千里光茎和叶的差异表达基因分析
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摘要
以千里光(Senecio scandens Buch.-Ham. ex D. Don)强抗菌性植株SC-32为研究对象,分别提取其茎和叶的总RNA,经质量检测合格后构建cDNA文库,利用Illumina HiSeq~(TM) 2500高通量测序平台对千里光茎和叶的cDNA文库进行转录组测序,筛选差异表达基因,并运用Nr、Swiss-Prot、KEGG和COG数据库对差异表达基因进行功能分析。结果表明:从千里光茎和叶的cDNA文库中分别获得26 147 016和26 996 119个clean reads,Q30值分别为95.17%和94.74%,说明其转录组测序结果良好。从千里光的茎和叶中共筛选到10 991个差异表达基因,以茎中差异表达基因的表达量为准,叶中上调的差异表达基因有5 542个,下调的差异表达基因有5 449个。千里光的茎和叶中共有7 683个差异表达基因被GO功能注释成生物过程、细胞组分和分子功能3个大类53个亚类,且这些差异表达基因与信号传导途径、次生代谢过程、细胞组分合成和酶催化活性等密切相关。KEGG代谢通路分析结果表明:共有4 527个差异表达基因,涉及50个代谢通路,主要参与碳代谢、氨基酸生物合成及淀粉和蔗糖代谢。研究结果显示:千里光茎和叶的差异表达基因具有器官特异性,并且,其茎和叶的分化和形成与多糖和蛋白质累积密切相关。
Taking strong anti-microbial plant SC-32 of Senecio scandens Buch.-Ham. ex D. Don as research object, total RNA from its stem and leaf was extracted, respectively, and cDNA library was constructed after qualified by quality test. Transcriptome sequencing of cDNA libraries of stem and leaf of S. scandens was conducted by using Illumina HiSeq~(TM) 2500 high-throughput sequencing platform, the differentially expressed genes were screened, and their functional analyses were conducted by using Nr, Swiss-Prot, KEGG, and COG databases. The results show that 26 147 016 and 26 996 119 clean reads are obtained from cDNA libraries of stem and leaf of S. scandens, and their Q30 values are 95.17% and 94.74%, respectively, indicating that its transcriptome sequencing result is fine. 10 991 differentially expressed genes are totally screened from stem and leaf of S. scandens. Taking expression level of differentially expressed gene in stem as standard, there are 5 542 up-regulated differentially expressed genes and 5 449 down-regulated differentially expressed genes in leaf. 7 683 differentially expressed genes in stem and leaf of S. scandens are totally annotated by GO function into 53 sub-categories of 3 major categories(including biological process, cellular component, and molecular function), and these differentially expressed genes are closely related with signal transduction pathway, secondary metabolic process, cell component synthesis, and enzyme catalyze activity, etc. The analysis result of KEGG metabolic pathway shows that there are 4 527 differentially expressed genes, which relate to 50 metabolic pathways, and mainly involve in carbon metabolism, biosynthesis of amino acids, and starch and sucrose metabolism. It is suggested that differentially expressed genes in stem and leaf of S. scandens have organ specificity, and the differentiation and formation of stem and leaf are closely related with accumulations of polysaccharide and protein.
Taking strong anti-microbial plant SC-32 of Senecio scandens Buch.-Ham. ex D. Don as research object, total RNA from its stem and leaf was extracted, respectively, and cDNA library was constructed after qualified by quality test. Transcriptome sequencing of cDNA libraries of stem and leaf of S. scandens was conducted by using Illumina HiSeq~(TM) 2500 high-throughput sequencing platform, the differentially expressed genes were screened, and their functional analyses were conducted by using Nr, Swiss-Prot, KEGG, and COG databases. The results show that 26 147 016 and 26 996 119 clean reads are obtained from cDNA libraries of stem and leaf of S. scandens, and their Q30 values are 95.17% and 94.74%, respectively, indicating that its transcriptome sequencing result is fine. 10 991 differentially expressed genes are totally screened from stem and leaf of S. scandens. Taking expression level of differentially expressed gene in stem as standard, there are 5 542 up-regulated differentially expressed genes and 5 449 down-regulated differentially expressed genes in leaf. 7 683 differentially expressed genes in stem and leaf of S. scandens are totally annotated by GO function into 53 sub-categories of 3 major categories(including biological process, cellular component, and molecular function), and these differentially expressed genes are closely related with signal transduction pathway, secondary metabolic process, cell component synthesis, and enzyme catalyze activity, etc. The analysis result of KEGG metabolic pathway shows that there are 4 527 differentially expressed genes, which relate to 50 metabolic pathways, and mainly involve in carbon metabolism, biosynthesis of amino acids, and starch and sucrose metabolism. It is suggested that differentially expressed genes in stem and leaf of S. scandens have organ specificity, and the differentiation and formation of stem and leaf are closely related with accumulations of polysaccharide and protein.
引文
[1] 祁云霞, 刘永斌, 荣威恒. 转录组研究新技术: RNA-Seq及其应用[J]. 遗传, 2011, 33(11): 1191-1202.
[2] 邹承武, 宋玮, 宋慈安, 等. 基于RNA-Seq技术分析在金属矿上部生长的芒萁的差异表达基因[J]. 植物资源与环境学报, 2017, 26(2): 1-9.
[3] 江香梅, 伍艳芳, 肖复明, 等. 樟树5种化学类型叶片转录组分析[J]. 遗传, 2014, 36(1): 58-68.
[4] 钱刚, 敖弟书, 段鹏敏, 等. 千里光抗菌作用的数量性状分析[J]. 武汉植物学研究, 2010, 28(1): 67-71.
[5] 李穆, 程志远, 石莹, 等. 基于RNA-Seq技术的甘蔗参考转录组建立及分析[J]. 分子植物育种, 2015, 13(2): 355-360.
[6] WANG X, YANG Z, WANG M, et al. The BRANCHING ENZYME1 gene, encoding a glycoside hydrolase family 13 protein, is required for in vitro plant regeneration in Arabidopsis[J]. Plant Cell, Tissue and Organ Culture, 2014, 117: 279-291.
[7] 王兴春, 杨致荣, 张树伟, 等. 拟南芥不定芽发生早期的数字基因表达谱分析[J]. 生物工程学报, 2013, 29(2): 189-202.
[8] MAGBANUA Z V, ARICK Ⅱ M, BUZA T, et al. Transcriptomic dissection of the rice-Burkholderia glumae interaction[J]. BMC Genomics, 2014, 15: 755.
[9] 徐定平, 周鑫堂, 郜红利, 等. 千里光化学成分和药理作用研究进展[J]. 中国药师, 2014, 17(9): 1562-1565.
[10] 李燕, 韩忠耀, 魏学军. 不同采收期和部位黔产千里光中总黄酮、绿原酸和金丝桃苷含量动态比较[J]. 天津中医药大学学报, 2018, 37(2): 155-160.
[11] ANDERS S, HUBER W. Differential expression analysis for sequence count data[J]. Genome Biology, 2010, 11: R106.
[12] YE J, FANG L, ZHENG H, et al. WEGO: a web tool for plotting GO annotations[J]. Nucleic Acids Research, 2006, 34: 293-297.
[13] 王梦夏, 郭方遒, 孙琼, 等. 高效液相色谱法结合化学计量学测定千里光中四种活性成分的含量[J]. 分析科学学报, 2014, 30(2): 219-222.
[14] 吴琼. 三种产萜类药用植物转录组分析和产地适宜性研究[D]. 北京: 中国医学科学院, 2010: 35-51.
[15] 赵振宇, 王仕玉, 郭凤根, 等. 转录组测序及其在药用植物上的应用[J]. 基因组学与应用生物学, 2017, 36(2): 820-825.
[16] 梁烨, 陈双燕, 刘公社. 新一代测序技术在植物转录组研究中的应用[J]. 遗传, 2011, 33(12): 1317-1326.
[17] 肖玉菲, 袁剑英, 刘海龙, 等. 桉树4个无性系茎部差异分析[J]. 中南林业科技大学学报, 2017, 37(10): 61-66.
[18] 夏叔芳, 于新建, 张振清. 叶片光合产物输出的抑制与淀粉和蔗糖的积累[J]. 植物生理学报, 1981, 7(2): 49-56.
[19] 张文平, 刘志春, 张文书, 等. 千里光对金黄色葡萄球菌和大肠埃希菌生物合成的影响[J]. 广东医学, 2009, 30(11): 1634-1635.
[2] 邹承武, 宋玮, 宋慈安, 等. 基于RNA-Seq技术分析在金属矿上部生长的芒萁的差异表达基因[J]. 植物资源与环境学报, 2017, 26(2): 1-9.
[3] 江香梅, 伍艳芳, 肖复明, 等. 樟树5种化学类型叶片转录组分析[J]. 遗传, 2014, 36(1): 58-68.
[4] 钱刚, 敖弟书, 段鹏敏, 等. 千里光抗菌作用的数量性状分析[J]. 武汉植物学研究, 2010, 28(1): 67-71.
[5] 李穆, 程志远, 石莹, 等. 基于RNA-Seq技术的甘蔗参考转录组建立及分析[J]. 分子植物育种, 2015, 13(2): 355-360.
[6] WANG X, YANG Z, WANG M, et al. The BRANCHING ENZYME1 gene, encoding a glycoside hydrolase family 13 protein, is required for in vitro plant regeneration in Arabidopsis[J]. Plant Cell, Tissue and Organ Culture, 2014, 117: 279-291.
[7] 王兴春, 杨致荣, 张树伟, 等. 拟南芥不定芽发生早期的数字基因表达谱分析[J]. 生物工程学报, 2013, 29(2): 189-202.
[8] MAGBANUA Z V, ARICK Ⅱ M, BUZA T, et al. Transcriptomic dissection of the rice-Burkholderia glumae interaction[J]. BMC Genomics, 2014, 15: 755.
[9] 徐定平, 周鑫堂, 郜红利, 等. 千里光化学成分和药理作用研究进展[J]. 中国药师, 2014, 17(9): 1562-1565.
[10] 李燕, 韩忠耀, 魏学军. 不同采收期和部位黔产千里光中总黄酮、绿原酸和金丝桃苷含量动态比较[J]. 天津中医药大学学报, 2018, 37(2): 155-160.
[11] ANDERS S, HUBER W. Differential expression analysis for sequence count data[J]. Genome Biology, 2010, 11: R106.
[12] YE J, FANG L, ZHENG H, et al. WEGO: a web tool for plotting GO annotations[J]. Nucleic Acids Research, 2006, 34: 293-297.
[13] 王梦夏, 郭方遒, 孙琼, 等. 高效液相色谱法结合化学计量学测定千里光中四种活性成分的含量[J]. 分析科学学报, 2014, 30(2): 219-222.
[14] 吴琼. 三种产萜类药用植物转录组分析和产地适宜性研究[D]. 北京: 中国医学科学院, 2010: 35-51.
[15] 赵振宇, 王仕玉, 郭凤根, 等. 转录组测序及其在药用植物上的应用[J]. 基因组学与应用生物学, 2017, 36(2): 820-825.
[16] 梁烨, 陈双燕, 刘公社. 新一代测序技术在植物转录组研究中的应用[J]. 遗传, 2011, 33(12): 1317-1326.
[17] 肖玉菲, 袁剑英, 刘海龙, 等. 桉树4个无性系茎部差异分析[J]. 中南林业科技大学学报, 2017, 37(10): 61-66.
[18] 夏叔芳, 于新建, 张振清. 叶片光合产物输出的抑制与淀粉和蔗糖的积累[J]. 植物生理学报, 1981, 7(2): 49-56.
[19] 张文平, 刘志春, 张文书, 等. 千里光对金黄色葡萄球菌和大肠埃希菌生物合成的影响[J]. 广东医学, 2009, 30(11): 1634-1635.
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