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Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus

View Article: PubMed Central - PubMed

ABSTRACT

Background: SBP-box genes belong to one of the largest families of transcription factors. Though members of this family have been characterized to be important regulators of diverse biological processes, information of SBP-box genes in the third most important oilseed crop Brassica napus is largely undefined.

Results: In the present study, by whole genome bioinformatics analysis and transcriptional profiling, 58 putative members of SBP-box gene family in oilseed rape (Brassica napus L.) were identified and their expression pattern in different tissues as well as possible interaction with miRNAs were analyzed. In addition, B. napus lines with contrasting branch angle were used for investigating the involvement of SBP-box genes in plant architecture regulation. Detailed gene information, including genomic organization, structural feature, conserved domain and phylogenetic relationship of the genes were systematically characterized. By phylogenetic analysis, BnaSBP proteins were classified into eight distinct groups representing the clear orthologous relationships to their family members in Arabidopsis and rice. Expression analysis in twelve tissues including vegetative and reproductive organs showed different expression patterns among the SBP-box genes and a number of the genes exhibit tissue specific expression, indicating their diverse functions involved in the developmental process. Forty-four SBP-box genes were ascertained to contain the putative miR156 binding site, with 30 and 14 of the genes targeted by miR156 at the coding and 3′UTR region, respectively. Relative expression level of miR156 is varied across tissues. Different expression pattern of some BnaSBP genes and the negative correlation of transcription levels between miR156 and its target BnaSBP gene were observed in lines with different branch angle.

Conclusions: Taken together, this study represents the first systematic analysis of the SBP-box gene family in Brassica napus. The data presented here provides base foundation for understanding the crucial roles of BnaSBP genes in plant development and other biological processes.

Electronic supplementary material: The online version of this article (doi:10.1186/s12870-016-0852-y) contains supplementary material, which is available to authorized users.

No MeSH data available.


Phylogenetic analysis of BnaSBP proteins. The protein sequences of SBP-box from Arabidopsis (AtSBP), rice (OsSBP) and B. napus (BnaSBP) were aligned using ClustalW. The phylogenetic tree was constructed using the neighbor-joining algorithm with 1000 replications. Nodes with bootstrap values of >50 % are dotted. Bar indicates 0.05 aa substitution per residue
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Fig5: Phylogenetic analysis of BnaSBP proteins. The protein sequences of SBP-box from Arabidopsis (AtSBP), rice (OsSBP) and B. napus (BnaSBP) were aligned using ClustalW. The phylogenetic tree was constructed using the neighbor-joining algorithm with 1000 replications. Nodes with bootstrap values of >50 % are dotted. Bar indicates 0.05 aa substitution per residue

Mentions: The phylogenetic relationship among BnaSBP genes and other SBP genes with known functions from other species is useful for predicting their roles in oilseed rape development. Sixteen SBP genes from Arabidopsis and nineteen SBP genes from rice, which are model plants for dicot and monocot species respectively, were extracted from the public gene pool. Fifty-eight SBP genes from oilseed rape together with the Arabidopsis and rice genes were used for the construction of an unrooted phylogenetic tree (Fig. 5, Additional file 2: Figure S2). According to phylogenetic analysis, SBP genes from these three plant species can be classified into seven groups (SBP-a to SBP-h). The largest group (SBP-e) contains 21 members which account for 23 % of the total SBPs, whereas group SBP-a forms the smallest group containing only five members. As shown in Fig. 5, genes in group SBP-a were more diverged than those in other groups. BnaSBP genes showed a high similarity to their orthologs from Arabidopsis and were classified into the same group. Among the groups revealed by phylogenetic analysis, group SBP-f only contain SBPs from Arabidopsis and oilseed rape, indicating the diversification of SBP genes between monocot and dicot plants.Fig. 5


Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus
Phylogenetic analysis of BnaSBP proteins. The protein sequences of SBP-box from Arabidopsis (AtSBP), rice (OsSBP) and B. napus (BnaSBP) were aligned using ClustalW. The phylogenetic tree was constructed using the neighbor-joining algorithm with 1000 replications. Nodes with bootstrap values of >50 % are dotted. Bar indicates 0.05 aa substitution per residue
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5017063&req=5

Fig5: Phylogenetic analysis of BnaSBP proteins. The protein sequences of SBP-box from Arabidopsis (AtSBP), rice (OsSBP) and B. napus (BnaSBP) were aligned using ClustalW. The phylogenetic tree was constructed using the neighbor-joining algorithm with 1000 replications. Nodes with bootstrap values of >50 % are dotted. Bar indicates 0.05 aa substitution per residue
Mentions: The phylogenetic relationship among BnaSBP genes and other SBP genes with known functions from other species is useful for predicting their roles in oilseed rape development. Sixteen SBP genes from Arabidopsis and nineteen SBP genes from rice, which are model plants for dicot and monocot species respectively, were extracted from the public gene pool. Fifty-eight SBP genes from oilseed rape together with the Arabidopsis and rice genes were used for the construction of an unrooted phylogenetic tree (Fig. 5, Additional file 2: Figure S2). According to phylogenetic analysis, SBP genes from these three plant species can be classified into seven groups (SBP-a to SBP-h). The largest group (SBP-e) contains 21 members which account for 23 % of the total SBPs, whereas group SBP-a forms the smallest group containing only five members. As shown in Fig. 5, genes in group SBP-a were more diverged than those in other groups. BnaSBP genes showed a high similarity to their orthologs from Arabidopsis and were classified into the same group. Among the groups revealed by phylogenetic analysis, group SBP-f only contain SBPs from Arabidopsis and oilseed rape, indicating the diversification of SBP genes between monocot and dicot plants.Fig. 5

View Article: PubMed Central - PubMed

ABSTRACT

Background: SBP-box genes belong to one of the largest families of transcription factors. Though members of this family have been characterized to be important regulators of diverse biological processes, information of SBP-box genes in the third most important oilseed crop Brassica napus is largely undefined.

Results: In the present study, by whole genome bioinformatics analysis and transcriptional profiling, 58 putative members of SBP-box gene family in oilseed rape (Brassica napus L.) were identified and their expression pattern in different tissues as well as possible interaction with miRNAs were analyzed. In addition, B. napus lines with contrasting branch angle were used for investigating the involvement of SBP-box genes in plant architecture regulation. Detailed gene information, including genomic organization, structural feature, conserved domain and phylogenetic relationship of the genes were systematically characterized. By phylogenetic analysis, BnaSBP proteins were classified into eight distinct groups representing the clear orthologous relationships to their family members in Arabidopsis and rice. Expression analysis in twelve tissues including vegetative and reproductive organs showed different expression patterns among the SBP-box genes and a number of the genes exhibit tissue specific expression, indicating their diverse functions involved in the developmental process. Forty-four SBP-box genes were ascertained to contain the putative miR156 binding site, with 30 and 14 of the genes targeted by miR156 at the coding and 3′UTR region, respectively. Relative expression level of miR156 is varied across tissues. Different expression pattern of some BnaSBP genes and the negative correlation of transcription levels between miR156 and its target BnaSBP gene were observed in lines with different branch angle.

Conclusions: Taken together, this study represents the first systematic analysis of the SBP-box gene family in Brassica napus. The data presented here provides base foundation for understanding the crucial roles of BnaSBP genes in plant development and other biological processes.

Electronic supplementary material: The online version of this article (doi:10.1186/s12870-016-0852-y) contains supplementary material, which is available to authorized users.

No MeSH data available.