Comparative Transcriptome Analysis

Comparative transcriptomics is an effective method for comparing gene expression patterns between specific tissues or species based on RNA sequencing data. We offer a one-stop comparative transcriptome analysis service to help you quickly and comprehensively resolve the evolutionary relationships between strains and subtypes, and to provide insights into biological processes.


CD Genomics offers next-generation sequencing (NGS) and long read sequencing (Pacbio SMRT and Nanopore platform) strategies for different sequencing needs. Comparative transcriptomics analyzes the affinities of closely related species by comparing the differences of transcripts and gene expression pattern, and uncovers genes that are clearly subject to positive or negative selection. Transcriptome sequencing, which does not require reference to the genome for data analysis, provides a rapid and comprehensive way to resolve the evolutionary relationships between species and to pull insights into biological processes. This tool has the advantages of short cycle time, comprehensiveness, and high-cost performance, which is suitable for species with overly large genomes, overly complex structures, and difficult to extract DNA samples. Comparative transcriptome analysis is now widely used in the study of evolution and biological processes in species such as rice, Arabidopsis, fungi, as well as ornamental and economic plants.


Any Species Efficient & Great Value Bioinformatics Analysis One-Stop Solution
This method can be applied to any species, including microorganisms, animals, plants and humans. Rapid and comprehensive analysis of the evolutionary relationships and specific tissue expression. Our integrated bioinformatics pipeline can be tailored to suit your project, data visualization. Customized analysis solutions for phylogenetic analysis, adaptability analysis, etc.

Project Workflow

Sample Preparation

1. Sample Preparation

Quality assessment and quantification

Library Preparation

2. Library Preparation

DNA library preparation.


3. Sequencing

Illumina NovaSeq, 150 bp paired-end; Circular consensus sequencing (CCS); continuous long read (CLR) sequencing

Data Analysis

4. Data Analysis & Delivery

Visualize and preprocess results, and custom bioinformatics analysis.

Bioinformatics Analysis Pipeline

Comparative Transcriptome Analysis

In-depth data analysis:

  • Splicing and alignment Clustering analysis
  • Gene function annotation (NR, GO, KEGG, KOG, etc.)
  • CDS prediction
  • SSR prediction
  • Identification of direct homologous genes
  • KA/KS analysis of direct homologous genes
  • Enrichment analysis
  • Construction and analysis of phylogenetic tree

Sample Requirements

RNA sample (concentration ≥ 20 ng/uL, amount ≥ 1 ug)

1.8 ≤ OD260/280 ≤ 2.2, OD260/230≥2.0, RIN ≥ 6.5, 28S/18S ≥1.0.

Please make sure that the RNA is not degraded.

Sample Storage: RNA can be dissolved in ethanol or RNA-free ultra-pure water and stored at -80°C. RNA should avoid repeated freezing and thawing.

Shipping Method: When shipping RNA samples, the RNA sample is stored in a 1.5 mL Eppendorf tube, sealed with a sealing film. Shipments are generally recommended to contain 5-10 pounds of dry ice per 24 hours.

Deliverable: FastQ, BAM, coverage summary, QC report, custom bioinformatics analysis report.


  1. Cai M, Tan Z, Wu X, et al. Comparative transcriptome analysis of genes and metabolic pathways involved in sporulation in Ganoderma lingzhi. G3 Genes| Genomes| Genetics, 2022.
  2. Irie N, Kuratani S. Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis. Nature communications, 2011, 2(1): 1-8.
* For Research Use Only. Not for use in diagnostic procedures.

Research Areas
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