Sequencing Service Based on Whole Genome cpDNA

Over the past few decades, there has been increasing interest in chloroplast genomic characterization, and the sequences of the chloroplast genomes of many land plants and algae have been sequenced to better understand their evolution. Traditional sequencing begins with the construction of a plastid or other genomic library. Furthermore, large-scale isolation of chloroplasts for rare or difficult-to-obtain taxa is impractical. Therefore, sequencing the chloroplast genome using traditional sequencing methods has been difficult. Due to the conserved features of genome size, gene arrangement, and coding sequences in chloroplast genomes, PCR-based methods have been used for their amplification, sequencing, and assembly. Although PCR combined with sequencing can eliminate the step of purifying cpDNA, it requires highly specific primers, which are difficult to identify without a reference chloroplast genome of the relevant species. Therefore, a simple and fast method to sequence the cp genome would greatly benefit studies that require cpDNA sequencing. At present, whole-genome DNA sequencing has become an important method for chloroplast researchers to obtain chloroplast genome sequences.

Fig. 1. Flowchart showing the major steps for the isolation of cpDNAs using the modified high salt method. (Shi C, et al., 2012)

Services

Since whole cellular DNA consists of chromosomal DNA, mitochondrial DNA and cp DNA, any of the three types of DNA sequences can be obtained by sequencing this DNA material. In addition, the development of next-generation sequencing technology has provided new ideas for easily sequencing the complete chloroplast genome. Over the years, the team at Lifeasible has accumulated rich experience in chloroplast gene sequencing, and provides you with professional sequencing services using whole-cell DNA as a sequencing template. We have successfully built a chloroplast whole genome cpDNA sequencing platform, dedicated to chloroplast genome sequencing through total DNA. Our scientists used advanced Solexa and Illumina sequencing technologies to generate highly accurate and essentially complete chloroplast genome sequences.The flow of sequencing service based on whole genome cpDNA is as follows:

(1) Preparing material (DNA source) for whole genome sequencing.
(2) Shearing, polishing, and preparation of isolated whole-cell DNA.
(3) Nucleotide sequences were determined according to Solexa or Illumina sequencing methods.
(4) The cpDNA sequence was screened for splicing and assembly to obtain a complete chloroplast genome.
(5) Gene annotation to identify putative protein-coding genes and identify transfer RNAs and ribosomal RNAs.
(6) Assessing the accuracy of chloroplast genome sequencing.

Competitive Advantages

• A faster and more economical method than traditional methods for rapid sequencing of chloroplast genomes.
• Using whole-cell DNA instead of cpDNA as sequencing template.
• Unlike PCR amplification-based sequencing, the possibility of introducing base errors during the PCR reaction is avoided.
• With the advantage that read coverage information can be used to reliably detect sequence variants.
• The microreads generated by this method can also be used to identify SNPs in species with whole genome sequences.

Lifeasible can meet the needs of customers on time and on budget through a wide range of chloroplast DNA sequencing  strategies. 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. Shi C, Hu N, Huang H, et al. (2012) An improved chloroplast DNA extraction procedure for whole plastid genome sequencing[J]. Plos one. 7(2): e31468.
2. Wu J, Liu B, Cheng F, et al. (2012) Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology[J]. Frontiers in plant science. 3: 243.