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Conserved transcriptional regulatory programs underlying rice and barley germination.

Lin L, Tian S, Kaeppler S, Liu Z, An YQ - PLoS ONE (2014)

Bottom Line: To gain insight into the conservation of their underlying gene regulatory programs, we compared transcriptomes of barley and rice at start, middle and end points of germination, and revealed that germination regulated barley and rice genes (BRs) diverged significantly in expression patterns and/or protein sequences.Preserving germination-regulated expression patterns and protein sequences of those cBRs for 50 million years strongly suggests that the cBRs are functionally significant and equivalent in germination, and contribute to the ancient characteristics of germination preserved in barley and rice.The functional significance and equivalence of the cBR genes predicted here can serve as a foundation to further characterize their biological functions and facilitate bridging rice and barley germination research with greater confidence.

View Article: PubMed Central - PubMed

Affiliation: USDA-ARS, Plant Genetics Research Unit, Donald Danforth Plant Sciences Center, Saint Louis, Missouri, United States of America ; Department of Agronomy, University of Wisconsin, Wisconsin, United States of America.

ABSTRACT
Germination is a biological process important to plant development and agricultural production. Barley and rice diverged 50 million years ago, but share a similar germination process. To gain insight into the conservation of their underlying gene regulatory programs, we compared transcriptomes of barley and rice at start, middle and end points of germination, and revealed that germination regulated barley and rice genes (BRs) diverged significantly in expression patterns and/or protein sequences. However, BRs with higher protein sequence similarity tended to have more conserved expression patterns. We identified and characterized 316 sets of conserved barley and rice genes (cBRs) with high similarity in both protein sequences and expression patterns, and provided a comprehensive depiction of the transcriptional regulatory program conserved in barley and rice germination at gene, pathway and systems levels. The cBRs encoded proteins involved in a variety of biological pathways and had a wide range of expression patterns. The cBRs encoding key regulatory components in signaling pathways often had diverse expression patterns. Early germination up-regulation of cell wall metabolic pathway and peroxidases, and late germination up-regulation of chromatin structure and remodeling pathways were conserved in both barley and rice. Protein sequence and expression pattern of a gene change quickly if it is not subjected to a functional constraint. Preserving germination-regulated expression patterns and protein sequences of those cBRs for 50 million years strongly suggests that the cBRs are functionally significant and equivalent in germination, and contribute to the ancient characteristics of germination preserved in barley and rice. The functional significance and equivalence of the cBR genes predicted here can serve as a foundation to further characterize their biological functions and facilitate bridging rice and barley germination research with greater confidence.

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Distribution of Pearson Correlation Co-efficiency between Expression Patterns of Barley and Rice Genes.The germination regulated barley and rice genes (BRs) were paired randomly and paired based on their sequence similarity with an e-value less than −50 respectively; and their PCC values were determined. The distribution of PCC value for BR genes with e-value less than −50 (dark blue) were compared with randomly paired BR genes (light blue). The percentage of BRs (Y-axis) in each defined PCC value range (X-axis) was graphed.
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pone-0087261-g001: Distribution of Pearson Correlation Co-efficiency between Expression Patterns of Barley and Rice Genes.The germination regulated barley and rice genes (BRs) were paired randomly and paired based on their sequence similarity with an e-value less than −50 respectively; and their PCC values were determined. The distribution of PCC value for BR genes with e-value less than −50 (dark blue) were compared with randomly paired BR genes (light blue). The percentage of BRs (Y-axis) in each defined PCC value range (X-axis) was graphed.

Mentions: A total of 1507 pairs of barley and rice genes (BRs) with protein sequence similarity at an e-value less than −50 were identified among the germination regulated barley and rice genes. The BRs contained 805 barley and 1054 rice genes (Table 1). Pearson correlation coefficients (PCC) between log2 signal intensities of each paired barley and rice genes at start-, mid- and end-stages of germination were calculated to determine the similarity of their expression patterns. Sixty percent of the BRs had a PCC value higher than 0.5, indicating that the barley and rice genes in each of the BRs had a good similarity in their transcript accumulation patterns (Figure 1, Table 2). However, forty percent of the BRs had PPC value lower than 0.5, indicating that a significant percentage of BRs had low similarity or no similarity in their expression patterns. Thus, the BRs with high protein sequence similarity preferentially preserved their expression patterns after rice and barley diverged from their most recent ancestor. However, a significant percentage of the BRs had evolved into different gene expression patterns.


Conserved transcriptional regulatory programs underlying rice and barley germination.

Lin L, Tian S, Kaeppler S, Liu Z, An YQ - PLoS ONE (2014)

Distribution of Pearson Correlation Co-efficiency between Expression Patterns of Barley and Rice Genes.The germination regulated barley and rice genes (BRs) were paired randomly and paired based on their sequence similarity with an e-value less than −50 respectively; and their PCC values were determined. The distribution of PCC value for BR genes with e-value less than −50 (dark blue) were compared with randomly paired BR genes (light blue). The percentage of BRs (Y-axis) in each defined PCC value range (X-axis) was graphed.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3928125&req=5

pone-0087261-g001: Distribution of Pearson Correlation Co-efficiency between Expression Patterns of Barley and Rice Genes.The germination regulated barley and rice genes (BRs) were paired randomly and paired based on their sequence similarity with an e-value less than −50 respectively; and their PCC values were determined. The distribution of PCC value for BR genes with e-value less than −50 (dark blue) were compared with randomly paired BR genes (light blue). The percentage of BRs (Y-axis) in each defined PCC value range (X-axis) was graphed.
Mentions: A total of 1507 pairs of barley and rice genes (BRs) with protein sequence similarity at an e-value less than −50 were identified among the germination regulated barley and rice genes. The BRs contained 805 barley and 1054 rice genes (Table 1). Pearson correlation coefficients (PCC) between log2 signal intensities of each paired barley and rice genes at start-, mid- and end-stages of germination were calculated to determine the similarity of their expression patterns. Sixty percent of the BRs had a PCC value higher than 0.5, indicating that the barley and rice genes in each of the BRs had a good similarity in their transcript accumulation patterns (Figure 1, Table 2). However, forty percent of the BRs had PPC value lower than 0.5, indicating that a significant percentage of BRs had low similarity or no similarity in their expression patterns. Thus, the BRs with high protein sequence similarity preferentially preserved their expression patterns after rice and barley diverged from their most recent ancestor. However, a significant percentage of the BRs had evolved into different gene expression patterns.

Bottom Line: To gain insight into the conservation of their underlying gene regulatory programs, we compared transcriptomes of barley and rice at start, middle and end points of germination, and revealed that germination regulated barley and rice genes (BRs) diverged significantly in expression patterns and/or protein sequences.Preserving germination-regulated expression patterns and protein sequences of those cBRs for 50 million years strongly suggests that the cBRs are functionally significant and equivalent in germination, and contribute to the ancient characteristics of germination preserved in barley and rice.The functional significance and equivalence of the cBR genes predicted here can serve as a foundation to further characterize their biological functions and facilitate bridging rice and barley germination research with greater confidence.

View Article: PubMed Central - PubMed

Affiliation: USDA-ARS, Plant Genetics Research Unit, Donald Danforth Plant Sciences Center, Saint Louis, Missouri, United States of America ; Department of Agronomy, University of Wisconsin, Wisconsin, United States of America.

ABSTRACT
Germination is a biological process important to plant development and agricultural production. Barley and rice diverged 50 million years ago, but share a similar germination process. To gain insight into the conservation of their underlying gene regulatory programs, we compared transcriptomes of barley and rice at start, middle and end points of germination, and revealed that germination regulated barley and rice genes (BRs) diverged significantly in expression patterns and/or protein sequences. However, BRs with higher protein sequence similarity tended to have more conserved expression patterns. We identified and characterized 316 sets of conserved barley and rice genes (cBRs) with high similarity in both protein sequences and expression patterns, and provided a comprehensive depiction of the transcriptional regulatory program conserved in barley and rice germination at gene, pathway and systems levels. The cBRs encoded proteins involved in a variety of biological pathways and had a wide range of expression patterns. The cBRs encoding key regulatory components in signaling pathways often had diverse expression patterns. Early germination up-regulation of cell wall metabolic pathway and peroxidases, and late germination up-regulation of chromatin structure and remodeling pathways were conserved in both barley and rice. Protein sequence and expression pattern of a gene change quickly if it is not subjected to a functional constraint. Preserving germination-regulated expression patterns and protein sequences of those cBRs for 50 million years strongly suggests that the cBRs are functionally significant and equivalent in germination, and contribute to the ancient characteristics of germination preserved in barley and rice. The functional significance and equivalence of the cBR genes predicted here can serve as a foundation to further characterize their biological functions and facilitate bridging rice and barley germination research with greater confidence.

Show MeSH