Identification and Analysis of Expansins in the Transcriptome of Sanyueli Plum and Its Red-flesh Mutant
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摘要:
目的 Expansin是广泛存在于植物中的一类细胞壁蛋白，通过调节细胞壁柔韧性在植物生长发育过程中发挥作用。本研究旨在分析Expansin基因家族特征及其在果实成熟过程中的表达模式，并比较Expansin基因在三月李及其红肉突变体之间的差异表达。 方法 基于三月李及其红肉突变体果实成熟过程的转录组数据，采用生物信息学分析方法进行Expansin家族基因鉴定与分析。 结果 鉴定出33个李Expansin基因家族成员，编码蛋白长度在176～460 aa，分子量在19.21～51.33 kD，等电点4.62～9.83，大部分为位于细胞外的稳定亲水蛋白。系统进化树分析表明李Expansin家族成员可分为4个组：22个EXPA、6个EXPB、1个EXPLA和4个EXPLB。所有李Expansin蛋白质均具有保守的DPBB_1和Pollen_allerg_1结构域。保守基序分析表明，同一组Expansin成员具有相似的基序组成。9个Expansin基因在三月李及其红肉突变体果实成熟过程中差异表达。 结论 Expansin在三月李及其红肉突变体果实成熟过程中的表达模式存在显著差异。本研究结果可为解析李Expansin家族基因在果实成熟过程中的功能奠定基础。 -
关键词:
- 李 /
- 转录组 /
- expansin家族 /
- 生物信息学分析 /
- 表达分析
Abstract:Objective Characteristics and expressions of Expansins, the widely existing gene family associated with plant cell wall, were studied during the fruit ripening stage to decipher the genetic functions relating to ripening of the plum fruits. Method Transcriptomes of fruits of Sanyueli ( Prunus salicina Lindl.) and its red-flesh mutant were used to identify Expansin genes as well as for a bioinformatic and expression comparison of identified genes. Result Thirty-three Expansins, with individual protein containing 176 to 460 amino acids, a molecular weight ranging from 19.21kD to 51.33kD, and an isoelectric point varying from 4.62 to 9.83, were identified from the fruit transcriptome data. Most of them were stable hydrophilic proteins located in the extracellular space. Phylogenetic analysis revealed that plum Expansin family included 22 EXPAs, 6 EXPBs, 1 EXPLA, and 4 EXPLBs. All of the proteins had DPBB_1 and Pollen_allerg_1 domains, and, within a same classification, they shared same conserved motif composition. Nine Expansins were differentially expressed in Sanyueli and the mutant during fruit ripening. The expressions of EVM0015785, EVM0016777, EVM0010710, EVM0022202, EVM0002390, and EVM0024996 significantly differed between Sanyueli and the red-flesh mutant. Conclusion The information obtained was to be used for further study on the functions of the Expansin family during ripening of plum fruits. -
Key words:
- Plum /
- transcriptome /
- expansin family /
- bioinformatics analysis /
- expression analysis
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图 1 李、桃、拟南芥和水稻Expansin家族蛋白质系统进化树
注：李Expansin家族蛋白质以粗体表示。
Figure 1. Phylogenetic tree of
Expansin family in plum, peach, Arabidopsis, and rice Note: Expansin in bold font.
图 2 Expansin家族蛋白质进化树及保守结构域分析
Figure 2. Phylogenetic tree and conserved domain of
Expansin family 
图 3 李Expansin家族蛋白质保守基序及结构域序列Logo
注：A：李Expansin家族蛋白质保守元件分布；B：李Expansin家族蛋白质保守元件序列特征。
Figure 3. Conserved motifs and domain sequence logo of Expansin family
Note：A：Distribution of the identified motifs in plum Expansin family proteins. B：The sequence constitution of identified motifs in plum Expansin family proteins.
图 4 李Expansin家族蛋白质的多重序列比对
注: Expansin蛋白质的保守结构域用黑色横线标出，上方的红色字表示保守的氨基酸残基。
Figure 4. Multiple sequence alignment analysis on
Expansin family Note: Conserved domains in Expansin indicated by horizontal black lines, and conserved amino acid residues by red letters.
图 5 Expansin家族基因在三月李及其红肉突变体果实成熟过程中的表达模式
注：上图基于三月李及其红肉突变体果实成熟过程的转录组数据计算得出。所有基因的FPKM值采用每个基因的最大FPKM值进行均一化处理。基因的表达水平由不同大小和颜色的实心圆表示，实心圆越大，表达量越高。右侧的数值为每个基因的最大FPKM值。
Figure 5. Expression pattern of Expansins in Sanyueli plum and its red-flesh mutant during fruit ripening
Note：Based on the transcriptome data of Sanyueli and the red-fleshed mutant fruits during ripening. All FPKM values of all genes were normalized with maximum FPKM values of each gene. The expression level of genes was indicated using filled circle with different size and colour. The larger the circle, the higher the expression. The values on the right indicates the highest FPKM value of each gene.
表 1 三月李及其红肉突变体Expansin蛋白质的理化性质和亚细胞定位
Table 1. Physicochemical properties and subcellular localization of Expansins in Sanyueli plum and its red-flesh mutant
序列编号
Sequnce ID蛋白质长度
Protein length/aa分子量
Molecular weight/kD等电点
pI不稳定系数
Instability index脂肪系数
Aliphatic index平均亲水系数
Grand average of hydropathicity细胞定位
Cell locationEVM0011615 252 26.78 9.36 35.7 64.29 −0.100 Extracellular EVM0015785 252 26.74 6.92 31.32 66.23 −0.108 Extracellular EVM0004461 254 27.27 8.43 30.26 63.43 −0.194 Extracellular EVM0027977 254 27.27 8.43 30.26 63.43 −0.194 Extracellular EVM0009515 257 27.47 8.79 35.46 74.47 −0.039 Extracellular EVM0008468 257 27.50 8.93 34.94 74.47 −0.042 Extracellular EVM0009923 257 27.74 9.14 32.88 67.24 −0.095 Extracellular EVM0010710 258 27.94 8.59 27.91 64.69 −0.066 Extracellular EVM0025415 259 28.39 8.89 22.2 73.9 −0.118 Extracellular EVM0019517 259 28.39 8.89 22.2 73.9 −0.118 Extracellular EVM0022202 259 27.84 9.41 33.23 71.2 −0.010 Extracellular EVM0002390 260 27.99 9.47 34.71 68.65 −0.007 Extracellular EVM0017357 260 28.74 8.07 17.38 66.81 −0.226 Extracellular EVM0018627 261 29.24 9.35 33.36 69.12 −0.338 Extracellular EVM0016646 263 28.99 9.22 35.71 65.32 0.006 Extracellular EVM0026183 265 29.18 9.83 45.17 73.21 −0.057 Extracellular EVM0016777 266 28.74 8.4 33.52 86.54 0.065 Extracellular EVM0010881 282 31.12 9.09 29.38 62.27 −0.388 Extracellular EVM0028371 291 31.89 5.77 39.08 72.03 −0.337 Extracellular EVM0018557 353 37.15 9.24 45.03 76.26 −0.001 Extracellular EVM0001651 367 40.65 9.53 48.28 83.41 −0.018 Extracellular EVM0020356 460 51.33 8.67 46.31 75.07 −0.258 Plasma membrane, Extracellular EVM0014217 176 19.21 4.98 36.08 77.1 −0.137 Extracellular EVM0016078 266 28.47 8.95 28.91 82.44 −0.032 Extracellular EVM0000548 272 28.58 4.62 43.47 76.4 −0.027 Extracellular EVM0006851 280 30.10 5.94 36.92 70.07 −0.168 Extracellular EVM0022596 282 30.33 7.52 35.18 72.02 −0.142 Extracellular EVM0026545 296 31.92 8.62 41.79 67.64 −0.269 Extracellular EVM0024996 260 28.16 8.73 37.26 85.62 0.035 Extracellular EVM0026062 252 28.00 6.87 30.3 69.33 −0.309 Extracellular EVM0028340 252 28.00 6.87 30.3 69.33 −0.309 Extracellular EVM0003805 252 28.00 6.87 30.3 69.33 −0.309 Extracellular EVM0013160 255 27.74 4.78 38.38 75.33 −0.170 Extracellular 
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