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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.


Sequence alignment of miR156 complementary sequences of the BnaSBP genes. a The complementary sequences are located in the coding regions. b The complementary sequences are located in the 3′UTR regions
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Fig6: Sequence alignment of miR156 complementary sequences of the BnaSBP genes. a The complementary sequences are located in the coding regions. b The complementary sequences are located in the 3′UTR regions

Mentions: Seven putative members of miR156 (BnaMiR156a-g) in oilseed rape were found after querying the miRBase database. Recently, thirty-two putative pre-mature structures of miR156 were predicted in B. napus by high throughput small RNA deep sequencing [47]. Previous results showed that miR156 complementarily bind to SBP genes either at the coding or 3′UTR region and reduced gene activity by translation suppression or cleavage [27, 29]. It was shown that 44 SBP proteins have miR156 binding site, with 30 and 14 at coding and 3′UTR regions, respectively (Fig. 6). According to previous results, 11 out of 17 SBP genes in Arabidopsis are targeted by miR156. The homologous genes in oilseed rape are also predicted to be target of miR156. These results suggest that relationship between miR156 and SBP genes is conserved across species. However, three BnaSBP genes targeted by miR156 differed from other genes. BnaSBP5c possesses the binding site within the coding region, while the other three BnaSBP5 genes are targeted by miR156 in 3′UTR. MiR156 was predicted to bind to 3′UTR sequence of BnaSBP6d and BnaSBP10a, while the relative homologous gene in Arabidopsis were bound by miR156 at the coding region. The distinct regulation pattern of the homologous genes between B. napus and Arabidopsis reveals the divergence of the SBP-box genes in oilseed rape.Fig. 6


Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus
Sequence alignment of miR156 complementary sequences of the BnaSBP genes. a The complementary sequences are located in the coding regions. b The complementary sequences are located in the 3′UTR regions
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig6: Sequence alignment of miR156 complementary sequences of the BnaSBP genes. a The complementary sequences are located in the coding regions. b The complementary sequences are located in the 3′UTR regions
Mentions: Seven putative members of miR156 (BnaMiR156a-g) in oilseed rape were found after querying the miRBase database. Recently, thirty-two putative pre-mature structures of miR156 were predicted in B. napus by high throughput small RNA deep sequencing [47]. Previous results showed that miR156 complementarily bind to SBP genes either at the coding or 3′UTR region and reduced gene activity by translation suppression or cleavage [27, 29]. It was shown that 44 SBP proteins have miR156 binding site, with 30 and 14 at coding and 3′UTR regions, respectively (Fig. 6). According to previous results, 11 out of 17 SBP genes in Arabidopsis are targeted by miR156. The homologous genes in oilseed rape are also predicted to be target of miR156. These results suggest that relationship between miR156 and SBP genes is conserved across species. However, three BnaSBP genes targeted by miR156 differed from other genes. BnaSBP5c possesses the binding site within the coding region, while the other three BnaSBP5 genes are targeted by miR156 in 3′UTR. MiR156 was predicted to bind to 3′UTR sequence of BnaSBP6d and BnaSBP10a, while the relative homologous gene in Arabidopsis were bound by miR156 at the coding region. The distinct regulation pattern of the homologous genes between B. napus and Arabidopsis reveals the divergence of the SBP-box genes in oilseed rape.Fig. 6

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.