Transcriptome analysis of regeneration process of primary cell wall in xylem protoplast of Betula platyphylla
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摘要:目的 木质部细胞壁的组成及特性是决定材性的重要因素,研究木质部细胞壁形成的分子调控机制对于木材改良具有重要意义。本研究探究了白桦木质部原生质体初生壁再生过程的分子调控机制,并鉴定出重要调控基因,旨在为林木材性性状研究提供数据和材料。方法 分别以培养0 h和2 h的白桦木质部原生质体为材料,通过荧光增白剂染色观察初生壁再生过程。利用转录组分析技术研究初生壁再生前后的差异表达基因及其参与的调控途径,将检测到的差异表达基因在GO、KEGG、PlantTFDB数据库中进行比对分析。结果 荧光显微镜观察结果显示:原生质体分离后不具有细胞壁,培养2 h再生初生细胞壁。以|log2(FC)| ≥ 1(FC为差异倍数)且q < 0.05为标准筛选差异基因,结果显示:相较于刚分离的原生质体,培养2 h的原生质体中检测到4 396个上调表达的基因,4 056个下调表达基因,总计8 452个差异表达基因。其中GO数据库共注释到10个显著上调条目,KEGG数据库注释到10个显著差异代谢通路,PlantTFDB数据库共注释到16个家族的360个差异表达转录因子。GO注释结果表明,DNA复制、细胞周期相关基因上调表达。KEGG注释结果表明,谷胱甘肽、α-亚麻酸等与抗逆代谢相关的基因下调表达,果胶脂酶相关基因上调表达。PlantTFDB注释结果表明,bHLH、NAC、MYB、bZIP等与细胞壁合成密切相关的转录因子均差异表达。结论 培养2 h的木质部原生质体处于细胞壁再生及分裂准备状态,DNA复制、细胞周期、多糖合成代谢等相关基因在白桦木质部原生质体培养及初生细胞壁形成过程中起调控作用。Abstract:Objective The properties of wood are determined by the composition and characteristics of xylem cell wall. It is important for wood improvement to study the molecular regulation mechanism of xylem cell wall formation. In this study, the molecular regulatory mechanisms in the process of regeneration of primary wall in the protoplast of birch (Betula platyphylla) xylem were analyzed and the important regulatory genes were identified, aiming to provide data and materials for the study of wood properties.Method The protoplasts of birch xylem cultured for 0 h and 2 h were used as materials, respectively, and the regeneration process of primary cell wall was observed by staining with calcofluor white. The differentially expressed genes (DEGs) and differential metabolic pathways participating before and after the regeneration of the primary wall were compared by transcriptomic analysis. The detected DEGs were aligned with GO, KEGG and PlantTFDB.Result Observation by fluorescence microscopy showed that protoplasts had no cell walls after enzymatic digestion and the primary cell walls had been regenerated after 2 h culture. The DEGs were screened using |log2(FC)| ≥ 1(fold change, FC) and q < 0.05 as the parameters. The results showed that compared with the protoplasts without cell wall, 4396 up-regulated genes and 4056 down-regulated genes were detected in the protoplasts cultured for 2 h, with a total number of 8452 DEGs. In the GO database, there were 10 significantly up-regulated terms. KEGG analysis noted 10 significantly different metabolic pathways. Total of 360 differentially expressed transcription factors from 16 families was annotated in PlantTFDB database. The GO database annotation results showed that DNA replication and cell cycle related genes were up-regulated in the cell wall regeneration lines compared with that in control. The results of KEGG database annotation showed that genes involved in glutathione, α-linolenic acid and other stress-related metabolism genes were down-regulated, and pectinester related genes were up-regulated. PlantTFDB annotation results showed that bHLH, NAC, MYB, bZIP and other transcription factors closely related to cell wall biosynthesis were differentially expressed.Conclusion Above results show that xylem protoplasts are in a state of cell wall regeneration and division preparation at 2 h culture. DNA replication, cell cycle, polysaccharide biosynthesis and other related genes play a regulatory role in xylem protoplast culture and primary cell wall formation of B. platyphylla.
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Keywords:
- Betula platyphilla /
- protoplast /
- regeneration of primary cell wall /
- transcriptome
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图 1 白桦原生质体细胞壁再生荧光显微镜观察结果
a. 培养0 h的原生质体;b. 培养0.5 h的原生质体;c. 培养1 h的原生质体;d. 培养2 h的原生质体。a, protoplasts cultured for 0 h; b, protoplasts cultured for 0.5 h; c, protoplasts cultured for 1 h; d, protoplasts cultured for 2 h.
Figure 1. Fluorescence microscope observation of cell wall regeneration in protoplasts of birch
图 8 糖酵解(a)、磷酸戊糖(b)、戊糖及葡萄糖互变异构体(c)、纤维素合成(d)和苯丙烷代谢(e)途径差异示意图
F16P. 果糖-1,6-二磷酸1.6-fructose diphosphate;F6P. 果糖-6-磷酸fructose 6-phosphate;G6P. 葡萄糖-6-磷酸glucose 6-phosphate;G1P. 磷酸葡萄糖 glucose 1-phosphate;红色文本代表基因的上调;绿色文本代表基因的下调;实线单箭头代表不可逆反应;实线双箭头代表可逆反应;虚线单箭头代表多步反应。Red text refers to gene up-regulation, the green text refers to gene down-regulation, the solid single arrow represents an irreversible reaction, the solid double arrow represents the reversible reaction, the dotted single arrow represents the multistep reaction.
Figure 8. Schematic diagram of differences in glycolysis (a), pentose phosphate (b), pentose and glucuronate interconversions (c), cellulose synthesis (d) and phenylpropanoid metabolism pathway (e)
表 1 Clean reads与参考基因组比对结果
Table 1 Clean reads and the sequence alignment results with reference genome
组别
Group过滤后序列总数
Total clean reads比对成功率
Mapping rate/%基因总数
Total gene numberQ30/% C1 44 905 836 92.04 19 835 93.36 C2 41 241 930 92.26 19 764 93.44 C3 45 786 950 92.28 19 885 93.22 T1 47 178 646 91.37 20 442 93.53 T2 44 340 702 91.13 20 310 93.22 T3 41 809 660 91.02 20 281 93.32 注:Q30为过滤后碱基质量值,表示碱基错误率小于0.001的测序碱基占测序总数的比例。Notes: Q30 is the base quality value after filtering, indicating the proportion of sequenced bases with a base error rate less than 0.001 in the total number of sequenced bases.
表 2 KEGG通路注释结果及富集分析统计表
Table 2 Results of KEGG notions and the significantly enriched KEGG pathway statistics
通路名称
Pathway nameMap编号
Map No.p值
p valueq值
q value上调数
Number of up-regulation下调数
Number of down-regulation谷胱甘肽代谢 Glutathione metabolism map00480 0.000 002 450 0.000 238 8 30 α-亚麻酸代谢
Alpha-Linolenic acid metabolismmap00592 0.000 029 600 0.001 353 6 17 DNA复制 DNA replication map03030 0.000 332 000 0.011 156 18 1 光合作用天线蛋白
Photosynthesis-antenna proteinsmap00196 0.001 147 000 0.026 197 7 0 黄酮代谢 Flavonoid biosynthesis map00941 0.001 623 000 0.027 359 9 5 戊糖及葡萄糖糖醛互变异构体
Pentose and glucuronate interconversionsmap00040 0.001 997 000 0.027 359 14 8 光合作用 Photosynthesis map00195 0.001 945 000 0.027 359 13 0 卟啉和叶绿素代谢
Porphyrin and chlorophyll metabolismmap00860 0.001 666 000 0.027 359 14 3 牛磺酸及亚牛磺酸代谢
Taurine and hypotaurine metabolismmap00430 0.002 319 000 0.028 882 2 5 黄酮及黄酮合成
Flavone and flavanol biosynthesismap00944 0.004 234 000 0.04 8340 6 1 表 3 原生质体细胞壁再生过程中相关差异基因统计
Table 3 DEGs in the process of cell wall regeneration
细胞壁发育相关代谢过程
Metabolic processes associated with
cell wall development差异表达基因编码的酶
Enzyme cluster of DEGs encoding差异基因总数(上调数 + 下调数)
Total DEGs number (up-regulation
number + down-regulation number)葡萄糖及葡萄糖酰代谢
Glucose and glucosyl metabolicUDP葡萄糖醛酸转移酶 UDP-glucosyl transferase (UDPGT) 37(13 + 24) UDP葡萄糖转移酶 UDP-glucose transferase (UDPG) 3(3 + 0) 果糖二磷酸酶 Fructose diphosphatase (FBP) 1(1 + 0) 果糖二磷酸醛缩酶 Fructose-bisphosphate aldolase (ALDO) 1(1 + 0) 羰基转移酶家族 Glycosyl transferase family 12(0 + 12) 糖基羟化酶家族 Glycosyl hydrolases family 9(9 + 0) 内质网二糖结合 Di-glucose binding within endoplasmic reticulum 5(2 + 3) 3-β葡萄糖苷酶 3-beta-glucosidase 3(3 + 0) 1,3-葡聚糖合成酶 1,3-beta-glucan synthase 1(1 + 0) 6-磷酸葡萄糖羟化酶 6-phosphogluconate dehydrogenase 1(0 + 1) 6-磷酸葡萄糖异构酶 Glucosamine-6-phosphate isomerases 1(1 + 0) 3-磷酸甘油醛脱氢酶 Glyceraldehyde 3-phosphate dehydrogenase 1(1 + 0) 木糖代谢
Xylose metabolicβ-1,4-木糖基转移酶 Beta-1,4-xylosyltransferase 1(1 + 0) β-1,2-木糖基转移酶 Beta-1,2-xylosyltransferase 1(1 + 0) 半乳糖代谢
Galactose metabolic细胞壁相关受体激酶半乳糖醛酸结合
Wall-associated receptor kinase galacturonan-binding10(4 + 6) 半乳糖基转移酶 Galactosyltransferase 5(3 + 2) 聚半乳糖醛酸酶 Polygalacturonase 5(2 + 3) 聚半乳糖醛酸酶抑制剂 Polygalacturonase inhibitor 3(0 + 3) 糖基水解酶 Glycosyl hydrolases 2(0 + 2) 磷酸戊糖代谢
Pentose phosphate metabolic核糖激酶 Ribokinase (RbsK) 3(3 + 0) 6-磷酸葡萄糖脱氢酶 Phosphogluconic dehydrogenase (G6PD) 2(2 + 0) 果胶代谢
Pectic metabolism果胶酯酶 Pectinester 6(0 + 6) 果胶裂解酶 Pectate lyase 7(7 + 0) 苯丙素生物合成
Phenylpropanoid biosynthesis月桂醇脱氢酶 Cinnamyl-alcihol dehydrogenase (CAD) 2(0 + 2) 过氧化物酶 Peroxidase (POD) 6(6 + 0) -
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