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International Journal of Genomics
Volume 2017, Article ID 3981031, 14 pages
Research Article

Genome-Wide Identification of bZIP Family Genes Involved in Drought and Heat Stresses in Strawberry (Fragaria vesca)

1College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
2Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996-4560, USA
3Food Quality Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
4Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996-4560, USA

Correspondence should be addressed to Zong-Ming Cheng; nc.ude.uajn@cmz

Received 11 October 2016; Revised 24 January 2017; Accepted 12 February 2017; Published 11 April 2017

Academic Editor: Ferenc Olasz

Copyright © 2017 Xiao-Long Wang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

Figure S1 Phylogenetic analysis (A) and copy number changes (B) of strawberry, Arabidopsis and rice bZIP proteins. In A, an N-J tree was constructed from a sequence alignment of predicted strawberry, Arabidopsis and rice bZIP proteins using MEGA 6.0 software. Number in branches indicae the bootstrap percentage values calculated from 1000 replicates, and only values >50% are shown. The nodes that represent the most recent common ancestral genes before the strawberry, Arabidopsis and rice split are indicated by red circles (bootstrap support >50%). Clades that contain only one species bZIP protein of are strawberry, Arabidopsis and rice indicated by red, green and yellow, respectively. In B, the numbers in circles and rectangles represent the numbers of bZIP genes in extant and ancestral species, respectively. Number on branch with plus and minus symbols represents the numbers of gene gains and losses, respectively. Figure S2 positions and patterns of introns within tha basic-hinge region of the bZIP domains for 50 FvbZIP transcription factors. The intron position is marked in red stripe. The five intron patterns in FvbZIP domain region were represented by a, b, c, d, and e. Figure S3 Classification of FvbZIP proteins based on the alignment of basic and hinge regions. The conserved amino acids in strawberry bZIP proteins are shadowed in red. The first leucine in leucine heptad repeats is numbered +1 and the last amino acid of hinge regions is -1. Some of the functional annotated bZIP proteins in Arabidopsis and rice sharing similar amino acid sequences in the basic and hinge regions are shown as references. The different amino acid residues at -10 and -18 positions like K and I are colored. Figure S4 Amino acid sequences alignments of the leucine zipper regions of FvbZIP proteins. The FvbZIP proteins are categorized into 20 types with similar predicted dimerization properties. The leucine zipper region is divided into heptad (gabcdef) from L0 to L9 to visualize the potential g ↔ e′pairs. Four colors are used to differentiate between different g ↔ e′pairs. Attractive basic-acidic (R↔E and K↔E) are colored green, attractive acidic-basic pairs (E↔R, E↔K, E↔R, and D↔K) are yellow, repulsive basic pairs (K↔K, R↔K, R↔Q, Q↔K and K↔Q) are blue, repulsive acidic pairs (E↔E, E↔D, E↔Q, and Q↔E) are red. If single amino acid at the positions e of g is charged, the residue is colored blue for basic amino acid and red for acidic acid. If the a or d position is charged, it is colored purple. Asparagines at a position are colored gray. The pralines and glycines are bold to indicate a potential bresk in the α-helix. The predicted C-terminal boundary is denoted by the symbol #, other than the natural terminals which are indicated by the symbol ∗. Table S1 Primer sequence information. Table S2 Additional conserved motifs identified from FvbZIP proteins. Table S3 DNA binding site specificity and classification of FvbZIP proteins. Table S4 Summary for the types of the dimerization properties predicted from FvbZIP proteins. Table S5 Transcriptome data of FvbZIP genes used in this study.

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