Abstract
BACKGROUND: Barley and particularly wheat are two grass species of immense agricultural importance. In spite of polyploidization events within the latter, studies have shown that genotypically and phenotypically these species are very closely related and, indeed, fertile hybrids can be created by interbreeding. The advent of two genome-scale Affymetrix GeneChips now allows studies of the comparison of their transcriptomes. RESULTS: We have used the Wheat GeneChip to create a "gene expression atlas" for the wheat transcriptome (cv. Chinese Spring). For this, we chose mRNA from a range of tissues and developmental stages closely mirroring a comparable study carried out for barley (cv. Morex) using the Barley1 GeneChip. This, together with large-scale clustering of the probesets from the two GeneChips into "homologous groups", has allowed us to perform a genomic-scale comparative study of expression patterns in these two species. We explore the influence of the polyploidy of wheat on the results obtained with the Wheat GeneChip and quantify the correlation between conservation in gene sequence and gene expression in wheat and barley. In addition, we show how the conservation of expression patterns can be used to elucidate, probeset by probeset, the reliability of the Wheat GeneChip. CONCLUSION: While there are many differences in expression on the level of individual genes and tissues, we demonstrate that the wheat and barley transcriptomes appear highly correlated. This finding is significant not only because given small evolutionary distance between the two species it is widely expected, but also because it demonstrates that it is possible to use the two GeneChips for comparative studies. This is the case even though their probeset composition reflects rather different design principles as well as, of course, the present incomplete knowledge of the gene content of the two species. We also show that, in general, the Wheat GeneChip is not able to distinguish contributions from individual homoeologs. Furthermore, the comparison between the two species leads us to conclude that the conservation of both gene sequence as well as gene expression is positively correlated with absolute expression levels, presumably reflecting increased selection pressure on genes coding for proteins present at high levels. In addition, the results indicate the presence of a correlation between sequence and expression conservation within the Triticeae.
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Claims 7
Claim · model-written summary
A wheat gene expression atlas was created using the Wheat GeneChip.
- Taxon
- wheat
Triticum aestivume0 - Material
- cv. Chinese Springe0
- Outcome
- "gene expression atlas"e0
Not reportedComparatorValue
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“used the Wheat GeneChip to create a "gene expression atlas" for the wheat transcriptome (cv. Chinese Spring)”
Claim · model-written summary
The wheat and barley transcriptomes appeared highly correlated despite individual gene and tissue differences.
- Taxon
- wheat and barley
.jpg?width=60)
Hordeum vulgareTriticum aestivume0 - Outcome
- transcriptomes appear highly correlatede0
- Comparator
- individual genes and tissuese0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
.jpg?width=500)
Verbatim
e0“While there are many differences in expression on the level of individual genes and tissues, we demonstrate that the wheat and barley transcriptomes appear highly correlated.”
Claim · model-written summary
The two GeneChips were usable for comparative studies.
- Taxon
- wheat and barleyHordeum vulgareTriticum aestivume1
- Outcome
- comparative studiese0
Not reportedComparatorValue
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“it is possible to use the two GeneChips for comparative studies”
e1“wheat and barley transcriptomes”
Claim · model-written summary
The Wheat GeneChip generally could not distinguish individual homoeolog contributions.
- Taxon
- wheatTriticum aestivume1
- Outcome
- contributions from individual homoeologse0
Not reportedComparatorValue
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the Wheat GeneChip is not able to distinguish contributions from individual homoeologs”
e1“wheat and barley transcriptomes”
Claim · model-written summary
Conservation of gene sequence was positively correlated with absolute expression levels.
- Taxon
- wheat and barleyHordeum vulgareTriticum aestivume1
- Outcome
- conservation of both gene sequencee0
- Direction
- positively correlatede0
- Comparator
- absolute expression levelse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the conservation of both gene sequence as well as gene expression is positively correlated with absolute expression levels”
e1“wheat and barley transcriptomes”
Claim · model-written summary
Conservation of gene expression was positively correlated with absolute expression levels.
- Taxon
- wheat and barleyHordeum vulgareTriticum aestivume1
- Outcome
- gene expressione0
- Direction
- positively correlatede0
- Comparator
- absolute expression levelse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the conservation of both gene sequence as well as gene expression is positively correlated with absolute expression levels”
e1“wheat and barley transcriptomes”
Claim · model-written summary
Sequence and expression conservation were correlated within Triticeae.
- Taxon
- wheat and barleyHordeum vulgareTriticum aestivume1
- Outcome
- expression conservatione0
- Comparator
- sequencee0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a correlation between sequence and expression conservation within the Triticeae”
e1“wheat and barley transcriptomes”