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A microarray for large-scale genomic and transcriptional analyses of the zebra finch (Taeniopygia guttata) and other passerines

Naurin, Sara LU ; Bensch, Staffan LU ; Hansson, Bengt LU ; Johansson, Tomas LU ; Clayton, David F; Albrekt, Ann-Sofie LU ; von Schantz, Torbjörn LU and Hasselquist, Dennis LU (2008) In Molecular Ecology Notes 8(2). p.275-281
Abstract
The microarray technology has revolutionized biological research in the last decade. By monitoring the expression of many genes simultaneously, microarrays can elucidate gene function, as well as scan entire genomes for candidate genes encoding complex traits. However, because of high costs of sequencing and design, microarrays have largely been restricted to a few model species. Cross-species microarray (CSM) analyses, where microarrays are used for other species than the one they were designed for, have had varied success. We have conducted a CSM analysis by hybridizing genomic DNA from the common whitethroat (Sylvia communis) on a newly developed Affymetrix array designed for the zebra finch (Taeniopygia guttata), the Lund-zf array. The... (More)
The microarray technology has revolutionized biological research in the last decade. By monitoring the expression of many genes simultaneously, microarrays can elucidate gene function, as well as scan entire genomes for candidate genes encoding complex traits. However, because of high costs of sequencing and design, microarrays have largely been restricted to a few model species. Cross-species microarray (CSM) analyses, where microarrays are used for other species than the one they were designed for, have had varied success. We have conducted a CSM analysis by hybridizing genomic DNA from the common whitethroat (Sylvia communis) on a newly developed Affymetrix array designed for the zebra finch (Taeniopygia guttata), the Lund-zf array. The results indicate a very high potential for the zebra finch array to act as a CSM utility in other passerine birds. When hybridizing zebra finch genomic DNA, 98% of the gene representatives had higher signal intensities than the background cut-off, and for the common whitethroat, we found the equivalent proportion to be as high as 96%. This was surprising given the fact that finches and warblers diverged 25-50 million years ago, but may be explained by a relatively low sequence divergence between passerines (89-93%). Passerine birds are widely used in studies of ecology and evolution, and a zebra finch array that can be used for many species may have a large impact on future research directions. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
cross-species, affymetrix, gene expression, Passeriformes, microarray, Taeniopygia guttata
in
Molecular Ecology Notes
volume
8
issue
2
pages
275 - 281
publisher
Wiley-Blackwell
external identifiers
  • wos:000253827300005
  • scopus:38949089254
ISSN
1471-8278
DOI
10.1111/j.1471-8286.2007.01979.x
project
CAnMove
language
English
LU publication?
yes
id
26ee5710-8d0c-4af5-b30c-3905868aaeff (old id 1185966)
date added to LUP
2008-09-03 11:37:14
date last changed
2017-08-27 04:09:53
@article{26ee5710-8d0c-4af5-b30c-3905868aaeff,
  abstract     = {The microarray technology has revolutionized biological research in the last decade. By monitoring the expression of many genes simultaneously, microarrays can elucidate gene function, as well as scan entire genomes for candidate genes encoding complex traits. However, because of high costs of sequencing and design, microarrays have largely been restricted to a few model species. Cross-species microarray (CSM) analyses, where microarrays are used for other species than the one they were designed for, have had varied success. We have conducted a CSM analysis by hybridizing genomic DNA from the common whitethroat (Sylvia communis) on a newly developed Affymetrix array designed for the zebra finch (Taeniopygia guttata), the Lund-zf array. The results indicate a very high potential for the zebra finch array to act as a CSM utility in other passerine birds. When hybridizing zebra finch genomic DNA, 98% of the gene representatives had higher signal intensities than the background cut-off, and for the common whitethroat, we found the equivalent proportion to be as high as 96%. This was surprising given the fact that finches and warblers diverged 25-50 million years ago, but may be explained by a relatively low sequence divergence between passerines (89-93%). Passerine birds are widely used in studies of ecology and evolution, and a zebra finch array that can be used for many species may have a large impact on future research directions.},
  author       = {Naurin, Sara and Bensch, Staffan and Hansson, Bengt and Johansson, Tomas and Clayton, David F and Albrekt, Ann-Sofie and von Schantz, Torbjörn and Hasselquist, Dennis},
  issn         = {1471-8278},
  keyword      = {cross-species,affymetrix,gene expression,Passeriformes,microarray,Taeniopygia guttata},
  language     = {eng},
  number       = {2},
  pages        = {275--281},
  publisher    = {Wiley-Blackwell},
  series       = {Molecular Ecology Notes},
  title        = {A microarray for large-scale genomic and transcriptional analyses of the zebra finch (Taeniopygia guttata) and other passerines},
  url          = {http://dx.doi.org/10.1111/j.1471-8286.2007.01979.x},
  volume       = {8},
  year         = {2008},
}