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月季插穗不定根起始的转录组分析和关键基因筛选

陈静 陈芸 热依麦阿依·阿布都艾尼 方志刚 凯迪日耶·玉苏普 马刘峰

陈静, 陈芸, 热依麦阿依·阿布都艾尼, 方志刚, 凯迪日耶·玉苏普, 马刘峰. 月季插穗不定根起始的转录组分析和关键基因筛选[J]. 华南师范大学学报(自然科学版), 2021, 53(3): 54-62. doi: 10.6054/j.jscnun.2021044
引用本文: 陈静, 陈芸, 热依麦阿依·阿布都艾尼, 方志刚, 凯迪日耶·玉苏普, 马刘峰. 月季插穗不定根起始的转录组分析和关键基因筛选[J]. 华南师范大学学报(自然科学版), 2021, 53(3): 54-62. doi: 10.6054/j.jscnun.2021044
CHEN Jing, CHEN Yun, Reyimaiayi·ABUDUAINI, FANG Zhigang, Kaidiriye·YUSUPU, MA Liufeng. A Transcriptomic Analysis of Early Adventitious Roots of Rosa chinensis Cuttings and Key Genes Screening[J]. Journal of South China normal University (Natural Science Edition), 2021, 53(3): 54-62. doi: 10.6054/j.jscnun.2021044
Citation: CHEN Jing, CHEN Yun, Reyimaiayi·ABUDUAINI, FANG Zhigang, Kaidiriye·YUSUPU, MA Liufeng. A Transcriptomic Analysis of Early Adventitious Roots of Rosa chinensis Cuttings and Key Genes Screening[J]. Journal of South China normal University (Natural Science Edition), 2021, 53(3): 54-62. doi: 10.6054/j.jscnun.2021044

月季插穗不定根起始的转录组分析和关键基因筛选

doi: 10.6054/j.jscnun.2021044
基金项目: 

新疆维吾尔自治区青年科技创新人才培养工程资助项目 QN2016YX0611

详细信息
    通讯作者:

    马刘峰, Email:maliufeng@126.com

  • 中图分类号: Q943.2;Q786

A Transcriptomic Analysis of Early Adventitious Roots of Rosa chinensis Cuttings and Key Genes Screening

  • 摘要: 为研究月季插穗在不定根发生过程中的关键基因调控机理,利用Illumina平台测序技术对切花月季品种‘卡罗拉’插穗的3个发育阶段(不定根未启动期、愈伤组织形成期和不定根伸长期)插穗基部1 cm皮层进行转录组测序分析,结果表明:月季插穗不定根发生的3个阶段中,在不定根未启动期与愈伤组织形成期之间共筛选出差异表达基因5 033个,其中2 313个基因上调,2 720个基因下调;在愈伤组织形成期与不定根伸长期之间共筛选出差异表达基因1 865个,其中1 332个基因上调,533个基因下调;GO功能分析表明,差异表达基因主要参与生物过程、分子功能和细胞组分3大功能;KEGG富集分析结果表明,差异表达基因主要参与植物激素信号转导、次生代谢产物的合成以及碳水化合物的合成等代谢通路;将月季插穗生根过程中差异性最为显著的8个基因通过实时荧光定量PCR检测其转录水平变化,结果表明: 实时荧光定量PCR的验证结果与转录组测序结果基本一致.
  • 图  1  月季扦插生根的3个时期

    Figure  1.  The 3 periods of rose cutting rooting

    图  2  差异表达基因火山图

    Figure  2.  The differentially expressed gene volcano plot

    图  3  不定根未启动期与愈伤组织阶段GO富集分析柱状图

    注:横坐标为Go level2等级的term,纵坐标为每个term富集的-log10(p值).

    Figure  3.  The histogram of the GO enrichment analysis at the cutting and callus stages

    图  4  KEGG富集分析图

    Figure  4.  The diagram of the KEGG enrichment analysis

    图  5  扦插生根不同时期的差异表达基因维恩图

    注:A-B: 不定根未启动期与愈伤组织期;A-C: 不定根未启动期与不定根伸长期;B-C: 愈伤组织期与不定根伸长期.

    Figure  5.  The Venn diagram of differentially expressed genes at different stages of rooting

    图  6  qRT-PCR检测月季扦插生根过程中2个阶段差异基因的表达

    Figure  6.  The differential gene expression at 2 rooting stages detected with qRT-PCR

    表  1  文库基本情况

    Table  1.   The basic information of the library

    样品 样品名称 文库名
    不定根未启动期 A1 LRA13418
    A2 LRA13419
    愈伤组织期 B1 LRA13420
    B2 LRA13421
    不定根伸长期 C1 LRA13422
    C2 LRA13423
    注:A1、A2为不定根未启动期的2个平行样本;B1、B2为愈伤组织期的2个平行样本;C1、C2为不定根伸长期的2个平行样本.
    下载: 导出CSV

    表  2  检测基因表达的引物序列

    Table  2.   The primer sequence of gene expression detected

    基因编号 正向序列(5'-3') 反向序列(5'-3') PCR产物/bp
    GAPDH GGAAAGGTTCTGCCTGCTC CTGGTCATAGGTTGCCTTCTTC 139
    LOC112189488 CTCTACCCTGCTGCCCCACT GCGACTCATCACCACCGTTT 187
    LOC112186298 GGAGCATTTGTCCAGTTCGT GCCATTAGTAGCCGCCTTT 180
    LOC112165178 GCATGGGAGTTGTGGAAAGA AGGTGCAGGTAATCGTGAGC 198
    LOC112172220 CCACCCTCTTGAGCCTTACC AGCATTTCCTCCATCTCCTTC 165
    LOC112179697 TCTATCCTCGCCAGCCACT ACCGTCCTCGAATACTCCTTC 187
    LOC112164736 TCCTAAGCAATGGTCTAAAGCC TCCGCATAGTCCCGAAAA 124
    LOC112193119 TGAAAACCCGATTCCCATC GGTCAAGAACCCACCCAATG 115
    LOC112194361 TGTTGTCATTCCTGCGTTTG TGGTGCTGCTGAGGTTGC 127
    下载: 导出CSV

    表  3  下机数据统计

    Table  3.   The statistics of offline data

    样品 Reads/条 碱基总数/bp Q30/bp N/% Q20占碱基数的百分数/% Q30占碱基数的百分数/% Clean Reads占Reads的百分数/%
    A1 41 432 804 6 214 920 600 5 608 791 753 0.003 266 95.89 90.24 92.26
    A2 44 353 390 6 653 008 500 6 057 901 035 0.003 008 96.30 91.05 92.80
    B1 39 577 678 5 936 651 700 5 384 791 893 0.003 314 96.09 90.70 92.83
    B2 43 275 996 6 491 399 400 5 900 420 774 0.003 278 96.19 90.89 92.73
    C1 45 240 742 6 786 111 300 6 172 944 331 0.003 262 96.26 90.96 92.52
    C2 48 695 120 7 304 268 000 6 625 080 997 0.003 226 96.11 90.70 92.91
    注:Q20(bp):碱基识别准确率在99%以上的碱基总数;Q30 (bp):碱基识别准确率在99.9%以上的碱基总数;N(%):模糊碱基所占百分比;Clean Reads占Reads的百分数(%):高质量序列碱基占测序碱基的百分比.
    下载: 导出CSV

    表  4  参考基因组信息

    Table  4.   The information of reference genome

    数据库 基因注释数 基因注释率/%
    NCBI_GeneID 30 216 100
    UniProt 25 170 83.30
    GO 19 242 63.68
    KEGG 8 754 28.97
    下载: 导出CSV
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出版历程
  • 收稿日期:  2020-12-19
  • 网络出版日期:  2021-07-06
  • 刊出日期:  2021-06-25

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