Identification of genome-specific transcripts in wheat-rye translocation lines

Tong Geon Lee, Yong Weon Seo

Research output: Contribution to journalArticle

Abstract

Studying gene expression in wheat-rye translocation lines is complicated due to the presence of homeologs in hexaploid wheat and high levels of synteny between wheat and rye genomes (Naranjo and Fernandez-Rueda, 1991 [. 1]; Devos et al., 1995 [. 2]; Lee et al., 2010 [. 3]; Lee et al., 2013 [. 4]). To overcome limitations of current gene expression studies on wheat-rye translocation lines and identify genome-specific transcripts, we developed a custom Roche NimbleGen Gene Expression microarray that contains probes derived from the sequence of hexaploid wheat, diploid rye and diploid progenitors of hexaploid wheat genome (Lee et al., 2014). Using the array developed, we identified genome-specific transcripts in a wheat-rye translocation line (Lee et al., 2014). Expression data are deposited in the NCBI Gene Expression Omnibus (GEO) under accession number GSE58678. Here we report the details of the methods used in the array workflow and data analysis.

Original languageEnglish
Pages (from-to)151-153
Number of pages3
JournalGenomics Data
Volume5
DOIs
Publication statusPublished - 2015 Sep 1

Fingerprint

Gene expression
Triticum
Genes
Genome
Gene Expression
Diploidy
Microarrays
Synteny
Workflow
Secale

Keywords

  • Homeologous
  • Microarray
  • Polyploidy
  • Synteny
  • Wheat-rye translocation

ASJC Scopus subject areas

  • Molecular Medicine
  • Biochemistry
  • Biotechnology
  • Genetics

Cite this

Identification of genome-specific transcripts in wheat-rye translocation lines. / Lee, Tong Geon; Seo, Yong Weon.

In: Genomics Data, Vol. 5, 01.09.2015, p. 151-153.

Research output: Contribution to journalArticle

@article{d1c262b590314f0587e89351a60a42fa,
title = "Identification of genome-specific transcripts in wheat-rye translocation lines",
abstract = "Studying gene expression in wheat-rye translocation lines is complicated due to the presence of homeologs in hexaploid wheat and high levels of synteny between wheat and rye genomes (Naranjo and Fernandez-Rueda, 1991 [. 1]; Devos et al., 1995 [. 2]; Lee et al., 2010 [. 3]; Lee et al., 2013 [. 4]). To overcome limitations of current gene expression studies on wheat-rye translocation lines and identify genome-specific transcripts, we developed a custom Roche NimbleGen Gene Expression microarray that contains probes derived from the sequence of hexaploid wheat, diploid rye and diploid progenitors of hexaploid wheat genome (Lee et al., 2014). Using the array developed, we identified genome-specific transcripts in a wheat-rye translocation line (Lee et al., 2014). Expression data are deposited in the NCBI Gene Expression Omnibus (GEO) under accession number GSE58678. Here we report the details of the methods used in the array workflow and data analysis.",
keywords = "Homeologous, Microarray, Polyploidy, Synteny, Wheat-rye translocation",
author = "Lee, {Tong Geon} and Seo, {Yong Weon}",
year = "2015",
month = "9",
day = "1",
doi = "10.1016/j.gdata.2015.05.045",
language = "English",
volume = "5",
pages = "151--153",
journal = "Genomics Data",
issn = "2213-5960",
publisher = "Elsevier Inc.",

}

TY - JOUR

T1 - Identification of genome-specific transcripts in wheat-rye translocation lines

AU - Lee, Tong Geon

AU - Seo, Yong Weon

PY - 2015/9/1

Y1 - 2015/9/1

N2 - Studying gene expression in wheat-rye translocation lines is complicated due to the presence of homeologs in hexaploid wheat and high levels of synteny between wheat and rye genomes (Naranjo and Fernandez-Rueda, 1991 [. 1]; Devos et al., 1995 [. 2]; Lee et al., 2010 [. 3]; Lee et al., 2013 [. 4]). To overcome limitations of current gene expression studies on wheat-rye translocation lines and identify genome-specific transcripts, we developed a custom Roche NimbleGen Gene Expression microarray that contains probes derived from the sequence of hexaploid wheat, diploid rye and diploid progenitors of hexaploid wheat genome (Lee et al., 2014). Using the array developed, we identified genome-specific transcripts in a wheat-rye translocation line (Lee et al., 2014). Expression data are deposited in the NCBI Gene Expression Omnibus (GEO) under accession number GSE58678. Here we report the details of the methods used in the array workflow and data analysis.

AB - Studying gene expression in wheat-rye translocation lines is complicated due to the presence of homeologs in hexaploid wheat and high levels of synteny between wheat and rye genomes (Naranjo and Fernandez-Rueda, 1991 [. 1]; Devos et al., 1995 [. 2]; Lee et al., 2010 [. 3]; Lee et al., 2013 [. 4]). To overcome limitations of current gene expression studies on wheat-rye translocation lines and identify genome-specific transcripts, we developed a custom Roche NimbleGen Gene Expression microarray that contains probes derived from the sequence of hexaploid wheat, diploid rye and diploid progenitors of hexaploid wheat genome (Lee et al., 2014). Using the array developed, we identified genome-specific transcripts in a wheat-rye translocation line (Lee et al., 2014). Expression data are deposited in the NCBI Gene Expression Omnibus (GEO) under accession number GSE58678. Here we report the details of the methods used in the array workflow and data analysis.

KW - Homeologous

KW - Microarray

KW - Polyploidy

KW - Synteny

KW - Wheat-rye translocation

UR - http://www.scopus.com/inward/record.url?scp=84930941875&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84930941875&partnerID=8YFLogxK

U2 - 10.1016/j.gdata.2015.05.045

DO - 10.1016/j.gdata.2015.05.045

M3 - Article

VL - 5

SP - 151

EP - 153

JO - Genomics Data

JF - Genomics Data

SN - 2213-5960

ER -