High-diversity genes in the arabidopsis genome

Jennifer M. Cork, Michael D. Purugganan

Research output: Contribution to journalArticle

Abstract

High-diversity genes represent an important class of loci in organismal genomes. Since elevated levels of nucleotide variation are a key component of the molecular signature for balancing selection or local adaptation, high-diversity genes may represent loci whose alleles are selectively maintained as balanced polymorphisms. Comparison of 4300 random shotgun sequence fragments of the Arabidopsis thaliana L er ecotype genome with the whole genomic sequence of the Col-0 ecotype identified 60 genes with putatively high levels of intraspecific variability. Eleven of these genes were sequenced in multiple A. thaliana accessions, 3 of which were found to display elevated levels of nucleotide polymorphism. These genes encode the myb-like transcription factor MYB103, a putative soluble starch synthase I, and a homeodomain-leucine zipper transcription factor. Analysis of these genes and 4-7 flanking genes in 14-20 A. thaliana ecotypes revealed that two of these loci show other characteristics of balanced polymorphisms, including broad peaks of nucleotide diversity spanning multiple linked genes and an excess of intermediate-frequency polymorphisms. Scanning genomes for high-diversity genomic regions may be useful in approaches to adaptive trait locus mapping for uncovering candidate balanced polymorphisms.

Original languageEnglish (US)
Pages (from-to)1897-1911
Number of pages15
JournalGenetics
Volume170
Issue number4
DOIs
StatePublished - Aug 2005

Fingerprint

Arabidopsis
Genome
Ecotype
Genes
Nucleotides
Transcription Factors
Starch Synthase
myb Genes
Leucine Zippers
Glycogen Synthase
Firearms
Alleles

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

High-diversity genes in the arabidopsis genome. / Cork, Jennifer M.; Purugganan, Michael D.

In: Genetics, Vol. 170, No. 4, 08.2005, p. 1897-1911.

Research output: Contribution to journalArticle

Cork, Jennifer M. ; Purugganan, Michael D. / High-diversity genes in the arabidopsis genome. In: Genetics. 2005 ; Vol. 170, No. 4. pp. 1897-1911.
@article{7df6787cc476415d9b26481618f1c05e,
title = "High-diversity genes in the arabidopsis genome",
abstract = "High-diversity genes represent an important class of loci in organismal genomes. Since elevated levels of nucleotide variation are a key component of the molecular signature for balancing selection or local adaptation, high-diversity genes may represent loci whose alleles are selectively maintained as balanced polymorphisms. Comparison of 4300 random shotgun sequence fragments of the Arabidopsis thaliana L er ecotype genome with the whole genomic sequence of the Col-0 ecotype identified 60 genes with putatively high levels of intraspecific variability. Eleven of these genes were sequenced in multiple A. thaliana accessions, 3 of which were found to display elevated levels of nucleotide polymorphism. These genes encode the myb-like transcription factor MYB103, a putative soluble starch synthase I, and a homeodomain-leucine zipper transcription factor. Analysis of these genes and 4-7 flanking genes in 14-20 A. thaliana ecotypes revealed that two of these loci show other characteristics of balanced polymorphisms, including broad peaks of nucleotide diversity spanning multiple linked genes and an excess of intermediate-frequency polymorphisms. Scanning genomes for high-diversity genomic regions may be useful in approaches to adaptive trait locus mapping for uncovering candidate balanced polymorphisms.",
author = "Cork, {Jennifer M.} and Purugganan, {Michael D.}",
year = "2005",
month = "8",
doi = "10.1534/genetics.104.036152",
language = "English (US)",
volume = "170",
pages = "1897--1911",
journal = "Genetics",
issn = "0016-6731",
publisher = "Genetics Society of America",
number = "4",

}

TY - JOUR

T1 - High-diversity genes in the arabidopsis genome

AU - Cork, Jennifer M.

AU - Purugganan, Michael D.

PY - 2005/8

Y1 - 2005/8

N2 - High-diversity genes represent an important class of loci in organismal genomes. Since elevated levels of nucleotide variation are a key component of the molecular signature for balancing selection or local adaptation, high-diversity genes may represent loci whose alleles are selectively maintained as balanced polymorphisms. Comparison of 4300 random shotgun sequence fragments of the Arabidopsis thaliana L er ecotype genome with the whole genomic sequence of the Col-0 ecotype identified 60 genes with putatively high levels of intraspecific variability. Eleven of these genes were sequenced in multiple A. thaliana accessions, 3 of which were found to display elevated levels of nucleotide polymorphism. These genes encode the myb-like transcription factor MYB103, a putative soluble starch synthase I, and a homeodomain-leucine zipper transcription factor. Analysis of these genes and 4-7 flanking genes in 14-20 A. thaliana ecotypes revealed that two of these loci show other characteristics of balanced polymorphisms, including broad peaks of nucleotide diversity spanning multiple linked genes and an excess of intermediate-frequency polymorphisms. Scanning genomes for high-diversity genomic regions may be useful in approaches to adaptive trait locus mapping for uncovering candidate balanced polymorphisms.

AB - High-diversity genes represent an important class of loci in organismal genomes. Since elevated levels of nucleotide variation are a key component of the molecular signature for balancing selection or local adaptation, high-diversity genes may represent loci whose alleles are selectively maintained as balanced polymorphisms. Comparison of 4300 random shotgun sequence fragments of the Arabidopsis thaliana L er ecotype genome with the whole genomic sequence of the Col-0 ecotype identified 60 genes with putatively high levels of intraspecific variability. Eleven of these genes were sequenced in multiple A. thaliana accessions, 3 of which were found to display elevated levels of nucleotide polymorphism. These genes encode the myb-like transcription factor MYB103, a putative soluble starch synthase I, and a homeodomain-leucine zipper transcription factor. Analysis of these genes and 4-7 flanking genes in 14-20 A. thaliana ecotypes revealed that two of these loci show other characteristics of balanced polymorphisms, including broad peaks of nucleotide diversity spanning multiple linked genes and an excess of intermediate-frequency polymorphisms. Scanning genomes for high-diversity genomic regions may be useful in approaches to adaptive trait locus mapping for uncovering candidate balanced polymorphisms.

UR - http://www.scopus.com/inward/record.url?scp=25444453446&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=25444453446&partnerID=8YFLogxK

U2 - 10.1534/genetics.104.036152

DO - 10.1534/genetics.104.036152

M3 - Article

C2 - 15911589

AN - SCOPUS:25444453446

VL - 170

SP - 1897

EP - 1911

JO - Genetics

JF - Genetics

SN - 0016-6731

IS - 4

ER -