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Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856

Thompson, OA; Snoek, LB; Nijveen, H; Sterken, MG; Volkers, RJM; Brenchley, RC; van't Hof, A; Bevers, RPJ; Cossins, AR; Yanai, I; Hajnal, A; Schmid, T; Perkins, JD; Spencer, D; Kruglyak, L; Andersen, EC; Moerman, DG; Hillier, LW; Kammenga, JE; Waterston, RH

Authors

OA Thompson

LB Snoek

H Nijveen

MG Sterken

RJM Volkers

A van't Hof

RPJ Bevers

AR Cossins

I Yanai

A Hajnal

T Schmid

JD Perkins

D Spencer

L Kruglyak

EC Andersen

DG Moerman

LW Hillier

JE Kammenga

RH Waterston



Abstract

The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. The CB4856 genome when compared against the N2 reference has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events (indels) that result in a total of 3.3 megabasepairs (Mb) of N2 sequence missing from CB4856 and 1.4 Mb of sequence present in CB4856 not present in N2. As previously reported, the density of SNVs varies along the chromosomes, with the arms of chromosomes showing greater average variation than the centers. In addition, we find 61 regions totaling 2.8 Mb, distributed across all six chromosomes, that have a greatly elevated SNV density, ranging from 2% to 16% SNVs. A survey of other wild isolates show that the two alternative haplotypes for each region are widely distributed, suggesting they have been maintained by balancing selection over long evolutionary times. These divergent regions contain an abundance of genes from large rapidly evolving families encoding F-box, MATH, BATH, seven-transmembrane G-coupled receptors, and nuclear hormone receptors suggesting that they provide selective advantages in natural environments. The draft sequence makes available a comprehensive catalog of sequence differences between the CB4856 and N2 strains that will facilitate the molecular dissection of their phenotypic differences. Our work also emphasizes the importance of going beyond simple alignment of reads to a reference genome when assessing differences between genomes.

Citation

Thompson, O., Snoek, L., Nijveen, H., Sterken, M., Volkers, R., Brenchley, R., …Waterston, R. (2015). Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856. Genetics, 200(3), 975-989. https://doi.org/10.1534/genetics.115.175950

Journal Article Type Article
Acceptance Date Apr 29, 2015
Online Publication Date May 19, 2015
Publication Date Jul 13, 2015
Deposit Date Jun 17, 2015
Journal Genetics
Print ISSN 0016-6731
Electronic ISSN 1943-2631
Publisher Genetics Society of America
Peer Reviewed Peer Reviewed
Volume 200
Issue 3
Pages 975-989
DOI https://doi.org/10.1534/genetics.115.175950
Publisher URL http://dx.doi.org/10.1534/genetics.115.175950
Related Public URLs http://www.genetics.org/
PMID 25995208
Additional Information Funders : National Human Genome Research Institute (NHGRI);William H. Gates Chair of Biomedical Sciences;Netherlands Organisation for Scientific Research
Projects : American Recovery and Reinvestment Act (ARRA) GO grant
Grant Number: HG005921 and HG007355
Grant Number: 823.01.001