Abstract
Homeodomain-Leu zipper (HD-Zip) gene family performs important biological functions related to organ development, photomorphogenesis and abiotic stress response in higher plants. However, systematic analysis of HD-Zip genes in Brassica rapa has not been performed. In the present study, a bioinformatics approach was used to identify and characterize the BraHD-Zip gene family in B. rapa. A total of 88 members were identified. All putative BraHD-Zip proteins contained a clear HD and LZ combined domain. Eighty-seven BraHD-Zips were non-randomly located on ten chromosomes. This gene family was mainly expanded following the whole genome triplication event and was preferentially over-retained relative to its neighboring genes in B. rapa. On phylogenetic analysis, the BraHD-Zips could be categorized into four distinct major groups (I–IV). Each group exhibited variant gene structures and motif distributions. Some syntenic orthologous gene pairs presented diverse expression profiles, which indicate that these gene pairs may be involved in the development of new functions during evolution. In summary, our analysis provided genome-wide insights into the expansion, preferential retention, expression profiles and functional diversity of BraHD-Zip genes following whole genome triplication in B. rapa.
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Acknowledgements
This work was supported by State Key Special Program “Seven Main Crops Breeding” (2016YFD0101701), National Science and Technology Support Program (2012BAD02B01), Independent Innovation of Agricultural Science and Technology Program of Jiangsu Province [CX(13)2006], Science and technology support program of Jiangsu Province (BE2013429), A Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions, National Natural Science Foundation of China (No. 31330067).
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10725_2017_268_MOESM1_ESM.eps
Fig. S1. Distribution of HD-Zip genes on chromosomes of Brassica rapa and Arabidopsis thaliana. (A) B. rapa chromosomes. (B) A. thaliana chromosomes. The synteny blocks are labeled on left of chromosomes (A to X). (EPS 1046 KB)
10725_2017_268_MOESM2_ESM.eps
Fig. S2. Prediction of physical/chemical characteristics of HD-Zip transcription factors family in eudicots. (A) Theoretical isoelectric point (pI). (B) Molecular weight (Mw). (EPS 548 KB)
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Fig. S4. An analytical view of the HD-Zip gene family in Brassica rapa. (A) Protein phylogenetic tree: The phylogenetic tree was constructed from a complete alignment of 88 BraHD-Zip proteins by maximum likelihood (ML) method with 1,000 bootstrap replicates using MEGA5.0. (B) Gene structure: Exon/intron structures of HD-Zip genes were drew by GSDS 2.0. Exons were represented by yellow boxes and introns by black lines. The sizes of exons and introns could be estimated using the scale below. (C) Protein structure: Schematic distributions of the conserved motifs among defined gene clusters. Motifs were identified by MEME software. The relative position of each identified motif in all HD-Zip proteins is shown. Multilevel consensus sequences for the MEME defined motifs were listed in Table S6. (EPS 3204 KB)
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Fig. S5. Heatmap of the expression profiles for HD-Zip genes across different tissues in Arabidopsis thaliana and Brassica rapa. (A) The A. thaliana expression profiling was analyzed using the AtGenExpress Visualization Tool with mean-normalized values (supplementary Table S10). (B) Gene expression FPKM values of RNA-Seq data were analyzed for Brassica rapa HD-Zip genes (supplementary Table S7). The color bar at the bottom of heat map represents relative expression values. (EPS 1065 KB)
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Jing, Z., Duan, W., Song, X. et al. Preferential retention, expression profile and potential functional diversity analysis of HD-Zip gene family in Brassica rapa . Plant Growth Regul 82, 421–430 (2017). https://doi.org/10.1007/s10725-017-0268-1
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DOI: https://doi.org/10.1007/s10725-017-0268-1