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Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans
BACKGROUND: Increasing genetic and phenotypic differences found among natural isolates of C. elegans have encouraged researchers to explore the natural variation of this nematode species. RESULTS: Here we report on the identification of genomic differences between the reference strain N2 and the Haw...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023591/ https://www.ncbi.nlm.nih.gov/pubmed/24694239 http://dx.doi.org/10.1186/1471-2164-15-255 |
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author | Vergara, Ismael A Tarailo-Graovac, Maja Frech, Christian Wang, Jun Qin, Zhaozhao Zhang, Ting She, Rong Chu, Jeffrey SC Wang, Ke Chen, Nansheng |
author_facet | Vergara, Ismael A Tarailo-Graovac, Maja Frech, Christian Wang, Jun Qin, Zhaozhao Zhang, Ting She, Rong Chu, Jeffrey SC Wang, Ke Chen, Nansheng |
author_sort | Vergara, Ismael A |
collection | PubMed |
description | BACKGROUND: Increasing genetic and phenotypic differences found among natural isolates of C. elegans have encouraged researchers to explore the natural variation of this nematode species. RESULTS: Here we report on the identification of genomic differences between the reference strain N2 and the Hawaiian strain CB4856, one of the most genetically distant strains from N2. To identify both small- and large-scale genomic variations (GVs), we have sequenced the CB4856 genome using both Roche 454 (~400 bps single reads) and Illumina GA DNA sequencing methods (101 bps paired-end reads). Compared to previously described variants (available in WormBase), our effort uncovered twice as many single nucleotide variants (SNVs) and increased the number of small InDels almost 20-fold. Moreover, we identified and validated large insertions, most of which range from 150 bps to 1.2 kb in length in the CB4856 strain. Identified GVs had a widespread impact on protein-coding sequences, including 585 single-copy genes that have associated severe phenotypes of reduced viability in RNAi and genetics studies. Sixty of these genes are homologs of human genes associated with diseases. Furthermore, our work confirms previously identified GVs associated with differences in behavioural and biological traits between the N2 and CB4856 strains. CONCLUSIONS: The identified GVs provide a rich resource for future studies that aim to explain the genetic basis for other trait differences between the N2 and CB4856 strains. |
format | Online Article Text |
id | pubmed-4023591 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40235912014-05-16 Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans Vergara, Ismael A Tarailo-Graovac, Maja Frech, Christian Wang, Jun Qin, Zhaozhao Zhang, Ting She, Rong Chu, Jeffrey SC Wang, Ke Chen, Nansheng BMC Genomics Research Article BACKGROUND: Increasing genetic and phenotypic differences found among natural isolates of C. elegans have encouraged researchers to explore the natural variation of this nematode species. RESULTS: Here we report on the identification of genomic differences between the reference strain N2 and the Hawaiian strain CB4856, one of the most genetically distant strains from N2. To identify both small- and large-scale genomic variations (GVs), we have sequenced the CB4856 genome using both Roche 454 (~400 bps single reads) and Illumina GA DNA sequencing methods (101 bps paired-end reads). Compared to previously described variants (available in WormBase), our effort uncovered twice as many single nucleotide variants (SNVs) and increased the number of small InDels almost 20-fold. Moreover, we identified and validated large insertions, most of which range from 150 bps to 1.2 kb in length in the CB4856 strain. Identified GVs had a widespread impact on protein-coding sequences, including 585 single-copy genes that have associated severe phenotypes of reduced viability in RNAi and genetics studies. Sixty of these genes are homologs of human genes associated with diseases. Furthermore, our work confirms previously identified GVs associated with differences in behavioural and biological traits between the N2 and CB4856 strains. CONCLUSIONS: The identified GVs provide a rich resource for future studies that aim to explain the genetic basis for other trait differences between the N2 and CB4856 strains. BioMed Central 2014-04-02 /pmc/articles/PMC4023591/ /pubmed/24694239 http://dx.doi.org/10.1186/1471-2164-15-255 Text en Copyright © 2014 Vergara et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. |
spellingShingle | Research Article Vergara, Ismael A Tarailo-Graovac, Maja Frech, Christian Wang, Jun Qin, Zhaozhao Zhang, Ting She, Rong Chu, Jeffrey SC Wang, Ke Chen, Nansheng Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans |
title | Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans |
title_full | Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans |
title_fullStr | Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans |
title_full_unstemmed | Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans |
title_short | Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans |
title_sort | genome-wide variations in a natural isolate of the nematode caenorhabditis elegans |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023591/ https://www.ncbi.nlm.nih.gov/pubmed/24694239 http://dx.doi.org/10.1186/1471-2164-15-255 |
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