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Related Concept Videos

Multi-species Conserved Sequences02:51

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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...
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CCS-Consensuser: A Haplotype-Aware Consensus Generator for PacBio Amplicon Sequences.

Carlos Congrains1,2, Forest Bremer2, Julian R Dupuis3

  • 1Entomology Section, Department of Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA.

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|April 4, 2025
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Summary
This summary is machine-generated.

A new pipeline, CCS-consensuser, analyzes amplicon long-read DNA sequencing data to generate high-quality consensus sequences. This tool accurately identifies intra-individual genetic variation, improving applications in biology and medicine.

Keywords:
amplicon sequencingcircular consensus sequencingconsensus sequenceintraindividual variationlong‐read sequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Third Generation Sequencing (TGS) platforms generate long-read data, advancing DNA sequencing capabilities.
  • Amplicon sequencing is widely used in biological sciences, but lacks dedicated software for analyzing intra-individual genetic variation from long-read data.

Purpose of the Study:

  • To introduce CCS-consensuser, an end-to-end pipeline for generating consensus sequences from PacBio circular consensus sequencing (CCS) amplicon data.
  • To evaluate the accuracy and concordance of CCS-consensuser with other sequencing platforms and simulated datasets.

Main Methods:

  • Utilized PacBio circular consensus sequencing (CCS) for high-fidelity long-read generation.
  • Developed and applied the CCS-consensuser pipeline for consensus sequence generation.
  • Assessed concordance with Illumina, Sanger sequencing, and simulated datasets.

Main Results:

  • CCS amplicon data with CCS-consensuser produced high-quality sequences (PHRED > 30).
  • Achieved high concordance rates: 94.94% with COI Sanger, 92.61% with nuclear Illumina (heterozygous loci), and 95.55% with simulated phased nuclear data.
  • Demonstrated capability in detecting mtDNA heteroplasmy, cross-contamination, and phasing nuclear genes.

Conclusions:

  • CCS-consensuser coupled with CCS amplicon data offers a robust method for high-quality sequence generation.
  • The pipeline is suitable for haploid data (e.g., DNA barcoding) and uniquely addresses within-individual haplotype variation.
  • Shows significant promise for diverse applications in biology and medicine previously limited by traditional techniques.