Related Experiment Video
Updated: Aug 12, 2026
09:40
Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
Fugu and human sequence comparison identifies novel human genes and conserved non-coding sequences
Patrick Gilligan1, Sydney Brenner, Byrappa Venkatesh
1Institute of Molecular and Cell Biology, 30 Medical Drive, 117609, Singapore.
Gene
|September 18, 2002
Summary
The pufferfish genome aids human gene discovery, revealing three novel human genes and conserved regulatory elements missed by prior analyses. This comparative genomics approach highlights Fugu's utility for human genome annotation.
Area of Science:
- Comparative genomics
- Human genome annotation
- Vertebrate evolution
Background:
- The compact pufferfish (Fugu rubripes) genome offers a valuable resource for human genome analysis.
- Previous gene prediction methods may have missed novel human genes.
Purpose of the Study:
- To annotate and compare Fugu and human genomic sequences.
- To identify novel human genes and regulatory elements using Fugu as a reference.
- To investigate conserved gene order and non-coding sequences between Fugu and humans.
Main Methods:
- Comparative sequence analysis of 85 kb of Fugu DNA against the human draft genome.
- Gene prediction and annotation.
- Identification of conserved non-coding sequences.
- Analysis of gene order and synteny.
Main Results:
- Three novel human genes (ZNF366, ZNF367, C9orf21) were identified, missed by previous methods.
- Two Fugu genes (chemokine, kinase) lacked human homologs, suggesting teleost-specific or human-lost genes.
- Conserved non-coding sequences in regulatory regions were found, indicating roles in gene regulation.
- Significant differences in gene order and locus dispersion were observed between Fugu and human genomes.
Conclusions:
- The Fugu genome is a powerful supplementary tool for uncovering novel human genes and regulatory regions.
- Comparative genomics with Fugu aids in understanding vertebrate gene evolution and conservation.
- Conserved synteny provides evidence for orthologous gene identification in distant species.
Related Concept Videos
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
02:51Multi-species Conserved Sequences
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
02:37Gene Duplication and Divergence
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...