Unknown

Dataset Information

0

Insertions/Deletions-Associated Nucleotide Polymorphism in Arabidopsis thaliana.

ABSTRACT: Although high levels of within-species variation are commonly observed, a general mechanism for the origin of such variation is still lacking. Insertions and deletions (indels) are a widespread feature of genomes and we hypothesize that there might be an association between indels and patterns of nucleotide polymorphism. Here, we investigate flanking sequences around 18 indels (>100 bp) among a large number of accessions of the plant, Arabidopsis thaliana. We found two distinct haplotypes, i.e., a nucleotide dimorphism, present around each of these indels and dimorphic haplotypes always corresponded to the indel-present/-absent patterns. In addition, the peaks of nucleotide diversity between the two divergent alleles were closely associated with these indels. Thus, there exists a close association between indels and dimorphisms. Further analysis suggests that indel-associated substitutions could be an important component of genetic variation shaping nucleotide polymorphism in Arabidopsis. Finally, we suggest a mechanism by which indels might generate these highly divergent haplotypes. This study provides evidence that nucleotide dimorphisms, which are frequently regarded as evidence of frequency-dependent selection, could be explained simply by structural variation in the genome.

SUBMITTER: Guo C 

PROVIDER: S-EPMC5127803 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

Json Xml
altmetric image

Publications

Insertions/Deletions-Associated Nucleotide Polymorphism in <i>Arabidopsis thaliana</i>.

Guo Changjiang C   Du Jianchang J   Wang Long L   Yang Sihai S   Mauricio Rodney R   Tian Dacheng D   Gu Tingting T  

Frontiers in plant science 20161130

Although high levels of within-species variation are commonly observed, a general mechanism for the origin of such variation is still lacking. Insertions and deletions (indels) are a widespread feature of genomes and we hypothesize that there might be an association between indels and patterns of nucleotide polymorphism. Here, we investigate flanking sequences around 18 indels (>100 bp) among a large number of accessions of the plant, <i>Arabidopsis thaliana</i>. We found two distinct haplotypes  ...[more]

Similar Datasets

Unknown Measuring Accelerated Rates of Insertions and Deletions Independent of Rates of Nucleotide Substitution.
| S-EPMC5080320 | biostudies-literature
Unknown The pattern of polymorphism in Arabidopsis thaliana.
| S-EPMC1135296 | biostudies-literature
Unknown Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm.
| S-EPMC2255072 | biostudies-literature
Unknown Strains of Escherichia coli O157:H7 differ primarily by insertions or deletions, not single-nucleotide polymorphisms.
| S-EPMC134921 | biostudies-literature
Unknown Strain-specific genotyping of Bifidobacterium animalis subsp. lactis by using single-nucleotide polymorphisms, insertions, and deletions.
| S-EPMC2786410 | biostudies-literature
Unknown Probabilistic phylogenetic inference with insertions and deletions.
| S-EPMC2527138 | biostudies-literature
Unknown Human gene targeting favors insertions over deletions.
| S-EPMC2940567 | biostudies-literature
Unknown Nucleotide insertions and deletions complement point mutations to massively expand the diversity created by somatic hypermutation of antibodies.
| S-EPMC4246108 | biostudies-literature
Unknown An efficient CRISPR vector toolbox for engineering large deletions in <i>Arabidopsis thaliana</i>.
| S-EPMC6071326 | biostudies-literature
Unknown Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana.
| S-EPMC1914337 | biostudies-literature