X

Quality Statement

Pacific Biosciences is committed to providing high-quality products that meet customer expectations and comply with regulations. We will achieve these goals by adhering to and maintaining an effective quality-management system designed to ensure product quality, performance, and safety.

X

Image Use Agreement

By downloading, copying, or making any use of the images located on this website (“Site”) you acknowledge that you have read and understand, and agree to, the terms of this Image Usage Agreement, as well as the terms provided on the Legal Notices webpage, which together govern your use of the images as provided below. If you do not agree to such terms, do not download, copy or use the images in any way, unless you have written permission signed by an authorized Pacific Biosciences representative.

Subject to the terms of this Agreement and the terms provided on the Legal Notices webpage (to the extent they do not conflict with the terms of this Agreement), you may use the images on the Site solely for (a) editorial use by press and/or industry analysts, (b) in connection with a normal, peer-reviewed, scientific publication, book or presentation, or the like. You may not alter or modify any image, in whole or in part, for any reason. You may not use any image in a manner that misrepresents the associated Pacific Biosciences product, service or technology or any associated characteristics, data, or properties thereof. You also may not use any image in a manner that denotes some representation or warranty (express, implied or statutory) from Pacific Biosciences of the product, service or technology. The rights granted by this Agreement are personal to you and are not transferable by you to another party.

You, and not Pacific Biosciences, are responsible for your use of the images. You acknowledge and agree that any misuse of the images or breach of this Agreement will cause Pacific Biosciences irreparable harm. Pacific Biosciences is either an owner or licensee of the image, and not an agent for the owner. You agree to give Pacific Biosciences a credit line as follows: "Courtesy of Pacific Biosciences of California, Inc., Menlo Park, CA, USA" and also include any other credits or acknowledgments noted by Pacific Biosciences. You must include any copyright notice originally included with the images on all copies.

IMAGES ARE PROVIDED BY Pacific Biosciences ON AN "AS-IS" BASIS. Pacific Biosciences DISCLAIMS ALL REPRESENTATIONS AND WARRANTIES, EXPRESS, IMPLIED OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, NON-INFRINGEMENT, OWNERSHIP, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL Pacific Biosciences BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, PUNITIVE, OR CONSEQUENTIAL DAMAGES OF ANY KIND WHATSOEVER WITH RESPECT TO THE IMAGES.

You agree that Pacific Biosciences may terminate your access to and use of the images located on the PacificBiosciences.com website at any time and without prior notice, if it considers you to have violated any of the terms of this Image Use Agreement. You agree to indemnify, defend and hold harmless Pacific Biosciences, its officers, directors, employees, agents, licensors, suppliers and any third party information providers to the Site from and against all losses, expenses, damages and costs, including reasonable attorneys' fees, resulting from any violation by you of the terms of this Image Use Agreement or Pacific Biosciences' termination of your access to or use of the Site. Termination will not affect Pacific Biosciences' rights or your obligations which accrued before the termination.

I have read and understand, and agree to, the Image Usage Agreement.

I disagree and would like to return to the Pacific Biosciences home page.

Pacific Biosciences
Contact:

New Nematode Assembly Simplifies Search for Evolutionary Clues

Thursday, December 28, 2017

Nematodes are both simple and complex, making them one of the most attractive animal taxa to study basic biological processes, including genome evolution. Studies in the nematode Caenorhabditis elegans, for instance, have provided invaluable insights into almost all aspects of biology, from developmental to neurobiology and human diseases.

However, the high degree of fragmentation of current genome assemblies for many organisms complicates almost all types of genomic analysis. As the authors of a recent Cell Reports paper, Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus, point out, “general questions of chromosome evolution cannot be addressed if genome assemblies consist of thousands of contigs.”

SMRT Sequencing was able to remedy this problem. By sequencing the genome of P. pacificus with the PacBio Sequel System, Christian Roedelsperger, Ralf J. Sommer, and other colleagues from the Max Planck Institute for Developmental Biology generated an assembly that reduced the number of contigs from 12,395 to 135 and simplified their search for clues into developmental systems drift, the genetics of phenotypic plasticity, and genome evolution.

pacificus has become an increasingly important model species, used in comparison to two other free-living nematode species, C. elegans and C. briggsae, to investigate how various biological pathways and their underlying regulatory programs are modified during evolution.

Populated primarily by self-fertilizing hermaphrodites with a low frequency of males, all three species undergo frequent recombination among different genetic lineages. Their genomes range in size from 100-160 Mb, but all have five autosomes and one sex chromosome. Many of their shared features are controlled by completely different molecular programs, a phenomenon referred to as ‘‘developmental systems drift,” making them particularly useful in comparative biology.

pacificus is also one of the most promising animal models in the investigation of “phenotypic plasticity,” the property of a single genotype to form distinct phenotypes in response to different environmental influences. In P. pacificus, for instance, young nematode larvae either develop directly into adults or into non-feeding, long-lived dauer larvae, which can disperse to find more suitable environments. They also exhibit two different mouth morphs that are specialized for either bacterial or predatory feeding.

For these reasons, the Max Planck team was particularly interested in unravelling some of their genetic mysteries. They sequenced the genome of the P. pacificus reference strain (PS312) on the Sequel System to 100-fold coverage. The resulting de novo assembly enabled ordering and orientation of contigs for all six P. pacificus chromosomes. “This allowed us to robustly characterize chromosomal patterns of gene density, repeat content, nucleotide diversity, linkage disequilibrium, and macrosynteny,” the authors write.

Among their findings was the discovery of a major translocation from autosomes to the sex chromosome during the evolution of the lineage leading to C. elegans.“These findings highlight the impact of large-scale chromosomal rearrangements in nematode genome evolution and emphasize the need for high-quality genome assemblies to robustly study these events,” add the authors. “The new P. pacificus assembly will allow more rigorous genomewide analysis in all fields of genomics, and will greatly enhance the capacity to map and identify causal genes for various phenotypes.”

 

 

Subscribe for blog updates:

Archives