Scientia Agricultura Sinica ›› 2021, Vol. 54 ›› Issue (21): 4694-4708.doi: 10.3864/j.issn.0578-1752.2021.21.018

• RESEARCH NOTES • Previous Articles    

Molecular Evolution and Function Analysis of bZIP Family in Nymphaea colorata

YE FangTing(),PAN XinFeng,MAO ZhiJun,LI ZhaoWei,FAN Kai()   

  1. College of Agriculture, FuJian Agriculture and Forestry University/Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fuzhou 350002
  • Received:2021-01-18 Accepted:2021-06-28 Online:2021-11-01 Published:2021-11-09
  • Contact: Kai FAN;


【Objective】The genome-wide analysis of the bZIP family in Nymphaea colorata was used to identify the bZIP (basic leucine zipper) family members in waterlily, and then which were further analyzed. This study revealed molecular evolution and function of the bZIP family in waterlily.【Method】The genome sequence of N. colorata was downloaded from Waterlily Pond database. The bZIP members in waterlily were identified by using HMMER 3.0 program, and the conserved bZIP domain was verified by using CDD program. The phylogenetic tree was constructed by the IQ-tree software. The ExPASy and SOPMA online website were performed to analyze protein structure characters. The conserved motifs were identified by using MEME program. The gene duplication events were found and visualized by the MCScan and Circos software. Transcriptome data of NcbZIP members were obtained from the NCBI website (SRA Study: SRP222853). The Pearson Correlation Coefficient (PCC) about the expression levels of the NcbZIP family members was calculated by using R software, and the network of the expression levels in the NcbZIP family was analyzed by using Cytoscape software.【Result】46 bZIP members were identified in N. colorata, and were named from NcbZIP01 to NcbZIP46 according to their chromosome distributions. The A subfamily contained the most NcbZIP members (11 NcbZIPs). There were 10 subfamilies (A, B, C, D, E, G, H, I, J and S) according to the phylogenetic analysis. The protein length in the NcbZIP family was from 101 aa to 1 898 aa, and the molecular weight ranged from 12.04 kD to 214.64 kD. The NcbZIP members from same subfamily had the similar distributions of the conserved motifs and gene structures. Waterlily had 14 chromosomes, and 46 NcbZIP members were unevenly distributed across 10 chromosomes. Chromosome 1 had the highest number of NcbZIP members. There were 10 gene duplication events in the NcbZIP family, including nine segmental duplication events and one tandem duplication event. The A subfamily had the most number of the gene duplication events (three). Based on the expression patterns in different tissues, the NcbZIP family could be divided into three groups (I, II and III). The NcbZIP members in Group I were highly expressed in all tissues, while the NcbZIP members in group II were not expressed in almost all tissues. The NcbZIP members in group III had tissue-specific expression profiles, and most of NcbZIP members in C, D and E subfamilies belonged to group III. The PPC analysis about the expression levels of NcbZIP members indicated NcbZIP45 had the highest connection with other members.【Conclusion】46 NcbZIP members were identified in Nymphaea colorata, and were unevenly distributed in 14 chromosomes. The NcbZIP family could be divided into 10 subfamilies with conserved motifs distributions and diverse expression levels. The current study could lay the foundation on the functional analysis of the bZIP family in N. colorata.

Key words: Nymphaea colorata, bZIP family, molecular evolution, expression profile, function analysis

Fig. 1

Phylogenetic analysis of the bZIP family in Arabidopsis thaliana and Nymphaea colorata"

Table 1

The identification and structural analysis of NcbZIP members in this study"

Locus name
Protein length (aa)
Molecular weight (kD)
Theoretical pI
α -helix
Extended strand
β -turn
Random coil
NcbZIP01 GWHPAAYW000832 D 418 46.54 6.09 215 19 9 175
NcbZIP02 GWHPAAYW000931 G 537 59.56 9.08 200 46 16 275
NcbZIP03 GWHPAAYW000954 A 425 45.47 9.24 155 44 25 201
NcbZIP04 GWHPAAYW000981 D 564 62.21 7.12 260 47 19 238
NcbZIP05 GWHPAAYW001299 C 415 44.86 6.11 164 6 5 240
NcbZIP06 GWHPAAYW001709 J 377 41.80 5.40 151 67 22 137
NcbZIP07 GWHPAAYW002908 A 336 37.46 7.80 115 19 5 197
NcbZIP08 GWHPAAYW002911 A 336 37.46 7.80 115 19 5 197
NcbZIP09 GWHPAAYW002993 D 461 50.44 7.20 242 30 7 182
NcbZIP10 GWHPAAYW003042 B 792 86.18 5.84 179 94 28 491
NcbZIP11 GWHPAAYW003339 E 266 29.16 6.15 107 16 10 133
NcbZIP12 GWHPAAYW011330 S 152 17.55 5.91 98 5 2 47
NcbZIP13 GWHPAAYW014950 S 1898 214.64 9.00 712 280 94 812
NcbZIP14 GWHPAAYW015527 A 167 18.44 9.48 87 22 5 53
NcbZIP15 GWHPAAYW015722 I 428 47.31 6.74 145 17 11 255
NcbZIP16 GWHPAAYW015723 I 217 23.98 9.92 72 37 9 99
NcbZIP17 GWHPAAYW019618 E 450 49.50 5.62 147 27 16 260
NcbZIP18 GWHPAAYW020485 S 160 18.11 5.48 94 6 4 56
NcbZIP19 GWHPAAYW020561 I 372 40.4 5.69 154 21 13 184
NcbZIP20 GWHPAAYW021201 H 166 18.22 9.90 76 7 0 83
NcbZIP21 GWHPAAYW021532 C 385 40.82 8.58 164 8 5 208
NcbZIP22 GWHPAAYW025680 A 310 34.00 5.30 110 24 6 170
NcbZIP23 GWHPAAYW025682 D 178 20.14 9.19 79 21 1 77
NcbZIP24 GWHPAAYW025732 A 488 51.90 9.37 141 55 17 275
NcbZIP25 GWHPAAYW025769 A 149 16.94 9.52 78 16 16 39
NcbZIP26 GWHPAAYW026086 D 429 46.68 7.70 211 30 15 173
NcbZIP27 GWHPAAYW026335 S 195 22.17 5.82 105 10 2 78
NcbZIP28 GWHPAAYW026612 G 371 39.05 8.48 118 27 9 217
NcbZIP29 GWHPAAYW026862 B 755 82.16 5.57 147 90 21 497
NcbZIP30 GWHPAAYW027461 G 298 30.89 4.79 94 19 6 179
NcbZIP31 GWHPAAYW027688 I 541 59.03 6.30 183 22 12 324
NcbZIP32 GWHPAAYW028327 A 268 30.70 6.11 132 30 5 101
NcbZIP33 GWHPAAYW004093 A 462 49.89 7.11 124 55 14 269
NcbZIP34 GWHPAAYW004840 A 362 40.15 6.13 143 24 10 185
NcbZIP35 GWHPAAYW004844 D 364 40.64 7.00 227 21 8 108
NcbZIP36 GWHPAAYW004881 G 283 32.04 8.68 147 54 24 58
NcbZIP37 GWHPAAYW005079 H 168 18.92 6.64 78 7 6 77
NcbZIP38 GWHPAAYW005229 E 452 49.64 5.71 162 33 9 248
NcbZIP39 GWHPAAYW005452 S 169 18.77 5.53 103 5 2 59
NcbZIP40 GWHPAAYW005509 I 355 38.40 5.68 145 28 11 171
NcbZIP41 GWHPAAYW005714 G 545 60.52 8.75 175 66 22 282
NcbZIP42 GWHPAAYW005783 C 410 44.35 5.67 153 36 17 204
NcbZIP43 GWHPAAYW005814 A 101 12.04 8.96 81 4 0 16
NcbZIP44 GWHPAAYW005854 D 511 56.99 7.75 245 23 19 224
NcbZIP45 GWHPAAYW009588 I 334 36.76 7.01 137 19 13 165
NcbZIP46 GWHPAAYW028567 C 264 28.72 6.13 119 10 7 128

Fig. 2

Identification of conserved motif (left) and gene structure (right) in the NcbZIP family"

Fig. 3

Chromosomal localization of bZIP members in waterlily"

Fig. 4

Syntenic analysis and Ks distribution of the duplicated bZIP members in Nymphaea colorata A: Syntenic analysis of the duplicated bZIP members in Nymphaea colorata; B: Subfamily distribution of the duplicated bZIP members in waterlily; C: Ks distribution of the duplicated bZIPs in waterlily, the arrow points topeak value of Ks"

Table 2

Ka and Ks analysis for the duplicated NcbZIP in N. colorata"

Duplicated gene 1
Duplicated gene 2
Purifying selection
Duplicated type
GWHPAAYW001299 GWHPAAYW021532 C 0.32 1.24 0.26 Yes Segmental duplication
GWHPAAYW000931 GWHPAAYW005714 G 0.36 0.95 0.38 Yes Segmental duplication
GWHPAAYW000954 GWHPAAYW005814 A 0.53 2.19 0.24 Yes Segmental duplication
GWHPAAYW000981 GWHPAAYW005854 D 0.11 0.78 0.15 Yes Segmental duplication
GWHPAAYW015527 GWHPAAYW025769 A 0.61 1.84 0.33 Yes Segmental duplication
GWHPAAYW020485 GWHPAAYW005452 S 0.09 1.29 0.07 Yes Segmental duplication
GWHPAAYW020561 GWHPAAYW005509 I 0.20 1.04 0.19 Yes Segmental duplication
GWHPAAYW019618 GWHPAAYW005229 E 0.22 1.29 0.17 Yes Segmental duplication
GWHPAAYW025680 GWHPAAYW004840 A 0.22 1.61 0.14 Yes Segmental duplication
GWHPAAYW015722 GWHPAAYW015723 I 0.28 0.96 0.30 Yes Tandem duplication

Fig. 5

Stress-responsive regulatory elements in the promoter regions of NcbZIP members"

Fig. 6

Expression patterns of NcbZIP members in different tissues"

Fig. 7

Heat map of PCC about the expression profiles of the bZIP family in N. colorata"

Fig. 8

The network of the bZIP family in N. colorata"

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