Transcriptome analysis of Idesia polycarpa Maxim. var vestita Diels flowers during sex differentiation

Abstract

Idesia polycarpa Maxim. var vestita Diels. is a dioecious tree species native to eastern Asia. There are difficulties associated with distinguishing the sex of the plant at the seedling stage. In order to explore the mechanism of sex differentiation in flower development, we conducted the transcriptome profiles of male and female flowers at early, metaphase and late developmental stages. Approximately 123,335 unigenes with a total length of 83,996 Mb and an average length of 168 bp were assembled. The unigenes were blasted into Nr, Nt, Pfam, KOG/COG, Swiss-prot, KEGG, GO databases. Homology analysis demonstrated that I. polycarpa and black cottonwood had the highest homology with the alignment of 92,871 sequences. This study identified 80 groups of transcription factor families with a total of 1475 unigenes, mainly including MYB, WRKY, AP2 and bHLH transcription factor families. KEGG pathway analysis showed that the expression of numerous plant hormones (cytokinin, gibberellin and ethylene) and flavonoid biosynthesis pathway were different at various stages of female and male flower development. In addition, a number of unigenes associated with flowering were identified which were key genes associated with photoperiodic, vernalization, thermosensory, gibberellin, and autonomic pathways. The results show that I. polycarpa floral organ development was in accordance with the ABCDE model, in which the down-regulation of the B gene family might affect stamen fertility in late stages of female flower development. qRT-PCR experiments validated that the expression patterns of 15 unigenes were consistent with those in RNA-seq results. The results highlight a central role for plant sex identification in seedling production and a sex-determining mechanism for dioecious plants. In addition, the transcriptome data provided a theoretical basis for I. polycarpa genetic diversity analysis and molecular- assisted breeding.

Keywords

Dioecious plants / Transcriptome sequencing / Sex differentiation / Idesia polycarpa / Floral organ development / Transcription factor

References

[1] Ai J, Li AM, Li CY, Wang J, Shen YJ. The effect of cytokinin on sex conversion of male plants of Vitis amurensis. Acta Hortic Sin, 2002, 29(2): 163-164.

[2] Amasino R. Seasonal and developmental timing of flowering. Plant J Cell Mol Biol, 2010 61 6 1001

[3] Aryal R, Ming R. Sex determination in flowering plants: papaya as a model system. Plant Sci Int J Exp Plant Biol, 2014 217–218 1 56

[4] Bai SNA. From ethylene promotion of female flowers to ethylene inhibition of stamen development: a review on the study of developmental fate of inappropriate organs in unisexual cucumber flowers. Sci Sin, 2010, 40(6): 469-475.

[5] Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR. Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 2008, 456(7218): 53-59.

[6] Blazquez MA, Ahn JD. A thermosensory pathway controlling flowering time in Arabidopsis thaliana. Nat Genet, 2003 33 2 168

[7] Bräutigam A, Gowik U. What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. Plant Biol, 2010, 12(6): 831-841.

[8] Chen MS, Pan BZ, Fu QT, Tao YB, Martínez-Herrera J, Niu LJ, Ni J, Dong YL, Zhao ML, Xu ZF. Comparative transcriptome analysis between gynoecious and monoecious plants identifies regulatory networks controlling sex determination in Jatropha curcas. Front Plant Sci, 2017, 7: 1953.

[9] Cheng H, Song SS, Xiao LT, Soo HM, Cheng ZW, Xie DX, Peng JR. Gibberellin acts through jasmonate to control the expression of MYB21, MYB24, and MYB57 to promote stamen filament growth in Arabidopsis. PLoS Genet, 2009 5 3 e1000440

[10] Chu QG, Cao YF, Jiang ZJ. Micro-morphological observations on flower bud differentiation of super prematurity cultivated strawberry. Acta Botanica Boreali-Occidentalia Sin, 2013, 1049(1049): 459-462.

[11] Conesa A, Götz S, García Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 2005, 21(18): 3674-3676.

[12] Cui RF, Han JK, Zhao SZ, Su KM, Wu F, Du XQ, Xu QJ, Chong K, Theissen G, Meng Z. Functional conservation and diversification of class E floral homeotic genes in rice (Oryza sativa). Plant J, 2010, 61(5): 767-781.

[13] Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L. MYB transcription factors in Arabidopsis. Trends Plant Sci, 2010, 15(10): 573-581.

[14] Eulgem T, Rushton PJ, Robatzek S, Somssich IE. The WRKY superfamily of plant transcription factors. Trends Plant Sci, 2000, 5(5): 199-206.

[15] Frerigmann H, Gigolashvili T. MYB34, MYB51, and MYB122 distinctly regulate indolic glucosinolate biosynthesis in Arabidopsis thaliana. Mol Plant, 2014, 7(5): 814-828.

[16] Gong BC, Da WL, Jiang XB, Kai YW, Bai JJ, Peng JL. Variation analysis of fruit oil content of Idesia polycarpa Maxim. from different populations. Acta Botanica Boreali-Occidentalia Sin, 2012, 32(8): 1680-1685.

[17] Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Xian A, Fan L, Raychowdhury R, Zeng Q. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol, 2011, 29(7): 644-652.

[18] Guo S, Zheng Y, Joung JG, Liu S, Zhang Z, Crasta OR, Sobral BW, Xu Y, Huang S, Fei Z. Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genom, 2010 11 1 384

[19] Guo H, Shen QW, Yao CH. Quality Analysis of Idesia polycarpa Maxim Seed Oil. Mod Food Sci Technol, 2012, 28(3): 345-347.

[20] Harborne JB, Williams CA. A chemotaxonomic survey of flavonoids and simple phenols in leaves of the Ericaceae. Bot J Linn Soc, 1973, 66(1): 37-54.

[21] Hobert O. Gene regulation by transcription factors and microRNAs. Science, 2008 319 5871 1785

[22] Hui ML, Huang XY, Gao CW, Qin XM. Sex identification of Siraidia grosvenorii by isozyme analysis. Guihaia, 2007, 27(5): 791-792.

[23] Jack T, Brockman LL, Meyerowitz EM. The homeotic gene APETALA3 of Arabidopsis thaliana encodes a MADS box and is expressed in petals and stamens. Cell, 1992 68 4 683

[24] Jiang XB, Gong BC, Da WL, Kai YW, Zhao XM, Deng QE. Selection of the plus trees of Idesia polycarpa maxim. from the natural seedlings. J Plant Genet Resour, 2014, 15(4): 738-745.

[25] Kai-Lin MO, Zhang ZX, Luo XL, Yang L. Exploitage of idesia polycarpa oil. Sci Technol Cereal, 2009, 17(6): 24-25.

[26] Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T. KEGG for linking genomes to life and the environment. Nucl Acids Res, 2007, 36((suppl_1)): D480-D484.

[27] Kang HG, Kim J, Kim B, Jeong H, Sun HC, Kim EK, Lee HY, Lim PO. Overexpression of FTL1/DDF1, an AP2 transcription factor, enhances tolerance to cold, drought, and heat stresses in Arabidopsis thaliana. Plant Sci, 2011 180 4 634

[28] Krol ARVD, Brunelle A, Tsuchimoto S, Chua NH. Functional analysis of petunia floral homeotic MADS box gene pMADS1. Genes Dev, 1993, 7(7A): 1214-1228.

[29] Laubinger S, Marchal V, Gentilhomme J, Wenkel S, Adrian J, Jang S, Kulajta C, Braun H, Coupland G, Hoecker U. Arabidopsis SPA proteins regulate photoperiodic flowering and interact with the floral inducer CONSTANS to regulate its stability. Development, 2006, 133(16): 3213-3222.

[30] Liu LJ, Zhang YC, Li QH, Sang Y, Mao J, Lian HL, Wang L, Yang HQ. COP1-mediated ubiquitination of CONSTANS is implicated in cryptochrome regulation of flowering in Arabidopsis. Plant Cell, 2008, 20(2): 292-306.

[31] Liu LH, Yang H, Wang YC, Wang LS. Extraction and separation of alcohol diterpenoids from Jatropha curcas oil. Guangdong Agric Sci, 2011, 38(6): 157-160.

[32] Liu JJ, Yin TM, Ye N, Chen YN, Yin TT, Liu M, Hassani D. Transcriptome analysis of the differentially expressed genes in the male and female shrub willows (Salix suchowensis). PLoS ONE, 2013 8 4 e60181

[33] Lü BB, Sun WW, Zhang SP, Zhang CL, Qian J, Wang XM, Gao R, Dong HS. HrpN Ea-induced deterrent effect on phloem feeding of the green peach aphid Myzus persicae requires AtGSL5 and AtMYB44 genes in Arabidopsis thaliana. J Biosci, 2011, 36(1): 123-137.

[34] Mahida SV, Valia RZ. Sitapara HH (2015) Growth, yield and sex-expression as influenced by plant growth regulators in sponge gourd cv. PUSA CHIKNI. Asian J Hortic, 2015, 10(1): 122-125.

[35] Makkena S, Lee E, Sack FD, Lamb RS. The R2R3 MYB transcription factors FOUR LIPS and MYB88 regulate female reproductive development. J Exp Bot, 2012, 63(15): 5545-5558.

[36] Mandaokar A, Browse J. MYB108 acts together with MYB24 to regulate jasmonate-mediated stamen maturation in Arabidopsis. Plant Physiol, 2009, 149(2): 851-862.

[37] Mao XZ, Cai T, Olyarchuk JG, Wei LP. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics, 2005, 21(19): 3787-3793.

[38] Mei LJ, Dong N, Li FS, Li N, Yao M, Chen F, Tang L. Transcriptome analysis of female and male flower buds of Idesia polycarpa Maxim. var. vestita Diels. Electron J Biotechnol EJB, 2017, 29: 39-46.

[39] Millar AA, Gubler F. The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. Plant Cell, 2005, 17(3): 705-721.

[40] Moon J, Lee H, Kim M, Lee I. Analysis of flowering pathway integrators in Arabidopsis. Plant Cell Physiol, 2005 46 2 292

[41] Moyroud E, Minguet EG, Ott F, Yant L, Posé D, Monniaux M, Blanchet S, Bastien O, Thévenon E, Weigel D. Prediction of regulatory interactions from genome sequences using a biophysical model for the Arabidopsis LEAFY transcription factor. Plant Cell, 2011, 23(4): 1293-1306.

[42] Nguyen XC, Hoang MHT, Kim HS, Lee K, Liu XM, Kim SH, Bahk S, Park HC, Chung WS. Phosphorylation of the transcriptional regulator MYB44 by mitogen activated protein kinase regulates Arabidopsis seed germination. Biochem Biophys Res Commun, 2012, 423(4): 703-708.

[43] Novaes E, Drost DR, Farmerie WG, Pappas GJ, Grattapaglia D, Sederoff RR, Kirst M. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genom, 2008 9 1 312

[44] Pan BZ, Xu ZF. Benzyladenine treatment significantly increases the seed yield of the biofuel plant Jatropha curcas. J Plant Growth Regul, 2011, 30(2): 166-174.

[45] Paul S, Andrew M, Owen O, Sbn TWJ, Daniel R, Nada A, Benno S, Trey I. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res, 2003, 13(11): 2498-2504.

[46] Pelaz S, Ditta GS, Baumann E, Wisman E, Yanofsky MF. B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature, 2000 405 6783 200

[47] Persak H, Pitzschke A. Tight interconnection and multi-level control of Arabidopsis MYB44 in MAPK cascade signalling. PLoS ONE, 2013 8 2 e57547

[48] Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucl Acids Res, 2001 29 9 e45

[49] Phan HA, Iacuone S, Li SF, Parish RW. The MYB80 transcription factor is required for pollen development and the regulation of tapetal programmed cell death in Arabidopsis thaliana. Plant Cell, 2011, 23(6): 2209-2224.

[50] Pinyopich A, Ditta GS, Savidge B, Liljegren SJ. Assessing the redundancy of MADS-box genes during carpel and ovule development. Nature, 2003 424 6944 85

[51] Renner SS. Dioecy and its correlates in flowering plants. Am J Bot, 1995, 82(5): 596-606.

[52] Richards AJ (1997) Plant breeding systems. Tamkang J Math 3

[53] Rocheta M, Sobral R, Magalhães J, Amorim MI, Ribeiro T, Pinheiro M, Egas C, Morais-Cecílio L, Costa MM. Comparative transcriptomic analysis of male and female flowers of monoecious Quercus suber. Front Plant Sci, 2014, 5(599): 1-16.

[54] Song SS, Qi TC, Wasternack C, Xie DX. Jasmonate signaling and crosstalk with gibberellin and ethylene. Curr Opin Plant Biol, 2014, 21: 112-119.

[55] Sorensen AM, Kröber S, Unte US, Huijser P, Dekker K, Saedler H. The Arabidopsis ABORTED MICROSPORES (AMS) gene encodes a MYC class transcription factor. Plant Journal, 2003, 33(2): 413-423.

[56] Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, Van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat biotechnol, 2010, 28(5): 511-515.

[57] Vandesompele J, Preter KD, Pattyn F, Poppe B, Roy NV, Paepe AD, Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol, 2002 3 7 research0034.0031

[58] Varshney RK, Nayak SN, May GD, Jackson SA. Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol, 2009, 27(9): 522-530.

[59] Wang LK, Feng ZX, Wang X, Wang XW, Zhang XG. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics, 2009, 26(1): 136-138.

[60] Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet, 2009, 10(1): 57-63.

[61] Wang SY, Lee PF, Lee YI, Hsiao YY, Chen YY, Pan ZJ, Liu ZJ, Tsai WC. Duplicated C-class MADS-box genes reveal distinct roles in gynostemium development in Cymbidium ensifolium (Orchidaceae). Plant Cell Physiol, 2011, 52(3): 563-577.

[62] Winter KU, Saedler H, Theissen G. On the origin of class B floral homeotic genes: functional substitution and dominant inhibition in Arabidopsis by expression of an orthologue from the gymnosperm Gnetum. Plant J, 2002, 31(4): 457-475.

[63] Wu ZW, Xie SX, Liu Q, Du WJ. Research progress and application prospect of Idesia polycarpa. Guizhou Agric Sci, 2010, 38(1): 161-164.

[64] Xu PZ, Liu T, Yang Y, Hu YQ. The role of abscisic acid in plant flowering. Acta Botanica Yunnanica, 2007, 29(2): 215-222.

[65] Yang CP, Liu GF, Jiang J, Liang Y. Changes of endogenous hormones in Betula platyphylla during the male flower development. J Northeast For Univ, 2002, 30(4): 1-4.

[66] Yang ZJ, Peng ZS, Wei SH, Liao ML, Yu Y, Jang ZY. Pistillody mutant reveals key insights into stamen and pistil development in wheat (Triticum aestivum L.). BMC Genom, 2015 16 1 211

[67] Yang WL, Wang WW, Zhang L, Chen ZY, Guo XY, Ma T. Characterization of the complete chloroplast genome of Idesia polycarpa. Conserv Genet Resour, 2016, 8: 1-3.

[68] Ye J, Fang L, Zheng HK, Zhang Y, Chen J, Zhang ZJ, Wang J, Li ST, Li RQ, Bolund L, Wang L. WEGO: a web tool for plotting GO annotations. Nucl Acids Res, 2006, 34: W293-W297.

[69] Young MD, Wakefield MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol, 2010 11 2 R14

[70] Yu H, Ito T, Zhao YX, Peng JR, Kumar PP, Meyerowitz EM. Floral homeotic genes are targets of gibberellin signaling in flower development. Proc Natl Acad Sci USA, 2004 101 20 7827

[71] Zhang XP. Great Potential of Idesia polycarpa as a Woody Edible Oil Resource. J Sichuan For Sci Technol, 2011, 32(2): 80-83.

[72] Zhang W, Sun YJ, Timofejeva L, Chen CB, Grossniklaus U, Ma H. Regulation of Arabidopsis tapetum development and function by dysfunctional tapetum1 (dyt1) encoding a putative bHLH transcription factor. Development, 2006, 133(16): 3085-3095.

[73] Zhang JX, Wu KL, Zeng SJ, da Silva JAT, Zhao XL, Tian CE, Xia HQ, Duan J. Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development. BMC Genom, 2013 14 1 279

[74] Zhang YC, Li WJ, Dou YJ, Zhang JX, Jiang GH, Miao LX, Han GF, Liu YX, Li H, Zhang ZH. Transcript quantification by RNA-Seq reveals differentially expressed genes in the red and yellow fruits of Fragaria vesca. PLoS ONE, 2015 10 12 e0144356

[75] Zhao SG, Zhang YX, Zhao YP. Effect of salicylic acid on pollen germinating and pollen tube growth of pear. Hubei Agric Sci, 2012, 51(7): 1366-1369.