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Identification of the mulberry genes involved in ethylene biosynthesis and signaling pathways and the expression of MaERF-B2-1 and MaERF-B2-2 in the response to flooding stress.

Shang J, Song P, Ma B, Qi X, Zeng Q, Xiang Z, He N - Funct. Integr. Genomics (2014)

Bottom Line: A total of 145 mulberry genes were identified by both homology-based and hidden Markov model (HMM) search, including 29 genes associated with ethylene biosynthesis and 116 genes in the AP2/ERF family.The differences in gene expression were also observed in different tissues.The expression of two mulberry genes in the AP2/ERF family, MaERF-B2-1 and MaERF-B2-2, was found to be associated with the response to flooding stress.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715, China.

ABSTRACT
The phytohormone ethylene is essential to plant growth and development. It plays crucial roles in responses to biotic and abiotic stress. The mulberry tree is an important crop plant in countries in which people rear silkworms for silk production. The availability of the mulberry genome has made it possible to identify mulberry genes involved in ethylene biosynthesis and signal pathways. A total of 145 mulberry genes were identified by both homology-based and hidden Markov model (HMM) search, including 29 genes associated with ethylene biosynthesis and 116 genes in the AP2/ERF family. Studies on gene structure have provided a genetic basis for understanding the functions of these genes. The differences in gene expression were also observed in different tissues. The expression of two mulberry genes in the AP2/ERF family, MaERF-B2-1 and MaERF-B2-2, was found to be associated with the response to flooding stress.

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Heat maps of hierarchical clustering of mulberry genes in the AP2/ERF family. a ERF subfamily; b DREB subfamily; c AP2 subfamily; and d RAV and Soloist subfamilies. The clustering analyses were carried out using Gene Cluster 3.0. The data were adjusted by log transformation and the mean center method. Hierarchical clustering (HCL) with average linkage was set to calculate K-medians with five clusters. Heat maps illustrating the gene expression data were generated using Java TreeView
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Fig4: Heat maps of hierarchical clustering of mulberry genes in the AP2/ERF family. a ERF subfamily; b DREB subfamily; c AP2 subfamily; and d RAV and Soloist subfamilies. The clustering analyses were carried out using Gene Cluster 3.0. The data were adjusted by log transformation and the mean center method. Hierarchical clustering (HCL) with average linkage was set to calculate K-medians with five clusters. Heat maps illustrating the gene expression data were generated using Java TreeView

Mentions: To investigate the levels of expression of AP2/ERF genes in different tissues, RPKM data of these genes were analyzed in roots, barks, leaves, flowers, and buds. Heat maps were constructed based on the RPKM data. Sixteen MnERF genes, including five genes in MnERF-B1, four in MnERF-B3, three in MnERF-B2, two in MnERF-B4, and one each in MnERF-B5 and MnERF-B6, had relatively high levels of expression in five tissues (Fig. 4a). This was also true of 8 of the 33 genes in the DREB subfamily, 6 of the 21 genes in the AP2 subfamily, and 1 of the 3 genes in the RAV subfamily. In addition, several genes were also found to be expressed in a tissue-biased manner. For example, MnERF-B3-21 was expressed solely in male flowers (Fig. 4a). MnDREB-A4-7 was more abundantly expressed in leaves than in other tissues (Fig. 4b). MnAP2-5 had high levels of expression in male flower (Fig. 4c). However, the expression of nine genes (MnERF-B6-1/8, MnDREB-A3-1, MnDREB-A4-4, MnDREB-A6-1/2, MnAP2-13/18/21) was not detectable in any tissue.Fig. 4


Identification of the mulberry genes involved in ethylene biosynthesis and signaling pathways and the expression of MaERF-B2-1 and MaERF-B2-2 in the response to flooding stress.

Shang J, Song P, Ma B, Qi X, Zeng Q, Xiang Z, He N - Funct. Integr. Genomics (2014)

Heat maps of hierarchical clustering of mulberry genes in the AP2/ERF family. a ERF subfamily; b DREB subfamily; c AP2 subfamily; and d RAV and Soloist subfamilies. The clustering analyses were carried out using Gene Cluster 3.0. The data were adjusted by log transformation and the mean center method. Hierarchical clustering (HCL) with average linkage was set to calculate K-medians with five clusters. Heat maps illustrating the gene expression data were generated using Java TreeView
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4233114&req=5

Fig4: Heat maps of hierarchical clustering of mulberry genes in the AP2/ERF family. a ERF subfamily; b DREB subfamily; c AP2 subfamily; and d RAV and Soloist subfamilies. The clustering analyses were carried out using Gene Cluster 3.0. The data were adjusted by log transformation and the mean center method. Hierarchical clustering (HCL) with average linkage was set to calculate K-medians with five clusters. Heat maps illustrating the gene expression data were generated using Java TreeView
Mentions: To investigate the levels of expression of AP2/ERF genes in different tissues, RPKM data of these genes were analyzed in roots, barks, leaves, flowers, and buds. Heat maps were constructed based on the RPKM data. Sixteen MnERF genes, including five genes in MnERF-B1, four in MnERF-B3, three in MnERF-B2, two in MnERF-B4, and one each in MnERF-B5 and MnERF-B6, had relatively high levels of expression in five tissues (Fig. 4a). This was also true of 8 of the 33 genes in the DREB subfamily, 6 of the 21 genes in the AP2 subfamily, and 1 of the 3 genes in the RAV subfamily. In addition, several genes were also found to be expressed in a tissue-biased manner. For example, MnERF-B3-21 was expressed solely in male flowers (Fig. 4a). MnDREB-A4-7 was more abundantly expressed in leaves than in other tissues (Fig. 4b). MnAP2-5 had high levels of expression in male flower (Fig. 4c). However, the expression of nine genes (MnERF-B6-1/8, MnDREB-A3-1, MnDREB-A4-4, MnDREB-A6-1/2, MnAP2-13/18/21) was not detectable in any tissue.Fig. 4

Bottom Line: A total of 145 mulberry genes were identified by both homology-based and hidden Markov model (HMM) search, including 29 genes associated with ethylene biosynthesis and 116 genes in the AP2/ERF family.The differences in gene expression were also observed in different tissues.The expression of two mulberry genes in the AP2/ERF family, MaERF-B2-1 and MaERF-B2-2, was found to be associated with the response to flooding stress.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715, China.

ABSTRACT
The phytohormone ethylene is essential to plant growth and development. It plays crucial roles in responses to biotic and abiotic stress. The mulberry tree is an important crop plant in countries in which people rear silkworms for silk production. The availability of the mulberry genome has made it possible to identify mulberry genes involved in ethylene biosynthesis and signal pathways. A total of 145 mulberry genes were identified by both homology-based and hidden Markov model (HMM) search, including 29 genes associated with ethylene biosynthesis and 116 genes in the AP2/ERF family. Studies on gene structure have provided a genetic basis for understanding the functions of these genes. The differences in gene expression were also observed in different tissues. The expression of two mulberry genes in the AP2/ERF family, MaERF-B2-1 and MaERF-B2-2, was found to be associated with the response to flooding stress.

Show MeSH
Related in: MedlinePlus