Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus
© The Author(s). 2016
Received: 9 December 2015
Accepted: 11 July 2016
Published: 8 September 2016
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.
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.
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.
Transcription factors play a critical role in the life-cycle of plants by activating or suppressing the expression of different target genes . The SQUAMOSA promoter-binding protein (SBP) box family represents one of the transcription factor families characterized by a highly conserved SBP domain, 76 amino acids in length [2–4]. Since the first SBP-box gene was identified in Antirrhinum majus, many such genes have been characterized from different plant species, thus identifying a moderately sized gene family. Sixteen SBP-box genes have been identified in model plant Arabidopsis and many genes have also been characterized in worldwide agriculturally important crops such as rice (Oryza sativa) and maize (Zea mays) [5–7]. The SBP-box genes have been shown to influence many aspects of development including leaf and trichome development, vegetative and reproductive phase transition, plant hormone signaling transduction and other physiological processes [8–15].
Among the identified SBP-box genes, many were proven to play essential roles in diverse development processes. Transgenic plants that constitutively express Arabidopsis gene SPL3 exhibited very early flowering and frequent morphology changes . Arabidopsis spl8 mutants show altered pollen sac development and overexpression of SPL8 influences plant fertility by mediating GA dependent signaling pathway [9, 17]. In addition, SPL8 and other SPL genes control gynoecium patterning through interference with auxin homeostasis . AtSBP7 is a central regulator for copper homeostasis in Arabidopsis . AtSPL2, AtSPL10 and AtSPL11 in Arabidopsis have been demonstrated to control morphological changes associated with shoot maturation in the reproductive phase . BraSPL9-2 is the target of microRNA bra-miR156 and controls the heading time of Chinese cabbage . Besides the important roles reported in dicot plants, SBP-box genes in monocot plant, such as rice and maize, were also shown to modulate essential developmental processes. Higher expression of OsSPL14 in the reproductive stage promotes panicle branching and higher grain yield in rice, suggesting the important roles of SPL genes in plant architecture regulation [22, 23]. Maize transcription factors unbranched2 and unbranched3 encoding SBP-box proteins also alter plant architecture and affect yield traits by regulating the rate of lateral primordia initiation .
MiRNAs are small non-coding 20–24 nt RNAs that can complementarily bind to their target mRNAs and reduce protein level through translational repression or transcript cleavage and degradation [25, 26]. Many development processes mediated by SBP-box genes are closely linked to miR156. Computational analysis indicated that many SBP-box genes are regulated by miR156 family in Arabidopsis . Some important developmental processes seem to be mediated by both miR156 and their target SBP-box genes since overexpression of miR156 resulted in various phenotypes, including increased number of leaves, delayed flowering and decreased apical dominance . Arabidopsis miR156 complementarily binds to the 3′UTR of SPL3 mRNA and regulates its expression through translation inhibition and transcript cleavage [16, 29]. Overexpression of rice miR156 also resulted in decreased expression of the SPL target genes, suggesting the correlative interaction of SPL and miR156 in monocot plants . Arabidopsis miR156 regulates tolerance to recurring heat stress and SPL genes are posttranscriptional regulated by miR156 after heat stress . Recently, it is reported that miR156/SPLs modulates Arabidopsis lateral root development . In addition to the regulatory roles of miR156, SBP-box genes were also shown to be regulated by miR529 in grasses . Interestingly, miR156 and miR529 are correlated at the nucleotide level sharing a 14–16 nt binding site . However, no miR529 candidates regulating SBP-box genes were found in core eudicots, such as Arabidopsis and poplar [34, 35].
Despite the essential roles of SBP-box genes in Arabidopsis or rice, information of SBP-box genes in oilseed rape (B. napus) is largely undefined. Genome-wide analysis of SBP-box genes has been performed in several species [36–40]. However, analysis of this gene family has not been conducted in Brassica species. Meanwhile, the interaction between the BnaSBP genes and BnaMiR156 was not clearly understood. In the light of recent findings about SBP-box gene function in Arabidopsis, rice and other organisms, analysis of SBP-box genes in B. napus will certainly accelerate the utilization of these genes. Here we report the systematically analysis of SBP-box genes in B. napus for their gene structure, phylogeny, motif composition, miRNA target site, chromosomal localization and expression pattern in various tissues and organs. Moreover, the relative transcript level of BnamiR156 in various tissues was also examined to study the functional relationship of SBP and miR156 genes.
Identification and annotation of SBP-box genes in the B. napus genome
Firstly, the HMM profiles of the SBP domains (PF03110) in the Pfam database (http://pfam.xfam.org/) were downloaded and used to search the genome database of B. napus (http://www.genoscope.cns.fr/brassicanapus/) using HHMER search program. All non-redundant sequences were submitted to Interpro (http://www.ebi.ac.uk/interpro) to confirm the presence of the SBP domain. Sequences without complete SBP domain were excluded from the result. We also performed HHMER search against Brassica rapa and Brassica oleracea genome databases to identify SBP proteins. Secondly, Arabidopsis SBP protein sequences were downloaded from TAIR (http://www.arabidopsis.org/) to use as query to perform the BLASTP against B. napus genome. SBP-box gene accession numbers in B. napus genome database were extracted. The nomenclature of putative SBP-box genes in B. napus was in accordance with the homologous gene IDs in Arabidopsis. For one SBP-box gene in Arabidopsis, the orthologous SBP-box genes in oilseed rape were drawn up alphabetically. As the sequence of AtSBP1 and AtSBP12 shows high similarity, only BnaSBP1 genes were named in oilseed rape. SBP-box genes in rice were downloaded from rice genome project (http://rice.plantbiology.msu.edu/).
Gene structure, chromosomal location, duplication and phylogenetic analysis of BnaSBP genes
All the BnaSBP genes were mapped to the B. napus genome chromosomes according to the approximate position information. The exon/intron structure of each BnaSBP genes was displayed in Gene Structure Display Server program (http://gsds.cbi.pku.edu.cn/index.php) by comparing the coding sequence and genomic sequence. MCScanX software (http://chibba.pgml.uga.edu/mcscan2/) was used to analyze the duplication pattern of BnaSBP genes in oilseed rape genome. The local blast + software was used to perform the BLASTP analysis of B. napus with the e-value under 1e-5. The position of SBP-box genes and the blast output were imported into MCScanX software to generate a circle plot under a default criterion. Multiple sequence alignment of SBP-box protein sequence from Oryza sativa, Arabidopsis thaliana and Brasscia napus was performed using ClustalX2.0 with the default parameters . Phylogenetic trees were constructed in MEGA6.0 software using the neighbor-joining (NJ) method and maximum likelihood (ML) method with 1000 bootstrap replications.
Conserved motif identification and miR156 target site prediction
The conserved motifs were identified using the MEME online tool (http://meme-suite.org/) with parameter setup as following: maximum number of motifs, 20; number of repetitions, any; the range of motif width was from 6 to 80. All the identified motifs were searched in InterPro database (http://www.ebi.ac.uk/interpro/) and sequence logos were created using Weblogo online software (http://weblogo.threeplusone.com/). To predict the putative target sites of miR156, full length of BnaSBP genes including exon, intron and UTR sequences were analyzed using psRNATarget tool (http://plantgrn.noble.org/psRNATarget/?function). The conserved target sequences were modified by Genedoc software.
Plant materials and growth condition
Plant samples used for expression pattern analysis and RNA-seq were collected from B. napus var. Zhongshuang 11 at the Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (OCRI-CAAS). The RNA-seq data were generated from twelve different tissues (root, leaf, bud, silique, stamen, new petal, blooming petal, wilting petal, stem, sepal, ovule and pericarp). The high resolution RNA-seq data of BnaSBP genes were kindly provided by Professor Shengyi Liu from OCRI-CAAS (data not published). The detailed FPKM value (Fragments Per Kilobase of exon model per Million mapped reads) was list in the supplemental data (Additional file 3: Table S2). The FPKM value was log2-transformed and the euclidean distances of all genes were calculated. Clustering tree was constructed and displayed by hierarchical cluster method of “complete linkage clustering” through R package.
To analyze the expression pattern of miR156 and BnaSBP genes, twelve tissue samples were also collected from the same tissue site at the same developmental stage as the sample for RNA-seq. All samples were collected and frozen in liquid nitrogen quickly and stored at the −80 °C. B. napus lines Purler and 6098B, harboring large and small branch angle respectively, were used for expression analysis. Results from different years showed that the branch angle of 6098B was 30−32° larger than that of Purler at the mature stage . Tissue samples at the branch sites were collected at the bolting and early flowering stages for RNA-seq analysis. RNA-seq data were analyzed as described for Zhongshuang 11. Other tissue samples from 6098B and Purler were taken as those from Zhongshuang 11 to perform RT-PCR to verify the RNA-seq result. All plant materials were grown at the field in OCRI-CAAS, Wuhan, China.
RNA extraction and quantitative real-time RT-PCR analysis
Total RNA from diverse tissues at different growth stage was extracted with Trizol Reagent (Invitrogen, America). Before reverse transcription, total RNA was treated with RNase-free DNase I (Promega, America) for 15 min to degrade genomic DNA. Stem-loop RT-PCR was used to examine miR156 expression level in different tissues following the procedure reported previously . miRNA sequences in B. napus were downloaded from miRBase Sequence Database . Primers used for stem-loop RT were designed according to Zhao et al. (2012) . U6 specific primer was added simultaneously as reference for accurate normalization in each reaction. As the mature sequence of miR156 family varies in the 5′ region, five different forward primers were designed for realtime qPCR. qRT-PCR was run in CFX96 Real Time System (Bio-Rad, Hercules, California, USA) using SYBR Green (Tiangen, China) according to the instructions. Briefly, 12.5 μl SYBR mixture, 1 μl universal reverse primer and 1 μl specific primer were added for each reaction. The U6 reaction as a control was conducted using the specific primer. Three replicate reactions were performed for each sample using following program: 10 min at 95 °C, 40 cycles of 5 s at 95 °C, and 30 s at 60 °C. The specificity of the amplification for each primer pair was verified by melting curve analysis. For RT-PCR, two μg of RNA was used for first strand cDNA synthesis with a Transcript First Strand cDNA Synthesis Kit (Tiangen, China) according to manufacturer’s instructions. The reaction was conducted using following program: 5 min at 95 °C, 31–37 cycles of 30 s at 95 °C, 40 s at 54–60 °C and 1 min at 72 °C. Primers used in the qPCR and RT-PCR were listed in Additional file 1: Table S1. The U6 and actin genes were selected as internal reference genes as described previously .
Identification of SBP genes in B. napus
Nomenclature of BnaSBP genes
Accession number a
MW (kd) c
Chromosome localization and gene duplication analysis
Structural organization and conserved domain identification
Phylogenetic analysis of SBP genes in B. napus, Arabidopsis and rice
MiR156 family in B. napus and their target site to BnaSBP genes
Expression profile of BnaSBP
Expression profile of miR156
SBP-box genes in Brasscia and their evolution
The SBP-box proteins are characterized by a conserved SBP domain with 76 amino acids and constitute one large family of transcription factors in plants. Plant specific SBP-box transcription factors were only detected in green plants suggesting that it might originate predating the divergence of green algae and the ancestor of land plants [5, 48]. Different numbers of SBP-box genes have been characterized in various land plants [39, 40, 49]. In present study, 58 SBP-box genes in B. napus genome were identified, which is about four times the number of Arabidopsis SBP-box genes. B. napus contains 13 more SBP-box genes than the sum of B. rapa (AA, 2n = 20) and B. oleracea (CC, 2n = 18), which are two immediate progenitor species of B. napus (AACC, 2n = 38) . For one gene family, tandem and segmental duplication events are the main reasons for gene expansion. SBP-box genes are unevenly distributed on 17 of the 19 chromosomes of B. napus, and four clusters each with two BnaSBPs were identified (Fig. 1). Uneven and cluster distribution of SBP-box gene family genes was also found in rice and peach . There are seven and 49 BnaSBP genes which were found to be tandem and segmental duplications respectively. Diversification of BnaSBP genes was observed from many aspects, including phylogenesis, genomic structure, as well as location of miR156 target site. This diversity of SBP-box gene structure is likely to be trigged by gene duplication followed by intron and exon loss.
Functional divergence of SBP-box genes
As the SBP-box genes possess the character of transcription factors, their expression pattern is expected to be correlated with their function on plant development. The expression profile of BnaSBP-box genes showed distinct expression patterns among different tissues. In Arabidopsis, some SPL genes are constitutively expressed, while the transcription level of others is under developmental control . Expression analysis of SBP-box genes in other organisms also presented diverse spatiotemporal expression patterns [39, 40, 49, 51]. SBP transcription factors in B. napus showed diverse expression patterns across tissues, indicating their possible functions in various biological processes. The transcription of a large number of BnaSBP genes was enriched in bud, stamen and pericarp, suggesting most of the SBP-box genes in oilseed rape may be involved in the development of reproductive organs.
SBP-box genes in many species, especially in rice and Arabidopsis, have been demonstrated to play essential roles in diverse developmental processes. The microRNA regulated SBP-box genes SPL9 and SPL15, which are the most close orthologous genes in Arabidopsis, was proven to control shoot maturation . Further support of possible roles for BnaSBP in development comes from the rice genes SPL14 in panicle development and ideal rice plant architecture regulation [22, 23]. We identified four BnaSBP9 genes in oilseed rape genome. Although the BnaSBP9 genes possess similar gene structure, diverse expression patterns were observed. It should be noted that the expression of BnaSBP9d in the compact material Purler is higher than in the loose material 6098B (Figs. 9 and 10). The expression of BnaSBP9d visibly decreased from bolting to early flowering. Further study should be performed to verify whether BnaSBP9d might play a role in regulating branch angle in oilseed rape.
Arabidopsis gene SPL8 affects pollen sac development and also controls gynoecium patterning . Three BnaSBP genes, BnaSBP8a, 8b and 8c showed most similarity to AtSBP8,joining the same group through phylogenetic analysis. BnaSBP8a and BnaSBP8b were highly expressed in the stamen. Further study may focus on the potential role of BnaSBP8 in flower development.
Constitutive expression of AtSPL3 resulted in early flowering . The SPL3 homologous genes in Antirrhinum majus and Silver birch also regulate flower development by binding to the MADS-box genes [16, 54]. Tomato LeSPL-CNR, which is most similar to AtSPL3 gene, is crucial for normal fruit development and ripening . In Arabidopsis, miR156-SPL3 module controls FT expression to regulate ambient temperature-responsive flowering . Among the five genes homologous to AtSPL3 identified in B. napus in our study, BnaSBP3c showed much higher expression level in bud, stamen, silique and pericarp, indicating a possible role in the reproduction phase. Arabidopsis gene AtSPL2, AtSPL10 and AtSPL11 were shown to play important roles in determining leaf shape and embryonic morphogenesis [20, 57]. All the BnaSBP2, 10 and 11 genes were classified into a same group of SBP-e. It would be interesting to explore the exact role of these group SBP-box genes by functional characterization.
Conservation of miR156 target site in SBP-box genes
A larger number of miRNAs targets are transcription factors, such as SBP, MYB, NAC, ARF, GRAS, and AP2 . MiRNAs play important roles in regulating the transcription of target genes. Previous results showed that overexpression of miR164, miR159a, and miR319 affected members of the NAC, MYB, and TCP families of transcription factor genes, respectively [58–60]. In present study, target prediction showed that 44 of the 58 BnaSBP genes were regulated by miR156. The complementary sites of miR156 locate in the coding region of 30 BnaSBP genes, and in the 3′ UTR of the other 14 BnaSBP genes. In Arabidopsis, 10 (AtSBP2, 3, 4, 5, 6, 9, 10, 11, 13, 15) out of 17 SBP genes were predicted or verified to be targeted by miR156. The other six AtSBP genes including (AtSBP1, 7, 8, 12, 14, 16) are not targets of miR156. AtSPL7 has been demonstrated to bind directly to the Cu-response element (CuRE) containing a core sequence of GTAC and regulate Cu homeostasis . The 44 BnaSBP genes predicted to be targeted by miR156 are the homologous genes in Arabidopsis, which also formed 10 gene clusters. Therefore, the miR156 target site in SBP-box genes is conserved across plant species.
Over-expression of miR156 in Arabidopsis significantly represses the SPL transcription and thus reduces apical dominance, leading to dwarfism and increases in total leaf number and plant biomass . The transcripts of the target SBP genes were also suppressed in other miR156 over-expression plants [29, 56]. In present study, the transcript level of miR156 was abundant in bud and silique (Fig. 11). By contrast, most putative target SBP genes with predicted miR156 target sites showed lower expression level in these tissues (Figs. 9 and 10). Among the floral organs, most BnaSBP genes showed a low expression level in petal and ovule, though transcript was relatively high in pericarp, which is a main component of silique. These results suggested that the transcript of miR156 is negatively correlated with the expression of most BnaSBP genes. The level of miR156 was declined with a concomitant rise in SPL levels during the aging time in Arabidopsis . SPL9 and SPL10 mediated the transition from high levels of miR156 to high levels of miR172 through direct activation of miR172 expression, thereby promoting the juvenile to adult phase transition [57, 62]. Our results showed that the lower expression level of miR156 in 6098B with bigger branch angle than in Purler with smaller branch angle (Fig. 11) is negatively correlated with the expression difference of many SBP-box genes, eg. BnaSBP2a, 2d, 3d, 3e, 5d, 8b, 9a, 9b, 10b, 11a, 11c, 13d and 15c (Figs. 9 and 10), indicating that the SBP/miR156 module is likely involved in regulating plant architecture in B. napus.
By genome wide analysis of SBP-box genes in oilseed rape (B. napus L), 58 SBP-box genes were identified in the B. napus genome. The BnaSBP proteins were classified into eight different groups and showed clear orthologous relationships of SBP members from rice and Arabidopsis. Our results showed that many SBP-box genes, which were predicted to be targeted by miR156, have tissue specific expression pattern and the expression pattern diverged after gene duplication. The expression level of miR156s was abundant in the root, flowers and silique samples. The different expression pattern between the miR156 and SBP-box genes in diverse tissues suggests that SBP/miR156 module may play an important role in the development processes. Eleven SBP-box gene groups, similar to those in Arabidopsis, were predicted to be targeted by miR156, implying the conservation of SBP/miR156 module regulation pattern. The involvement of some BnaSBP genes as well as the SBP/miR156 module in plant architecture regulation was also implicated from the results. Taken together, our data presented here provide valuable information for further study on the function of SBP-box in B. napus.
CuRE, Cu-response element; Mw, The molecular weight; SBP, squamosa promoter binding protein
We would like to thank Dr. Rachel Wells in John Innes Centre for revision and comments on the manuscript.
This work was supported by the Science and technology innovation project of Chinese Academy of Agricultural Sciences(Group No. 118),the Earmarked Fund for China Agriculture Research System (CARS-13), the Hubei Agricultural Science and Technology Innovation Center and Hubei National Science Foundation (2015CFA103).
Availability of supporting data
The data sets supporting the results of this article are included within the article and its additional files. Materials described in the article will be freely available upon request to any scientist wishing to use them for non-commercial purposes. Phylogenetic and genomic data could be achieved from Dryad database (http://dx.doi.org/10.5061/dryad.3rk33).
HTC and QH designed research; HTC, WXW performed the bioinformatics analysis, HTC, MYH performed qRT-PCR experiments and miRNA analysis, DSM, JL performed RNA-seq analysis, CBT carried out expression pattern analysis, HW, LF provided plant material and prepared RNA samples, HTC and QH wrote the paper. All authors have read and approved the version of manuscript.
The authors declare that they have no competing interests.
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