基于转录组测序的青蟹寿锦化相关基因分析

陈汉鑫; 鞠玉栋; 万学锋

doi:10.19303/j.issn.1008-0384.2019.02.006

基于转录组测序的青蟹寿锦化相关基因分析

doi: 10.19303/j.issn.1008-0384.2019.02.006

1.
福建省漳州市农业科学研究所, 福建漳州 363005
2.
福建省农业科学院亚热带农业研究所, 福建漳州 363005

基金项目:

福建省科技厅农业引导性（重点）项目 2017N0063

详细信息

作者简介:
陈汉鑫(1978-), 男, 副研究员, 主要从事生物技术研究(E-mail:zzche@163.com)

中图分类号: Q943.2
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- 被引次数: 0
出版历程
- 收稿日期: 2018-05-12
- 修回日期: 2018-11-14
- 刊出日期: 2019-02-28

Preliminary Study on Molecular Mechanism of Variegated Haworthia magnifica Formation

1.
Zhangzhou Agriculture Science Institute, Zhangzhou, Fujian 363005, China
2.
Subtropical Agriculture Institute, Fujian Academy of Agriculture Sciences, Zhangzhou Fujian 363005, China

摘要

摘要: 目的以青蟹寿及其全锦突变体qj为材料，研究多肉植物锦化变异分子机理。方法利用分光光度计法、转录组测序（RNA-seq），分别测量其叶绿素、类胡萝卜素含量及其相关基因的表达水平，并筛选差异显著的相关代谢途径。结果结果表明，qj的叶绿素a、叶绿素b、类胡萝卜素的含量显著下降；对青蟹寿及qj叶片转录组测序分别获得44 988 938和37 271 576条Reads，经过滤拼接组装得到45 226条Unigene；所得Unigene的Nr注释分类中有26 999条，Swissport注释有20 279条，KOG注释有16 943条，KEGG注释有10 775条；筛选获得表达差异显著基因共20 305条，涉及130个途径，其中21个途径差异显著。筛选得到的叶绿素合成途径（ko00860）、天线蛋白（ko00196）和光合作用途径（ko00195）的基因表达对比分析，结果表明这3个途径的基因普遍显著下调表达。结论初步探索了多肉植物锦化变异的转录组信息，筛选到表达差异显著的基因及途径，为进一步研究多肉植物锦化变异机制提供了基础。
- 多肉植物 /
- 锦化突变 /
- 转录组 /
- 光合作用
Abstract: Objective Molecular mechanism responsible for the formation of variegated succulent plants, Haworthia magnifica, was investigated using the mutant qj for the comparison. Method Contents of chlorophylls and carotenoids in the plants were determined by spectrophotometry, and gene expression by transcriptome sequencing (RNA-seq). Result The contents of chlorophyll a, chlorophyll b and carotenoids in the variegated qj were significantly lower than those of wild-type H. magnifica. Using RNA-seq, 44 988 938 Reads were obtained for H. magnifica and 37 271 576 for qj which were assembled into 45 226 Unigenes. There were 26 999 Unigenes assigned to Nr annotations, 20 279 to Swissport, 16 943 to KOG categories, and 10 775 to KEGG pathway. A total of 20 305 genes exhibited significantly different expressions that involved 130 pathways, of which 21 significantly differed from the others. The gene expression analysis showed that the genes associated with the chlorophyll synthesis (ko00860), antenna protein (ko00196) and photosynthesis (ko00195) pathways were generally significantly down-regulated. Conclusion The significant variations on the transcriptome sequences, genes and pathways of H. magnifica and its variegated counterpart obtained from this study provided the fundamental information for further study to unveil the underlaying mechanism.
- succulent plants /
- variegated variation /
- transcriptome /
- photosynthesis

HTML全文

图 1 WT与qj中叶绿素a、b和类胡萝卜素含量

注：A为野生型(WT)与突变体(qj)的表型，标尺=0.5 cm；B为WT和qj的叶绿素a、b、类胡萝卜素含量；*为P＜0.05显著差异，**为P＜0.01极显著差异。

Figure 1. The content difference of Chlorophyll a, chlorophyll b and carotenoid in WT and qj

Note:A: Phenotype of WT and qj, scale bar=0.5 cm; B: Differences on contents of chlorophyll a, chlorophyll b and carotenoids in WT and qj; *P<0.05, **P < 0.01.

下载: 全尺寸图片幻灯片

图 2 测序拼接后Unigene长度分布情况

Figure 2. Distribution of Unigenes by length

下载: 全尺寸图片幻灯片

图 3 unigene注释及分类

注：A为四大数据库注释韦恩图; B为GO功能分类图; C为KOG功能分类图。

Figure 3. Annotations and classification of Unigenes

Note:A: Venn of annotated gene (mapped from KEGG, KOG, Nr, Swissprot database); B: Classification of gene ontology annotation; C: Classification of KOG annotation.

下载: 全尺寸图片幻灯片

图 4 样品间差异分析

注：A为样品间差异基因散点图；B为样品间差异基因GO分类图；C为样品间差异基因KEGG富集图。

Figure 4. Difference analysis among samples

Note:A: Scatter plot of differentially expressed genes; B: GO annotation of differentially expressed genes; C: KEGG metabolism pathway categories of differentially expressed genes.

下载: 全尺寸图片幻灯片

图 5 光合途径基因下调表达

注：A为光系统Ⅰ差异基因下调表达；B为F型ATP酶差异基因下调表达；C为细胞色素b6/f复合体差异基因下调表达；D为光系统Ⅱ差异基因下调表达；E为光合作用电子传递链差异基因下调表达。

Figure 5. Down-regulated expressions of genes in photosynthetic pathway

Note:A: Down-regulated expression of genes in photosystem Ⅰ; B: Down-regulated expression of genes in F-type ATPase; C: Down-regulated expression of genes in cytochrome b6/f complex; D: Down-regulated expression of genes in photosystem Ⅱ; E: Down-regulated expression of genes in photosystem in photosynthetic electron transport.

下载: 全尺寸图片幻灯片

图 6 天线蛋白基因下调表达

注：A为光系统Ⅰ中天线蛋白差异基因下调表达；B为光系统Ⅱ中天线蛋白差异基因下调表达。

Figure 6. Down-regulated expressions of genes in antenna proteins

Note:A.The down-regulated expression genes in photosystem Ⅰ; B.The down-regulated expression genes in F-type ATPase.

下载: 全尺寸图片幻灯片

图 7 叶绿素合成酶基因下调表达

Figure 7. Down-regulated expressions of genes in chlorophyll synthesis

下载: 全尺寸图片幻灯片

表 1 测序质量评估

Table 1. Statistics on sequencing

样品 Sample	过滤前read数 Before filter read number	Q20/%	Q30/%	G+C/%	过滤后read数 After filter read number	Q20/%	Q30/%
WT	44988938	97.26	93.13	49.52	43871136(97.52)	98.38	94.88
qj	37271576	97.13	92.94	48.86	36263612(97.30)	98.35	94.82

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