Transcriptome sequencing, de novo assembly and expression analysis of 
several genes related to internode development in Pseudosasa japonica

doi:10.3969/j.issn.1000-2006.201601006

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2017, Vol. 41 ›› Issue (05): 42-48.doi: 10.3969/j.issn.1000-2006.201601006

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Transcriptome sequencing, de novo assembly and expression analysis of several genes related to internode development in Pseudosasa japonica

WEI Qiang, DING Yulong

Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China

Online:2017-10-18 Published:2017-10-18

Abstract

Abstract: 【Objective】Describe the molecular basis of bamboo rhizome development. 【Methods】 We used next-generation sequencing technology and qRT-PCR to analyze the transcriptome profile of the underground stems of Pseudosasa japonica and the expression pattern of genes related to internode elongation, respectively. 【Results】 A total of 119 767 unigenes, with an average length of 1 008 bp were determined, 63.8% of which had annotated results. A total of 16 254 unigenes were annotated to 137 KEGG(kyo to Encyclopedia of Genes and Genomes)pathways. MapMan software identified 1 864 transcription factors, 603 hormone related genes, and 564 cell-wall building related genes, including 92 unigenes related to lignin biosynthesis. The qRT-PCR analysis showed that, among the nine genes used for detecting, gibberellin-related genes had the highest expression level in the elongation initiation stage of internode development, whereas cell wall growth- and cytoskeleton-related genes had the strongest expression in the rapid elongation of internodes. 【Conclusion】 These results illustrate the molecular basis for rhizome development in Ps. japonica. The molecular mechanism underlying the development of rhizomes is a complex network consisting of hormones, transcription factors and downstream functional genes.

CLC Number:

S795
Q781

WEI Qiang, DING Yulong. Transcriptome sequencing, de novo assembly and expression analysis of several genes related to internode development in Pseudosasa japonica[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2017, 41(05): 42-48.

References

[1] 熊文愈, 丁祖福, 李又芬. 竹类植物的居间分生组织与节间生长Ⅰ:秆茎的居间分生组织与节间生长[J]. 林业科学, 1980, 16(2):81-89. XIONG W Y, DIN Z F, LI Y F. Intercalary meristem and internodal elongation of bamboo rhizome shoots[J]. Sciontia Silvae Sinicae, 1980, 6(2):81-89.
[2] MORGAN M, ANDERS S, LAWRENCE M, et al. ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data[J]. Bioinformatics, 2009, 25(19): 2607-2608. DOI:10.1093/bioinformatics/btp450.
[3] GRABHERR MG, HAAS BJ, YASSOUR M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J]. Nat Biotechnol, 2011, 29(7): 644-652. DOI:10.1038/nbt.1883.
[4] ZHENG Y, ZHAO L, GAO J, et al. iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences[J]. BMC Bioinformatics, 2011, 12: 453. DOI:10.1186/1471-2105-12-453.
[5] CONESA A, GÖTZ S, GARCÍA-GÓMEZ JM, et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research[J]. Bioinformatics, 2005, 21(18): 3674-3676. DOI:10.1093/bioinformatics/bti610.
[6] ASHBURNER M, BALL CA, BLAKE JA, et al. Gene ontology: tool for the unification of biology[J]. Nat Genet, 2000, 25(1): 25-29. DOI:10.1038/75556.
[7] THIMM O, BLÄSING O, GIBON Y, et al. Mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes[J]. The Plant Journal, 2004, 37(6): 914-939. DOI:10.1111/j.1365-313x.2004.02016.x.
[8] LOHSE M, NAGEL A, HERTER T, et al. Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data[J]. Plant Cell Environ, 2014, 37(5): 1250-1258. DOI:10.1111/pce.12231.
[9] LIVAK KJ, SCHMITTGEN TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T))Method[J]. Methods, 2001, 25(4): 402-408. DOI:10.1006/meth.2001.1262.
[10] ZHANG X M, ZHAO L, LARSON-RABIN Z, et al. De novo sequencing and characterization of the floral transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae)[J]. PLoS ONE, 2012, 7(8): e42082. DOI:10.1371/journal.pone.0042082.
[11] LIU M, QIAO G, JIANG J, et al. Transcriptome sequencing and de novo analysis for Ma bamboo(Dendrocalamus latiflorus Munro)using the Illumina platform[J]. PLoS ONE, 2012, 7(10): e46766. DOI:10.1371/journal.pone.0046766.
[12] HE CY, CUI K, ZHANG JG, et al. Next-generation sequencing-based mRNA and microRNA expression profiling analysis revealed pathways involved in the rapid growth of developing culms in Moso bamboo[J]. BMC Plant Biol, 2013, 13: 119. DOI:10.1186/1471-2229-13-119.
[13] CUI K, WANG H, LIAO S, et al. Transcriptome sequencing and analysis for culm elongation of the world's largest bamboo(Dendrocalamus sinicus)[J]. PLoS ONE, 2016, 11(6): e0157362. DOI:10.1371/journal.pone.0157362.
[14] 王身昌, 胡尚连, 曹颖, 等. 梁山慈竹高通量转录组测序及差异表达基因分析[J]. 华北农学报, 2016, 31(3): 65-71. DOI:10.7668/hbnxb.2016.03.010. WANG S C, HU S L, CAO Y, et al. High-throughput RNA-seq and analysis on differential expressed gene from Dendrocalamus farinosus[J].Acta Agriculturae Boreali-Sinica, 2016, 3:65-71.
[15] STASOLLA C, KATAHIRA R, THORPE TA, et al. Purine and pyrimidine nucleotide metabolism in higher plants[J]. J Plant Physiol, 2003, 160(11): 1271-1295. DOI:10.1078/0176-1617-01169.
[16] PENG Z, LU Y, LI L, et al. The draft genome of the fast-growing non-timber forest species moso bamboo(Phyllostachys heterocycla)[J]. Nat Genet, 2013, 45(4): 456-461. DOI:10.1038/ng.2569.
[17] 陈宇鹏, 曹颖, 胡尚连, 等. 基于高通量测序的慈竹笋转录组分析与基因功能注释[J]. 生物工程学报, 2016, 32(11): 1610-1623. DOI:10.13345/j.cjb.160095. CHEN Y P, CAO Y, HU S L, et al. Transcriptome analysis and gene function annotation of bambusa emeiensis shoots based on high-throughput sequencing technology[J]. Chinese Journal of Biotechnology, 2016, 32(11): 1610-1623.
[18] OHASHI-ITO K, FUKUDA H. Transcriptional regulation of vascular cell fates[J]. Curr Opin Plant Biol, 2010, 13(6): 670-676. DOI:10.1016/j.pbi.2010.08.011.
[19] YANG JH, WANG H. Molecular mechanisms for vascular development and secondary cell wall formation[J]. Front Plant Sci, 2016, 7: 356. DOI:10.3389/fpls.2016.00356.

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Transcriptome sequencing, de novo assembly and expression analysis of several genes related to internode development in Pseudosasa japonica

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