High-throughput RNA-seq and Analysis on Differential Expressed Gene from Dendrocalamus farinosus

doi:10.7668/hbnxb.2016.03.010

Abstract

Abstract: The transcriptome from the shoots of Dendrocalamus farinosus and its somatic mutant was sequenced using the RNA-Seq technology to elucidate its functional gene and analyze its differential expressed gene,providing a theoretical basis for its genetic improvement.The sequencing data was assembled by de novo assembly and the differential expressed gene screened was annotated in COG,GO and KEGG database.In addition,the differential expression of gene related to cellulose and lignin biosynthesis was analyzed,basing on the Swiss-Prot function annotation.The sequencing results showed that a total of 86 575 631 reads were produced and assembled into a total of 84 741 unigenes by de novo,among which 49 829 were annotated in Nonredundant protein,Cluster of Orthologous Groups of proteins,Gene Ontology,Kyoto Encyclopedia of Genes and Genomes and Swiss-Prot database.Besides,a total of 3 572 differential expressed unigenes were identified from the plant of seeds (CK) and the somatic mutant No.30.Of these differential expressed genes,757 unigenes had a detailed protein functions in the COG classification system,2 213 unigenes had the function definition in the GO database,385 unigenes were annotated to 94 KEGG Pathways.The expression of genes encoding CesA,Prx,Ubiquitin-conjugating enzyme and Heat shock proteins increased in somatic mutant No.30,while,the expression of genes encoding MYB4,4CL,CAD,CCR and LAC decreased.Our data provide the most comprehensive transcriptomic resource for Dendrocalamus farinosus and the transcript sequences with important function related to cellulose and lignin biosynthesis were found,which provide the most precious information resources for the further research on bamboo.

Key words: Dendrocalamus farinosus, Somatic mutant, Transcriptome, Differential expressed gene

CLC Number:

WANG Shenchang, HU Shanglian, CAO Ying, XU Gang. High-throughput RNA-seq and Analysis on Differential Expressed Gene from Dendrocalamus farinosus[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2016, 31(3): 65-71. doi: 10.7668/hbnxb.2016.03.010.

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References

[1] 刘红亮,郑丽明,刘青青,等.非模式生物转录组研究[J].遗传,2013,35(8):955-970.
[2] Li X,Sun H,Pei J,et al.De novo sequencing and comparative analysis of the blueberry transcriptome to discover putative genes related to antioxidants[J].Gene,2012,511(1):54-61.
[3] 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.
[4] 熊壮,扶志宏,鄢武先,等.四川梁山慈竹纸浆林生产现状及培育技术初步研究[J].世界竹藤通讯,2012,10(5):7-11.
[5] 李永全,张安刚,龚兆全,等.梁山慈竹特性及育苗技术[J].四川林勘设计,2012(2):34-37.
[6] 胡尚连,蒋瑶,陈其兵,等.四川2种丛生竹理化特性及纤维形态研究[J].植物研究,2010,30(6):708-712.
[7] Yang X,Tian G L,Shang L L,et al.Variation in the cell wall mechanical properties of Dendrocalamus farinosus bamboo by nanoindentation[J].BioResources,2014,9(2):2289-2298.
[8] Hu S L,Jy Z,Cao Y,et al. In vitro callus induction and plant regeneration from mature seed embryo and young shoots in a giant sympodial bamboo,Dendrocalamus farinosus(Keng et Keng f.)Chia et HL Fung[J].African Journal of Biotechnology,2011,10(16):3120-3125.
[9] 郭鹏飞.梁山慈竹体细胞无性系再生植株变异研究[D].绵阳:西南科技大学,2013.
[10] Grabherr M G,Haas B J,Yassour M,et al.Full-length transcriptome assembly from RNA-Seq data without a reference genome[J].Nature Biotechnology,2011,29(7):644-652.
[11] Mortazavi A,Williams B A,Mccue K,et al.Mapping and quantifying mammalian transcriptomes by RNA-Seq[J].Nature Methods,2008,5(7):621-628.
[12] Kaul S,Koo H L,Jenkins J,et al.Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J].Nature,2000,408(6814):796-815.
[13] Goff S A,Ricke D,Lan T H,et al.A draft sequence of the rice genome ( Oryza sativa L.ssp.japonica)[ J].Science,2002,296(5565):92-100.
[14] Peng Z,Lu Y,Li L,et al.The draft genome of the fast-growing non-timber forest species moso bamboo ( Phyllostachys heterocycla )[ J].Nature Genetics,2013,45(4):456-461,461e1-2.
[15] Fullwood M J,Wei C L,Liu E T,et al.Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses[J].Genome Research,2009,19(4):521-532.
[16] Li C F,Wang X Q,Lu W X,et al.A poplar R2R3-MYB transcription factor,PtrMYB152,is involved in regulation of lignin biosynthesis during secondary cell wall formation[J].Plant Cell,Tissue and Organ Culture,2014,119(3):553-563.
[17] Patzlaff A,Mcinnis S,Courtenay A,et al.Characterisation of a pine MYB that regulates lignification[J].The Plant Journal,2003,36(6):743-754.
[18] Ma Q H,Wang C,Zhu H H. TaMYB4 cloned from wheat regulates lignin biosynthesis through negatively controlling the transcripts of both cinnamyl alcohol dehydrogenase and cinnamoyl-CoA reductase genes[J].Biochimie,2011,93(7):1179-1186.
[19] Li S F,Milliken O N,Pham H,et al.The Arabidopsis MYB5 transcription factor regulates mucilage synthesis,seed coat development,and trichome morphogenesis[J].The Plant Cell,2009,21(1):72-89.
[20] Taylor N G,Laurie S,Turner S R.Multiple cellulose synthase catalytic subunits are required for cellulose synthesis in Arabidopsis [J].The Plant Cell,2000,12(12):2529-2540.
[21] Hovav R,Udall J A,Chaudhary B,et al.The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism[J].PLOS Genetics,2008,4(2):e25.
[22] Sengar A S,Thind K S,Kumar B,et al. In vitro selection at cellular level for red rot resistance in sugarcane ( Saccharum sp.)[J].Plant Growth Regulation,2009,58(2):201-209.
[23] 梁芳,蒋素华,王洁琼,等.濒危植物太行菊组织培养及快繁技术研究[J].中国农学通报,2015,31(16):115-120.
[24] 王鹏姬.荞麦愈伤组织培养及其黄酮合成研究[D].杨凌:西北农林科技大学,2013.
[25] Sheidai M,Aminpoor H,Noormohammadi Z,et al.RAPD analysis of somaclonal variation in banana ( Musaacuminate L.) cultivar Valery[J].Acta Biol Szeged,2008,52:307-311.
[26] Carsono N,Yoshida T.Variation in spikelet-related traits of rice plants regenerated from mature seed-derived callus culture[J].Plant Production Science,2007,10(1):86-90.
[27] Mohanty S,Panda M K,Subudhi E,et al.Plant regeneration from callus culture of Curcuma aromatica and in vitro detection of somaclonal variation through cytophotometric analysis[J].Biologia Plantarum,2008,52(4):783-786.

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