基于Illumina高通量测序的泡桐转录组研究

doi:10.11707/j.1001-7488.20130605

摘要/Abstract

摘要：

利用新一代高通量测序技术平台Illumina Solexa对泡桐进行转录组测序和数据de novo组装,并对得到的unigene进行功能注释、分类及代谢通路分析。结果表明,N50值为2 278 bp、平均长度为1 410 bp的泡桐unigene共有188 019条,将其与NCBI的Nr和Swiss-Prot数据库比对后发现,分别有120 808条和85 880条unigene与其他物种的基因具有同源性。利用COG数据库可将有关的41 914条泡桐unigene分成25类,KEGG数据库分析发现共有43 553个unigene参与215种代谢通路。找到与木质素合成相关的泡桐unigene。

关键词: 泡桐, 转录组, Illumina高通量测序, 从头组装

Abstract:

The transcriptome Paulownia plant was sequenced by using Illumina technology, and the functional annotations and metabolic pathways analyses of some unigenes were conducted in this present paper. The results indicated that 188 019 unigenes with an average length of 1 410 bp and N50 value of 2 278 bp were obtained with de novo assembly. Comparison with NCBI and Swiss-Prot protein databases showed that 120 808 and 85 880 unigenes had homology with the genes from other species, respectively. The 41 914 unigenes were able to be assigned to 25 categories with the COG (Clusters of Orthologous Groups) database. Functional annotation against KEGG (Kyoto Encyclopedia of Genes and Genomes) database identified 43 553 unigenes which were mapped to 215 metabolic pathways. Moreover, some Paulownia unigenes related to lignin biosynthesis were found using this information platform. The result provides reference for future excavations of new genes, as well as screening and identifying miRNA of Paulownia plants.

Key words: Paulownia, transcriptome, Illumina sequencing, de novo assembly

中图分类号:

S718.46

邓敏捷, 董焱鹏, 赵振利, 张晓申, 范国强. 基于Illumina高通量测序的泡桐转录组研究[J]. 林业科学, 2013, 49(6): 30-36.

Deng Minjie, Dong Yanpeng, Zhao Zhenli, Zhang Xiaoshen, Fan Guoqiang. Illumina-Based de novo Sequencing and Characterization of the Transcriptome of Paulownia Plant[J]. Scientia Silvae Sinicae, 2013, 49(6): 30-36.

参考文献

陈占宽, 杨艳坤,叶金山,等. 2011. 白花泡桐羟基肉桂酰辅酶A还原酶mRNA全序列克隆及序列分析. 西北林学院学报,26(4): 99-103.

范国强,李有,郑建伟,等. 2003. 泡桐丛枝病发生相关蛋白质的电泳分析. 林业科学,39(2): 119-122.

范国强,杨志清,曹艳春,等. 2006. 秋水仙素诱导兰考泡桐同源四倍体. 核农学报,20(6): 473-476.

范国强,曹艳春,赵振利,等. 2007a. 白花泡桐同源四倍体的诱导. 林业科学,43(4): 30-36.

范国强,杨志清,曹艳春,等. 2007b. 毛泡桐同源四倍体的诱导. 植物生理学通讯,43(1): 109-111.

范国强,张胜,翟晓巧,等. 2007c. 抗生素对泡桐丛枝病植原体和发病相关蛋白质的影响. 林业科学,43(3): 138-142.

范国强,曾辉,翟晓巧. 2008. 泡桐丛枝病发生特异相关蛋白质亚细胞定位及质谱鉴定. 林业科学,44(4): 83-86.

范国强,魏真真,杨志清. 2009. 南方泡桐同源四倍体的诱导及其体外植株再生研究. 西北农林科技大学学报: 自然科学版,37(10): 83-90.

范国强,翟晓巧,魏真真,等. 2010. 豫杂一号泡桐体细胞同源四倍体诱导及其体外植株再生. 东北林业大学学报,38(12): 22-26.

范国强,赵改丽,翟晓巧,等. 2011. 硫酸二甲酯处理豫杂一号泡桐丛枝病幼苗形态变化及其SSR分析. 东北林业大学学报,39(5): 30-33.

范国强,赵改丽,翟晓巧,等. 2012. 硫酸二甲酯对毛泡桐丛枝病幼苗植原体及SSR扩增位点的影响. 南京林业大学学报: 自然科学版,36(3): 5-8.

黎明,翟晓巧,范国强,等. 2008. 土霉素对豫杂一号泡桐丛枝病幼苗形态和DNA甲基化水平的影响. 林业科学,44(9): 152-156.

祁云霞,刘永斌,荣威恒. 2011. 转录组研究新技术: RNA-Seq及其应用. 遗传, 33(11): 1191-1202.

田国忠,李永,梁文星,等. 2010. 丛枝病植原体侵染对泡桐组培苗组织内H₂O₂产生的影响. 林业科学,46(9): 96-104.

翟晓巧,曹喜兵,范国强. 2010. 甲基磺酸甲酯处理的豫杂一号泡桐丛枝病幼苗的生长及SSR分析. 林业科学,46(12): 176-181.

赵振利,何佳,赵晓改,等. 2011. 泡桐9501体外植株再生体系的建立及体细胞同源四倍体诱导. 河南农业大学学报,45(1): 59-65.

Akyildiz M H, Kol H S. 2010. Some technological properties and uses of Paulownia (Paulownia tomentosa Steud.) wood. J Environ Biol, 31(3): 351-355.

Altschul S F, Madden T L, Schäffer A A,et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 25(17): 3389-3402.

Annadurai R S, Jayakumar V, Mugasimangalam R C, et al. 2012. Next generation sequencing and de novo transcriptome analysis of Costus pictus D. Don, a non-model plant with potent anti-diabetic properties. BMC Genomics, 13: 663.

Barash Y, Calarco J A, Gao W,et al. 2010. Deciphering the splicing code. Nature, 465(7294): 53-59.

Barrero R A, Chapman B, Yang Y,et al. 2011. De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes. BMC Genomics, 12: 600.

Fan G Q, Jiang J Q. 1997. Relationship between witches' broom protein and dynamic of some amino acids in Paulownia tree leaves. Journal of Forestry Research, 8(3): 164-166.

Gao C, Wang Y, Liu G,et al. 2008. Expression profiling of salinity-alkali stress responses by large-scale expressed sequence tag analysis in Tamarix hispida. Plant Mol Biol, 66 (3): 245-258.

Garg R, Patel R K, Jhanwar S,et al. 2011. Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol, 156(4): 1661-1678.

Hao D C, Ge G, Xiao P,et al. 2011. The first insight into the tissue specific Taxus transcriptome via Illumina second generation sequencing. PLoS ONE, 6(6): e21220.

Hsiao Y Y, Chen Y W, Huang S C,et al. 2011. Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchids. BMC Genomics, 12: 360.

Huang L L, Yang X, Sun P,et al. 2012. The first Illumina-based de novo transcriptome sequencing and analysis of Safflower flowers. PLoS ONE, 7(6): e38653. doi: 10.1371/journal.pone.0038653.

Kristiansson E, Asker N, Forlin L,et al. 2009. Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing. BMC Genomics, 10: 345.

Li D, Deng Z, Qin B,et al. 2012. De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics, 13: 192.

Llano-Sotelo J M, Alcaraz-Melendez L, Castellanos Villegas A E. 2010. Gas exchange in Paulownia species growing under different soil moisture conditions in the field. J Environ Biol, 31(4): 497-502.

Miyama M, Tada Y. 2008. Transcriptional and physiological study of the response of Burma mangrove (Bruguiera gymnorhiza) to salt and osmotic stress. Plant Mol Biol, 68(1-2): 119-129.

Mizrachi E, Hefer C A, Ranik M,et al. 2010. De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNASeq. BMC Genomics, 11: 681.

Parchman T L, Geist K S, Grahnen J A,et al. 2010. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics, 11: 180.

Schatz M C, Witkowski J, McCombie W R,et al. 2012. Current challenges in de novo plant genome sequencing and assembly. Genome Biol, 13: 243.

Schulz M H, Zerbino D R, Vingron M,et al. 2012. Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics, 28(8): 1086-1092.

Shi C Y, Yang H, Wei C L,et al. 2011. Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics, 12: 131.

Sloan D B, Keller S R, Berardi A E,et al. 2012. De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae). Mol Ecol Resour, 12(2): 333-43.

Vera J C, Wheat C W, Fescemyer H W,et al. 2008. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular Ecology, 17(7): 1636-1647.

Wang Y, Zeng X, Iyer N J,et al. 2012. Exploring the switchgrass transcriptome using second-generation sequencing technology. PLoS ONE, 7(3): e34225. doi: 10.1371/journal.pone.0034225.

Ye J, Fang L, Zheng H,et al. 2006. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res, 34(Web Server issue): W293-W297.

Zdobnov E M, Apweiler R. 2001. InterProScan: an integration platform for thesignature-recognition methods in InterPro. Bioinformatics, 17(9): 847-848.

Zerbino D R, Birney E. 2008. Velvet: Algorithms for de novo short read assembly using de Brujin graphs. Genome Res, 18(5): 821-829.

Zhang Y, Zhang S G, Han S Y,et al. 2012. Transcriptome profiling and in silico analysis of somatic embryos in Japanese larch (Larix leptolepis). Plant Cell Rep, 31(9): 1637-1657.

Zhou Y, Gao F, Liu R,et al. 2012. De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus. BMC Genomics, 13: 266.

[1]	韩小红, 卢赐鼎, 华银, 林浩宇, 是雨霏, 吴松青, 张飞萍, 梁光红. 星天牛转录组及三大解毒酶家族相关基因系统发育分析[J]. 林业科学, 2019, 55(5): 104-113.
[2]	刘果, 陈鸿鹏, 吴志华, 彭彦, 谢耀坚. 南美油藤种子发育过程的代谢组学和转录组学联合分析[J]. 林业科学, 2019, 55(5): 169-179.
[3]	张恩亮, 马玲玲, 杨如同, 李林芳, 汪庆, 李亚, 王鹏. IBA诱导楸树嫩枝扦插不定根发育的转录组分析[J]. 林业科学, 2018, 54(5): 48-61.
[4]	曹亚兵, 翟晓巧, 邓敏捷, 赵振利, 范国强. 泡桐丛枝病发生与代谢组变化的关系[J]. 林业科学, 2017, 53(6): 85-93.
[5]	毛伟兵, 陈发菊, 王长兰, 梁宏伟. 楸树雄性不育花芽转录组测序及分析[J]. 林业科学, 2017, 53(6): 141-150.
[6]	唐海霞, 杜淑辉, 邢世岩, 桑亚林, 李际红, 刘晓静, 孙立民. 银杏性别决定相关基因的筛选[J]. 林业科学, 2017, 53(2): 76-82.
[7]	郭丽丽, 尹伟伦, 郭大龙, 侯小改. 油用凤丹牡丹不同种植时间根际细菌群落多样性变化[J]. 林业科学, 2017, 53(11): 131-141.
[8]	王艳梅, 张龙冲, 马天晓, 刘震, 任雪敏, 耿晓东, 宋良红. 人工调控对泡桐顶芽生长发育的影响[J]. 林业科学, 2016, 52(8): 53-59.
[9]	曹艳春, 曹亚兵, 赵振利, 翟晓巧, 范国强. 泡桐新品种‘南四泡桐1号’[J]. 林业科学, 2016, 52(8): 168-168.
[10]	李康琴, 龚斌, 徐海宁, 戴小英, 彭纪南, 朱培林. 泡桐良种‘天桐C22’[J]. 林业科学, 2016, 52(7): 171-171.
[11]	丁昌俊, 张伟溪, 高暝, 黄秦军, 褚延广, 苏晓华. 不同生长势美洲黑杨转录组差异分析[J]. 林业科学, 2016, 52(3): 47-58.
[12]	时小东, 朱学慧, 盛玉珍, 庄国庆, 陈放. 基于转录组序列的楠木SSR分子标记开发[J]. 林业科学, 2016, 52(11): 71-78.
[13]	张振, 张含国, 莫迟, 张磊. 红松转录组SSR分析及EST-SSR标记开发[J]. 林业科学, 2015, 51(8): 114-120.
[14]	陈昊, 谭晓风. 基于油脂合成期油桐种仁转录组数据的α-亚麻酸代谢途径解析[J]. 林业科学, 2015, 51(3): 41-48.
[15]	文亚峰, 韩文军, 周宏, 徐刚标. 杉木转录组SSR挖掘及EST-SSR标记规模化开发[J]. 林业科学, 2015, 51(11): 40-49.