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Genome-wide analysis of auxin response factor gene family members in medicinal model plant Salvia miltiorrhiza.

Xu Z, Ji A, Song J, Chen S - Biol Open (2016)

Bottom Line: Based on a genome-wide strategy using the medicinal model plant Salvia miltiorrhiza, 25 S. miltiorrhiza ARF (SmARF) gene family members in four classes (class Ia, IIa, IIb and III) were comprehensively analyzed to identify characteristics including gene structures, conserved domains, phylogenetic relationships and expression patterns.In a hybrid analysis of the phylogenetic tree, microRNA targets, and expression patterns of SmARFs in different organs, root tissues, and methyl jasmonate or indole-3-acetic acid treatment conditions, we screened for candidate SmARFs involved in various developmental processes of S. miltiorrhiza Based on this analysis, we predicted that SmARF25, SmARF7, SmARF16 and SmARF20 are involved in flower, leaf, stem and root development, respectively.With the further insight into the targets of miR160 and miR167, specific SmARF genes in S. miltiorrhiza might encode products that participate in biological processes as described for ARF genes in Arabidopsis Our results provide a foundation for understanding the molecular basis and regulatory mechanisms of SmARFs in S. miltiorrhiza.

View Article: PubMed Central - PubMed

Affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100193, China Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing 100193, China.

No MeSH data available.


Related in: MedlinePlus

A heat map showing SmARF gene expression patterns in different organs. The red color represents upregulation of expression, the white color represents an unchanged expression level, and the blue color represents downregulation of expression. Red dot (SmARF6) is not belong to the Class III.
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BIO017178F3: A heat map showing SmARF gene expression patterns in different organs. The red color represents upregulation of expression, the white color represents an unchanged expression level, and the blue color represents downregulation of expression. Red dot (SmARF6) is not belong to the Class III.

Mentions: To better probe the physiological function of SmARFs, the tissue-specific expression of 25 SmARF genes in different danshen organs (leaf, root, stem and flower) was determined by analyzing the RNA-seq data (Fig. 3; Table S4). Most SmARF genes, but not SmARF9, 12 or 17 presented ubiquitous expression and high variability in all studied organs, and this result implies that these SmARFs might function in danshen growth and development. There were significant differences in SmARF expression between organs. SmARF3, 7 and 21, all of which belong to class Ia based on phylogenetic analysis, showed higher expression in danshen leaf than in other organs. SmARF4, 5, 11, 18, 20 and 23 were expressed more strongly in danshen root than in other organs, however, only SmARF16 showed stem-specific expression in S. miltiorrhiza. When comparing phylogenetic tree analysis with the expression cluster analysis, SmARF8, 10, 19, 22, 24 and 25, which belong to class IIa, showed significantly lower expression in danshen leaf than in other organs. Most of the SmARF genes from class III (SmARF13-17) also clustered in one expression branch. These results indicated that ARF genes from the same class might perform a similar physiological function in plants.Fig. 3.


Genome-wide analysis of auxin response factor gene family members in medicinal model plant Salvia miltiorrhiza.

Xu Z, Ji A, Song J, Chen S - Biol Open (2016)

A heat map showing SmARF gene expression patterns in different organs. The red color represents upregulation of expression, the white color represents an unchanged expression level, and the blue color represents downregulation of expression. Red dot (SmARF6) is not belong to the Class III.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4920185&req=5

BIO017178F3: A heat map showing SmARF gene expression patterns in different organs. The red color represents upregulation of expression, the white color represents an unchanged expression level, and the blue color represents downregulation of expression. Red dot (SmARF6) is not belong to the Class III.
Mentions: To better probe the physiological function of SmARFs, the tissue-specific expression of 25 SmARF genes in different danshen organs (leaf, root, stem and flower) was determined by analyzing the RNA-seq data (Fig. 3; Table S4). Most SmARF genes, but not SmARF9, 12 or 17 presented ubiquitous expression and high variability in all studied organs, and this result implies that these SmARFs might function in danshen growth and development. There were significant differences in SmARF expression between organs. SmARF3, 7 and 21, all of which belong to class Ia based on phylogenetic analysis, showed higher expression in danshen leaf than in other organs. SmARF4, 5, 11, 18, 20 and 23 were expressed more strongly in danshen root than in other organs, however, only SmARF16 showed stem-specific expression in S. miltiorrhiza. When comparing phylogenetic tree analysis with the expression cluster analysis, SmARF8, 10, 19, 22, 24 and 25, which belong to class IIa, showed significantly lower expression in danshen leaf than in other organs. Most of the SmARF genes from class III (SmARF13-17) also clustered in one expression branch. These results indicated that ARF genes from the same class might perform a similar physiological function in plants.Fig. 3.

Bottom Line: Based on a genome-wide strategy using the medicinal model plant Salvia miltiorrhiza, 25 S. miltiorrhiza ARF (SmARF) gene family members in four classes (class Ia, IIa, IIb and III) were comprehensively analyzed to identify characteristics including gene structures, conserved domains, phylogenetic relationships and expression patterns.In a hybrid analysis of the phylogenetic tree, microRNA targets, and expression patterns of SmARFs in different organs, root tissues, and methyl jasmonate or indole-3-acetic acid treatment conditions, we screened for candidate SmARFs involved in various developmental processes of S. miltiorrhiza Based on this analysis, we predicted that SmARF25, SmARF7, SmARF16 and SmARF20 are involved in flower, leaf, stem and root development, respectively.With the further insight into the targets of miR160 and miR167, specific SmARF genes in S. miltiorrhiza might encode products that participate in biological processes as described for ARF genes in Arabidopsis Our results provide a foundation for understanding the molecular basis and regulatory mechanisms of SmARFs in S. miltiorrhiza.

View Article: PubMed Central - PubMed

Affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100193, China Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing 100193, China.

No MeSH data available.


Related in: MedlinePlus