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Multi-species Conserved Sequences

Multi-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.
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Updated: Jun 4, 2025

In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression

In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression

Published on: March 29, 2019

Optimising Exome Captures in Species With Large Genomes Using Species-Specific Repetitive DNA Blocker.

Robert Kesälahti^1,2, Timo A Kumpula¹, Sandra Cervantes^1,3

¹Department of Ecology and Genetics, University of Oulu, Oulu, Finland.

Molecular Ecology Resources

|December 18, 2024

Summary

Species-specific C0t-1 DNA blockers significantly improve exome capture efficiency in large, repetitive genomes like Pinus sylvestris. This method enhances single nucleotide polymorphism discovery and reduces repetitive DNA sequencing compared to universal blockers.

Keywords:

Pinus sylvestris c0t‐1 DNA conifer exome capture large genome repetitive DNA

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Last Updated: Jun 4, 2025

In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression

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Published on: March 29, 2019

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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Novel Sequence Discovery by Subtractive Genomics

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Published on: January 25, 2019

Area of Science:

Genomics
Molecular Evolution
Bioinformatics

Background:

Large, repetitive genomes pose challenges for functional genetic studies.
Exome capture is a cost-effective method for sequencing protein-coding regions.
C0t-1 DNA blockers are crucial for preventing repetitive DNA hybridization during exome capture.

Purpose of the Study:

To evaluate the effectiveness of species-specific C0t-1 DNA blockers in exome capture for Pinus sylvestris.
To compare species-specific blockers with universal blockers for optimizing exome capture in a non-model organism.

Main Methods:

Exome capture experiments were performed on Pinus sylvestris DNA.
Treatments included a commercial universal blocker and species-specific C0t-1 DNA (30,000 and 60,000 ng).
Performance was assessed by comparing unique exon capture, SNP discovery, and repetitive DNA sequencing.

Main Results:

Species-specific C0t-1 DNA captured more unique exons than the universal blocker.
Increased single nucleotide polymorphism discovery was observed with species-specific blockers.
Sequencing of tandem repeats was reduced when using species-specific C0t-1 DNA.

Conclusions:

Species-specific C0t-1 DNA blockers are highly effective for exome capture in large, repetitive genomes.
Optimizing exome capture requires at least 60,000 ng of species-specific C0t-1 DNA.
This method is practical for non-model species and compatible with existing bait designs.