Phylogenetic Shadowing

Phylogenetic Shadowing

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CD Genomics offers phylogenetic shadowing services to help you understand the complex and often myriad mechanisms of gene regulation in humans and other higher eukaryotes. We offer comprehensive and tailored solutions to help you gain valuable insights into the phylogenetic shadowing of your species of interest.

Overview of Phylogenetic Shadowing

Understanding the complex and often myriad mechanisms of gene regulation has been a great challenge. Recent genome sequencing combined with gene prediction algorithms has yielded a wealth of gene sequences, but our understanding of gene regulation is still very limited. In humans and other higher eukaryotes, gene expression is regulated through the binding of various transcription factors to cis-regulatory regions of genes. The binding of different combinations of transcription factors may lead to gene expression in different tissue types or at different developmental stages. Therefore, to fully understand gene function, it is essential to identify the transcription factors that regulate genes and the corresponding transcription factor binding sites (TFBSs) in DNA sequences. Phylogenetic footprinting provides a systematic approach to identify conserved noncoding sequences that often contain TFBSs critical for gene regulation. when this approach is used for a large number of closely related species, it is referred to as phylogenetic shadowing.

Fig. 1. Using phylogenetic footprinting to detect conserved transcription-factor-binding sites.Fig. 1. Using phylogenetic footprinting to detect conserved transcription-factor-binding sites. (Zhang Z, et al, 2023)

Application Field

CD Genomics has extensive genomic data and comparative genomics expertise to provide a suite of bioinformatics solutions specifically tailored for phylogenetic shadowing. Our experts can provide comprehensive services for motif discovery, regulatory element identification, and functional annotation. Working closely with our clients, we will analyze large genomic datasets for you, unravel conserved regulatory motifs, and provide valuable insights into gene regulatory networks.

Our phylogenetic shadowing services are used in a wide range of fields:

  • Understanding developmental biology. Our phylogenetic shadowingg can identify conserved regulatory elements involved in the development and reveal the complex processes that control embryogenesis. By comparing direct homologous sequences from different species, our technical teams can identify evolutionarily conserved regions critical to developmental gene regulation.
  • Exploring disease mechanisms. Our phylogenetic shadowing provides a powerful way to identify regulatory elements associated with the disease. By comparing the non-coding sequences of disease-associated genes from different species, conserved motifs can be identified, providing insight into the dysregulation of gene expression that leads to pathological conditions.
  • Learning evolutionary biology. Our phylogenetic shadowing can also be used to study the evolution of regulatory elements across species. By comparing genomes from different taxonomic levels, we can help you identify conserved motifs that have stood the test of time and point to essential functional elements in gene regulation.

Workflow of Phylogenetic Shadowing

CD Genomics offers a customized phylogenetic shadowing workflow that integrates various computational and experimental steps.

(1) Data collection and alignment: CD Genomics collects genomic sequences of interest from different species and compares these sequences using a robust multiple-sequence alignment algorithm to identify conserved regions.

(2) Motif discovery and statistical analysis: CD Genomics uses motif discovery algorithms to identify putative TFBSs within conserved regions.

(3) Motif validation and functional annotation: we validate the discovered motifs by experimental techniques such as reporter gene analysis, chromatin immunoprecipitation (ChIP) or DNA shadowing. In addition, we perform functional annotation to assign biological significance to the identified motifs and understand their role in gene regulation.

(4) Comparative analysis and visualization:we can perform a comparative analysis of patterns identified across species to help you gain insight into their conservation and differentiation. We also reveal the evolutionary dynamics of regulatory elements by constructing classification trees and mapping motifs to branches. CD Genomics provides visualization tools to explore and interpret the results obtained.

By leveraging comparative genomics, CD Genomics offers comprehensive bioinformatics services for phylogenetic shadowing to help you unlock the regulatory code hidden in the genome. From motif discovery to comparative analysis, CD Genomics supports researchers in gaining insight into the regulation of gene expression and its impact on biological processes. If you are interested in our services, please contact us for more detailed information.


  1. Zhang Z, Gerstein M. Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements. J Biol. 2003;2(2):11.
* For Research Use Only. Not for use in diagnostic procedures.
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