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Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression - PubMed

  • ️Sun Jan 01 2012

Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression

Elie Raherison et al. BMC Genomics. 2012.

Abstract

Background: Conifers have very large genomes (13 to 30 Gigabases) that are mostly uncharacterized although extensive cDNA resources have recently become available. This report presents a global overview of transcriptome variation in a conifer tree and documents conservation and diversity of gene expression patterns among major vegetative tissues.

Results: An oligonucleotide microarray was developed from Picea glauca and P. sitchensis cDNA datasets. It represents 23,853 unique genes and was shown to be suitable for transcriptome profiling in several species. A comparison of secondary xylem and phelloderm tissues showed that preferential expression in these vascular tissues was highly conserved among Picea spp. RNA-Sequencing strongly confirmed tissue preferential expression and provided a robust validation of the microarray design. A small database of transcription profiles called PiceaGenExpress was developed from over 150 hybridizations spanning eight major tissue types. In total, transcripts were detected for 92% of the genes on the microarray, in at least one tissue. Non-annotated genes were predominantly expressed at low levels in fewer tissues than genes of known or predicted function. Diversity of expression within gene families may be rapidly assessed from PiceaGenExpress. In conifer trees, dehydrins and late embryogenesis abundant (LEA) osmotic regulation proteins occur in large gene families compared to angiosperms. Strong contrasts and low diversity was observed in the dehydrin family, while diverse patterns suggested a greater degree of diversification among LEAs.

Conclusion: Together, the oligonucleotide microarray and the PiceaGenExpress database represent the first resource of this kind for gymnosperm plants. The spruce transcriptome analysis reported here is expected to accelerate genetic studies in the large and important group comprised of conifer trees.

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Figures

Figure 1
Figure 1

Interspecific comparison of hybridization intensities in secondary xylem.A-F: Pair-wise comparison of white spruce and six other species based on the number of shared positive probes indicated in the plots. The squared correlation coefficients (r2) are as follows 0.86 (A), 0.85 (B), 0.89 (C), 0.29 (D), 0.22 (E) and 0.27 (F). G: Analysis of signal intensity variation between species; the fold change (FC) was determined from the average normalized signal intensities (log2 scale). An FC of 1 or −1 represents a two-fold signal increase or decrease, respectively. For phelloderm results, see Additional file 4: Figure S3.

Figure 2
Figure 2

Preferential expression in secondary vascular tissues of three spruce species. The FC data in the plot represent genes with differential expression in all three spruces. The scale is the log2 fold change.

Figure 3
Figure 3

The PiceaGenExpress database reveals tissue preferential and conserved expression patterns within three gene families.A: Cellulose synthases. B: Photosystem I and II proteins. C: Ubiquitins. NA: Not detected. Tissues: B (Vegetative buds), F (Foliage), X-M (Xylem - mature), X-J (Xylem - juvenile), P (Phelloderm), R (Adventitious roots), M (Megagametophytes), E (Embryogenic cells).

Figure 4
Figure 4

Expression classes and numbers of tissue of annotated and non annotated sequences.A-C: Number of annotated and nonannotated sequences per expression class for xylem from juvenile trees (A), roots (B) and young foliage (C). Other tissues are shown in Additional file 8: Figure S5. D: Number of tissues in which each annotated and non-annotated sequence was detected. Frequency, number of genes in a given intensity class or detected in a given number of tissues types.

Figure 5
Figure 5

Gene expression patterns in two osmotic regulation protein families based on the PiceaGenExpress database.A: Dehydrins. B: Late Embryogenesis Abundant proteins. C: Distribution of Euclidean distances between the members of each protein family. The order of the bars is not representative of the order of the genes in panels A and B. A, B: Tissues: B (Vegetative buds), F (Foliage), X-M (Xylem - mature), X-J (Xylem - juvenile), P (Phelloderm), R (Adventitious roots), M (Megagametophytes), E (Embryogenic cells).

Figure 6
Figure 6

Expression patterns of LTR retrotransposons based on the PiceaGenExpress database.A: Sequences containing protein domains of LTR retroelements. Pfam annotations: a: Integrase core domain; b: Retrotransposon gag protein; c: Retroviral aspartyl protease; d: Reverse transcriptase (RNA-dependent DNA polymerase); e: RNAse. Tissues: B (Vegetative buds), F (Foliage), X-M (Xylem - mature), X-J (Xylem - juvenile), P (Phelloderm), R (Adventitious roots), M (Megagametophytes), E (Embryogenic cells). B: Expression levels are not correlated with the number of genomic copies.

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