity, which can more easily assemble a large number of chloroplast genomes. With the rapid development of next-generation sequencing technology, scientists can obtain chloroplast genome sequences more efficiently and economically. About 4100 plant chloroplast genomes have been published and are available in the NCBI database. The chloroplast genome contains a large number of functional genes, and its application value in species identification and phylogenetic research has gradually been widely accepted. However, due to the large genome and complex genetic background of many plants, it is difficult to accurately determine the genetic information of the nuclear genome.

Fig. 1. Comparison of the borders of LSC, SSC, and IR regions of chloroplast genomes of Vasconcellea pubescens and Carica papaya. (Shi C, et al., 2012)

Services

Over the years, the team at Lifeasible has extensive experience in chloroplast genome analysis. We have built a rich database of chloroplast genomes from multiple plants. Here, our scientists analyzed all protein sequences from more than 55 complete chloroplast genomes using advanced computational methods, enabling you to analyze the correlations between a range of protein sequences contained in complete genomes. In addition, we can help you compare the obtained chloroplast genomes of multiple species with the chloroplast genomes in the database, which can achieve an understanding of genetic differences between species and identify potential DNA barcodes for species identification. We mainly perform comparative analysis on the genomes of multiple species in the following ways:

• All gene sequences of cpDNA were compared with genomic sequences in databases to find functionally related orthologous proteins.
• Pairwise comparisons of cpDNA genomes to discover orthologous groups not present in plants.
• Gene annotations were used as a reference for functional assignment.

Competitive Advantages

• A rich database of chloroplast genomes.
• Advanced computer software automatically creates nucleotide comparison maps.
• Reveal regions of increased genetic variation.
• Genome composition and size differences between species were obtained by comparative analysis.
• Helping analyze species evolution, genetic structure, and chloroplast DNA markers.
• Suitable for species with complex nuclear genomes.

Lifeasible can meet the needs of customers on time and on budget through a wide range of strategies for analyzing chloroplast genome sequences. Our aim is to be customer-centric and to provide the highest quality service to customers around the world. Our skilled and dedicated scientific researchers ensure that the most appropriate methods and techniques are selected for each specialized chloroplast project. Our customer service representatives are enthusiastic and trustworthy 24 hours a day, 7 days a week. If you are interested in our services, please feel free to contact us for more information or a detailed discussion.

References

1. Lin Z, Zhou P, Ma X, et al. (2020) Comparative analysis of chloroplast genomes in Vasconcellea pubescens A. DC. and Carica papaya L[J]. Scientific reports. 10(1): 1-12.
2. De Las Rivas J, Lozano J J, Ortiz A R. (2002) Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns[J]. Genome research. 12(4): 567-583.