Mitochondrial/Chloroplast Genome Sequencing

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Mitochondrial/Chloroplast Genome Sequencing

Chloroplasts (cp) and mitochondria (mt) are subcellular organelles that play an important role in cellular energy metabolism. They both possess their own genomes and genetic systems. These small genomes are often used to investigate the evolution of eukaryotes, especially in plants. Based on the long-read sequencing technologies, the assembly of complete mt and cp DNA sequences is more intuitive, accurate, and comprehensive. With PacBio SMRT sequencing and ONT nanopore sequencing, CD Genomics can sequence organelle genomes of plants as well as animals, providing reliable genome data for further genetics studies and taxonomic/phylogenetic analysis. Our services are cost-effective, straightforward, and highly flexible to meet the specific needs of our clients worldwide.

Overview of Mitochondrial (mt)/Chloroplast (cp) Genome

Chloroplasts (cp) and mitochondria (mt).

Mitochondrial (mt) and chloroplast (cp), as essential organelles in eukaryotic cells, have both retained some prokaryotic properties and acquired some new ones during the evolutionary process. Different evolutionary pathways in animals and plants have led to significant differences in the mt and cp genomes of animals and plants. Plant mt and cp genomes are bigger than animal mt genomes. Similar to most prokaryotic genomes, plant mt and cp genomes have introns, while there are no introns present in animal mt genomes. In addition, in plants, pc genome is more conserved than mt genome and contains more genes. pc genomes are more similar to their prokaryotic genome in terms of regulatory sequences and the arrangement of many gene clusters. In the past years, there has been a dramatic increase in sequences of complete organelle genomes due to the development of sequencing technologies.

Services Offering at CD Genomics

Sequencing Platform Library Construction Analytic Strategy Delivery Cycle
Pacific Biosciences (PacBio) Sequel II system 10Kb SMRTbell library, ≥100X coverage Standard analysis and advanced analysis Minimum of 23 working days
Oxford Nanopore Technologies (ONT) PromethION 1D library, ≥100X coverage Standard analysis and advanced analysis Minimum of 20 working days

Workflow of Our Services

Workflow of Our Services-CD Genomics.

Analysis Pipeline and Contents

Dna sequence visualization, genetic mapping, gene barcoding.
  • Data output and quality control.
  • Mt/cp genome assembly and evaluation of assembly results.
  • Genome annotation and generation of circular genome map.
  • Repeat sequence analysis.
  • Identification of protein-coding genes.
  • RNA-editing and substitution rate analysis.
  • Phylogenetic analysis.

Benefits of Our Services

  • Ready to start your project once the contract is signed.
  • Optimized and well-established long-read sequencing platforms.
  • Fully developed and improved analytical methods.
  • Fast and traceable testing for urgent project needs.

CD Genomics is a leading custom service provider in the field of long-read sequencing. Our goal is to help clients accelerate their research and support their careers by using advanced third-generation sequencing platforms. By developing innovative, tailored, and cost-effective strategies, we can greatly accelerate the success of their projects. Please feel free to contact us. Our customer service representatives are available 24 hours a day from Monday to Sunday.


  1. Franco-Sierra, N. D., & Díaz-Nieto, J. F. (2020). "Rapid mitochondrial genome sequencing based on Oxford Nanopore Sequencing and a proxy for vertebrate species identification." Ecology and evolution, 10(7), 3544-3560.
  2. Bi, C., et al. (2016). "Analysis of the complete mitochondrial genome sequence of the diploid cotton Gossypium raimondii by comparative genomics approaches." BioMed Research International, 2016.
For Research Use Only. Not for use in diagnostic procedures.

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