Limits...
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

Gene structure analysis of SmARF genes and prediction of their miRNA target sites according to their phylogenetic relationships. The yellow boxes represent exons; the gray lines represent introns. The red box denotes the targets of At-miR160 in SmARF genes; the purple box denotes the targets of At-miR167 in SmARF genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4920185&req=5

BIO017178F2: Gene structure analysis of SmARF genes and prediction of their miRNA target sites according to their phylogenetic relationships. The yellow boxes represent exons; the gray lines represent introns. The red box denotes the targets of At-miR160 in SmARF genes; the purple box denotes the targets of At-miR167 in SmARF genes.

Mentions: To better understand the gene structure of SmARFs, the exon-intron features among SmARFs were aligned via phylogenetic analysis (Fig. 2). The phylogenetic analysis revealed four clusters in accordance with the group data presented in Fig. 1. Gene structure analysis of all of the SmARF genes revealed that the number of exons ranges from 1 to 18, however, SmARF12 is intronless. The genes in the four groups have an average exon number ranging from three (class III) to 15 (class Ia). The results showed that the exon number of class I-II was significantly greater than that of class III; these findings were identical to the structure of AtARF genes.Fig. 2.


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)

Gene structure analysis of SmARF genes and prediction of their miRNA target sites according to their phylogenetic relationships. The yellow boxes represent exons; the gray lines represent introns. The red box denotes the targets of At-miR160 in SmARF genes; the purple box denotes the targets of At-miR167 in SmARF genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

BIO017178F2: Gene structure analysis of SmARF genes and prediction of their miRNA target sites according to their phylogenetic relationships. The yellow boxes represent exons; the gray lines represent introns. The red box denotes the targets of At-miR160 in SmARF genes; the purple box denotes the targets of At-miR167 in SmARF genes.
Mentions: To better understand the gene structure of SmARFs, the exon-intron features among SmARFs were aligned via phylogenetic analysis (Fig. 2). The phylogenetic analysis revealed four clusters in accordance with the group data presented in Fig. 1. Gene structure analysis of all of the SmARF genes revealed that the number of exons ranges from 1 to 18, however, SmARF12 is intronless. The genes in the four groups have an average exon number ranging from three (class III) to 15 (class Ia). The results showed that the exon number of class I-II was significantly greater than that of class III; these findings were identical to the structure of AtARF genes.Fig. 2.

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