Molecular Breeding

, 35:208 | Cite as

De novo transcriptome sequencing and comparative analysis of differentially expressed genes in kiwifruit under waterlogging stress

  • Ji-Yu Zhang
  • Sheng-Nan Huang
  • Zheng-Hai Mo
  • Ji-Ping Xuan
  • Xiao-Dong Jia
  • Gang Wang
  • Zhong-Ren Guo


Kiwifruit plants are particularly sensitive to soil waterlogging. Enhancement of waterlogging tolerance in kiwifruit can potentially considerably increase its fruit production and extend the shelf life of the fruit. We generated 95,945,496 bases of high-quality sequence from kiwifruit roots after 4-day waterlogging treatment using Illumina sequencing technology, and demonstrated de novo assembly and annotation of genes. These reads were assembled into 140,187 unigenes (mean length 556 bp). Based on a similarity search with known proteins in the non-redundant (nr) protein database, 56,912 unigenes (40.60 %) were functionally annotated with a cutoff E-value of 10−5. Using the RPKM method, we investigated differentially expressed genes by applying the Benjamini and Hochberg correction. Overall, 14,843 transcripts were identified as differentially expressed unigenes (DEG) in two samples. Among these unigenes, 5697 DEGs (about 38.5 %) were found to be induced by waterlogging, and 9146 DEGs (about 61.5 %) decreased in abundance. To identify the most important pathways represented by DEGs, we compared these genes to those in the KEGG database. The categories “ribosome,” “plant hormone signal transduction,” and “starch and sucrose metabolism” pathways contained the three highest numbers of differentially expressed unigenes and, thus, appear to play important roles in waterlogging perception. We identified many transcription factors, belonging to AP2/ERF, WRKY, TGA, MYB, bZIP families, implicating a potential function for them in waterlogging responses in kiwifruit. Our results provide a transcriptome profile that is associated with waterlogging stress induction in kiwifruit plants. The potential waterlogging stress-related transcripts identified in this study represent candidate genes and molecular resources to further understand the molecular mechanisms of the waterlogging response in kiwifruit.


Actinidia Illumina Waterlogging Transcriptome 



Alcohol dehydrogenase


Kyoto encyclopedia of genes and genomes


Clusters of orthologous groups


Gene ontology


Reads per kilobase of exon region in a given gene per million mapped fragments


Differential expression genes


False discovery rate


Pyruvate decarboxylase





This study was supported by grants from the Natural Science Foundation of Jiangsu Province (Grant No. BK20140760) and the National Natural Science Foundation of China (NSFC) (31401854).

Supplementary material

11032_2015_408_MOESM1_ESM.tif (168 kb)
Supplemental Fig. 1 Length frequency distribution of unigenes (TIFF 168 kb)
11032_2015_408_MOESM2_ESM.tif (10.3 mb)
Supplemental Fig. 2 Expression analysis of 10 DEGs by qRT-PCR performed on 10 members randomly selected from among the regulated genes (TIFF 10514 kb)
11032_2015_408_MOESM3_ESM.docx (16 kb)
Supplemental Tab. 1 Primers for RT-qPCR in this study (DOCX 16 kb)
11032_2015_408_MOESM4_ESM.docx (17 kb)
Supplemental Tab. 2 Length distribution of assembled contigs and unigenes (DOCX 17 kb)
11032_2015_408_MOESM5_ESM.xls (8.2 mb)
Supplemental Tab. 3 Differentially expressed genes between two samples (p < 0.05) (XLS 8413 kb)
11032_2015_408_MOESM6_ESM.xls (54 kb)
Supplemental Tab. 4 Most highly significantly regulated differentially expressed 200 genes between the two samples (q < 0.001) (XLS 53 kb)
11032_2015_408_MOESM7_ESM.xls (50 kb)
Supplemental Tab. 5 Over-representative GO terms of DEGs in waterlogging-stressed kiwifruit (q < 0.05) (XLS 49 kb)
11032_2015_408_MOESM8_ESM.xls (31 kb)
Supplemental Tab. 6 Pathway enrichment analyses for DEGs (q < 0.05) (XLS 31 kb)
11032_2015_408_MOESM9_ESM.xls (27 kb)
Supplemental Tab. 7 Expression of the ADH and PDC gene families between two samples (q < 0.05) (XLS 27 kb)


  1. Bailey-Serres J, Voesenek LACJ (2008) Flooding stress: acclimations and genetic diversity. Ann Rev Plant Biol 59:313–339CrossRefGoogle Scholar
  2. Bailey-Serres J, Voesenek LACJ (2010) Life in the balance: a signaling network controlling survival of flooding. Curr Opin Plant Biol 13:489–494CrossRefPubMedGoogle Scholar
  3. Branco-Price C, Kaiser KA, Jang CJH, Larive CK, Bailey-Serres J (2008) Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. Plant J 56:743–755CrossRefPubMedGoogle Scholar
  4. Cai BH, Zhang JY, Gao ZH, Qu SC, Tong ZG, Mi L, Qiao YS, Zhang Z (2008) An improved method for isolation of total RNA from the leaves of Fragaria spp. Jiangsu J Agric Sci 24:875–877Google Scholar
  5. Chen J, Tian Q, Pang T, Jiang L, Wu R, Xia X, Yin W (2014) Deep-sequencing transcriptome analysis of low temperature perception in a desert tree, Populus euphratica. BMC Genomics 15:326PubMedCentralCrossRefPubMedGoogle Scholar
  6. Cheng R-l, Feng J, Zhang B-X, Huang Y, Cheng J, Zhang C-X (2014) Transcriptome and gene expression analysis of an oleaginous diatom under different salinity conditions. BioEnergy Res 7:192–205CrossRefGoogle Scholar
  7. Christianson JA, Llewellyn DJ, Dennis ES, Wilson IW (2010) Global gene expression responses to waterlogging in roots and leaves of cotton (Gossypium hirsutum L.). Plant Cell Physiol 51:21–37CrossRefPubMedGoogle Scholar
  8. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676CrossRefPubMedGoogle Scholar
  9. Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38:W64–W70PubMedCentralCrossRefPubMedGoogle Scholar
  10. Fukao T (2006) A variable cluster of ethylene response factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice. Plant Cell 18:2021–2034PubMedCentralCrossRefPubMedGoogle Scholar
  11. Fukao T, Bailey-Serres J (2004) Plant responses to hypoxia—is survival a balancing act? Trends Plant Sci 9:449–456CrossRefPubMedGoogle Scholar
  12. Garabagi F, Duns G, Strommer S (2005) Selective recruitment of Adh genes for distinct enzymatic functions in Petunia hybrida. Plant Mol Biol 58:283–294CrossRefPubMedGoogle Scholar
  13. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652PubMedCentralCrossRefPubMedGoogle Scholar
  14. Grossman AR, Catalanotti C, Yang W, Dubini A, Magneschi L, Subramanian V, Posewitz MC, Seibert M (2011) Multiple facets of anoxic metabolism and hydrogen production in the unicellular green alga Chlamydomonas reinhardtii. New Phytol 190:279–288CrossRefPubMedGoogle Scholar
  15. Hattori Y, Nagai K, Furukawa S, Song X-J, Kawano R, Sakakibara H, Wu J, Matsumoto T, Yoshimura A, Kitano H, Matsuoka M, Mori H, Ashikari M (2009) The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature 460:1026–1030CrossRefPubMedGoogle Scholar
  16. Hinz M, Wilson IW, Yang J, Buerstenbinder K, Llewellyn D, Dennis ES, Sauter M, Dolferus R (2010) Arabidopsis RAP2.2: an ethylene response transcription factor that is important for hypoxia survival. Plant Physiol 153:757–772PubMedCentralCrossRefPubMedGoogle Scholar
  17. Ismond KP, Dolferus R, De Pauw M, Dennis ES, Good AG (2003) Enhanced low oxygen survival in Arabidopsis through increased metabolic flux in the fermentative pathway. Plant Physiol 132:1292–1302PubMedCentralCrossRefPubMedGoogle Scholar
  18. Jackson MB, Colmer TD (2005) Response and adaptation by plants to flooding stress. Ann Bot (Lond) 96:501–505CrossRefGoogle Scholar
  19. Jung KH, Seo YS, Walia H, Cao P, Fukao T, Canlas PE, Amonpant F, Bailey-Serres J, Ronald PC (2010) The submergence tolerance regulator Sub1A mediates stress-responsive expression of AP2/ERF transcription factors. Plant Physiol 152:1674–1692PubMedCentralCrossRefPubMedGoogle Scholar
  20. Junttila S, Laiho A, Gyenesei A, Rudd S (2013) Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen. BMC Genomics 14:870PubMedCentralCrossRefPubMedGoogle Scholar
  21. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2011) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40:109–114CrossRefGoogle Scholar
  22. Kende H, van der Knaap E, Cho H (1998) Deepwater rice a model plant to study stem elongation. Plant Physiol 118:1105–1110PubMedCentralCrossRefPubMedGoogle Scholar
  23. Komatsu S, Sugimoto T, Hoshino T, Nanjo Y, Furukawa K (2010) Identification of flooding stress responsible cascades in root and hypocotyl of soybean using proteome analysis. Amino Acids 38:729–738CrossRefPubMedGoogle Scholar
  24. Komatsu S, Thibaut D, Hiraga S, Kato M, Chiba M, Hashiguchi A, Tougou M, Shimamura S, Yasue H (2011) Characterization of a novel flooding stress-responsive alcohol dehydrogenase expressed in soybean roots. Plant Mol Biol 77:309–322CrossRefPubMedGoogle Scholar
  25. Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, Harper JF (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 130:2129–2141PubMedCentralCrossRefPubMedGoogle Scholar
  26. Kreuzwieser J, Rennenberg H (2014) Molecular and physiological responses of trees to waterlogging stress. Plant Cell Environ 37:2245–2259PubMedGoogle Scholar
  27. Lee J, Noh EK, Choi H-S, Shin SC, Park H, Lee H (2012) Transcriptome sequencing of the Antarctic vascular plant Deschampsia antarctica Desv. under abiotic stress. Planta 237:823–836CrossRefPubMedGoogle Scholar
  28. Licausi F, Van Dongen JT, Giuntoli B, Novi G, Santaniello A, Geigenberger P, Perata P (2010) HRE1 and HRE2, two hypoxia-inducible ethylene response factors, affect anaerobic responses in Arabidopsis thaliana. Plant J 62:302–315CrossRefPubMedGoogle Scholar
  29. Liu Z, Adams KL (2007) Expression partitioning between genes duplicated by polyploidy under abiotic stress and during organ development. Curr Biol 17:1669–1674CrossRefPubMedGoogle Scholar
  30. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−∆∆Ct method. Methods 25:402–408CrossRefPubMedGoogle Scholar
  31. Mi YF (2009) Research on tolerance identification and physiological mechanism of kiwifruit seeding to root zone hypoxia. Thesis for doctor degree, Northwest A&F UniversityGoogle Scholar
  32. Mustroph A, Lee SC, Oosumi T, Zanetti ME, Yang H, Ma K, Yaghoubi-Masihi A, Fukao T, Bailey-Serres J (2010) Cross-kingdom comparison of transcriptomic adjustments to low-oxygen stress highlights conserved and plant-specific responses. Plant Physiol 152:1484–1500PubMedCentralCrossRefPubMedGoogle Scholar
  33. Mustroph A, Barding GA Jr, Kaiser KA, Larive CK, Bailey-Serres J (2014) Characterization of distinct root and shoot responses to low-oxygen stress in Arabidopsis with a focus on primary C-and N-metabolism. Plant Cell Environ 37:2366–2380PubMedGoogle Scholar
  34. Nanjo Y, Maruyama K, Yasue H, Yamaguchi-Shinozaki K, Shinozaki K, Komatsu S (2011) Transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings. Plant Mol Biol 77:129–144CrossRefPubMedGoogle Scholar
  35. Narsai R, Whelan J (2013) How unique is the low oxygen response? An analysis of the anaerobic response during germination and comparison with abiotic stress in rice and Arabidopsis. Front Plant Sci 4:349PubMedCentralCrossRefPubMedGoogle Scholar
  36. Narsai R, Rocha M, Geigenberger P, Whelan J, van Dongen JT (2011) Comparative analysis between plant species of transcriptional and metabolic responses to hypoxia. New Phytol 190:472–487CrossRefPubMedGoogle Scholar
  37. Peng HP, Chan CS, Shih MC, Yang SF (2001) Signaling events in the hypoxic induction of alcohol dehydrogenase gene in Arabidopsis. Plant Physiol 126:742–749PubMedCentralCrossRefPubMedGoogle Scholar
  38. Peng HP, Lin TY, Wang NN, Shih MC (2005) Differential expression of genes encoding 1-aminocyclopropane-1-carboxylate synthase in Arabidopsis during hypoxia. Plant Mol Biol 58:15–25CrossRefPubMedGoogle Scholar
  39. Pierik R, van Aken JM, Voesenek LACJ (2009) Is elongation-induced leaf emergence beneficial for submerged Rumex species? Ann Bot 103:353–357PubMedCentralCrossRefPubMedGoogle Scholar
  40. Rushton PJ, Somssich IE, Ringler P, Shen QJ (2010) WRKY transcription factors. Trends Plant Sci. 15:247–258CrossRefPubMedGoogle Scholar
  41. Sairam RK, Dharmar K, Chinnusamy V, Meena RC (2009) Waterlogging-induced increase in sugar mobilization, fermentation, and related gene expression in the roots of mung bean (Vigna radiata). J Plant Physiol 166:602–616CrossRefPubMedGoogle Scholar
  42. Sasidharan R, Mustroph A, Boonman A, Akman M, Ammerlaan AMH, Breit T, Schranz ME, Voesenek LACJ, van Tienderen PH (2013) Root transcript profiling of two Rorippa species reveals gene clusters associated with extreme submergence tolerance. Plant Physiol 163:1277–1292PubMedCentralCrossRefPubMedGoogle Scholar
  43. Sauter M (2000) Rice in deep water: how to take heed against a sea of troubles. Naturwissenschaften 87:289–303CrossRefPubMedGoogle Scholar
  44. Steffens B, Sauter M (2005) Epidermal cell death in rice is regulated by ethylene, gibberellin, and abscisic acid. Plant Physiol 139:713–721PubMedCentralCrossRefPubMedGoogle Scholar
  45. Steffens B, Wang J, Sauter M (2006) Interactions between ethylene, gibberellin and abscisic acid regulate emergence and growth rate of adventitious roots in deepwater rice. Planta 223:604–612CrossRefPubMedGoogle Scholar
  46. Tamang BG, Magliozzi JO, Maroof MAS, Fukao T (2014) Physiological and transcriptomic characterization of submergence and reoxygenation responses in soybean seedlings. Plant Cell Environ 37:2350–2365PubMedGoogle Scholar
  47. Tougou M, Hashiguchi A, Yukawa K, Nanjo Y, Hiraga S, Nakamura T, Nishizawa K, Komatsu S (2012) Responses to flooding stress in soybean seedlings with the alcohol dehydrogenase transgene. Plant Biotechnol 29:301–305CrossRefGoogle Scholar
  48. van Veen H, Mustroph A, Barding GA, Vergeer-van Eijk M, Welschen-Evertman RAM, Pedersen O, Visser EJW, Larive CK, Pierik R, Bailey-Serres J (2013) Two Rumex species from contrasting hydrological niches regulate flooding tolerance through distinct mechanisms. Plant Cell 25:4691–4707PubMedCentralCrossRefPubMedGoogle Scholar
  49. Voesenek LACJ, Bailey-Serres J (2013) Flooding tolerance: O2 sensing and survival strategies. Curr Opin Plant Biol 16:1–7CrossRefGoogle Scholar
  50. Voesenek LACJ, Bailey-Serres J (2015) Flood adaptive traits and processes: an overview. New Phytol 206:57–73CrossRefPubMedGoogle Scholar
  51. Voesenek LACJ, Sasidharan R (2013) Ethylene—and oxygen signalling—drive plant survival during flooding. Plant Biol 15:426–435CrossRefPubMedGoogle Scholar
  52. Voesenek LACJ, Rijnders JH, Peeters AJM, Van de Steeg HM, De Kroon H (2004) Plant hormones regulate fast shoot elongation under water: from genes to communities. Ecology 85:16–27CrossRefGoogle Scholar
  53. Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708CrossRefPubMedGoogle Scholar
  54. Xu Y, Gao S, Yang Y, Huang M, Cheng L, Wei Q, Fei Z, Gao J, Hong B (2013) Transcriptome sequencing and whole genome expression profiling of chrysanthemum under dehydration stress. BMC Genom 14:662CrossRefGoogle Scholar
  55. Yamaguchi-Shinozaki K, Shinozaki K (2006) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol 57:781–803CrossRefPubMedGoogle Scholar
  56. Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:W293–W297PubMedCentralCrossRefPubMedGoogle Scholar
  57. Yin D, Chen S, Chen F, Guan Z, Fang W (2009) Morphological and physiological responses of two chrysanthemum cultivars differing in their tolerance to waterlogging. Environ Exp Bot 67:87–93CrossRefGoogle Scholar
  58. Yin X, Allan AC, Xu Q, Burdon J, Dejnoprat S, Chen K (2012) Differential expression of kiwifruit ERF genes in response to postharvest abiotic stress. Postharvest Biol Technol 66:1–7CrossRefGoogle Scholar
  59. Zhang J-Y, Wang Q-J, Guo Z-R (2012) Progresses on plant AP2/ERF transcription factors. Hereditas 34(7):835–847CrossRefPubMedGoogle Scholar
  60. Zhuang J, Cai B, Peng R-H, Zhu B, Jin X-F, Xue Y, Gao F, Fu X-Y, Tian Y-S, Zhao W, Qiao Y-S, Zhang Z, Xiong A-S, Yao Q-H (2008) Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa. Biochem Biophys Res Commun 371:468–474CrossRefPubMedGoogle Scholar
  61. Zhuang J, Peng R-H, Cheng Z-M, Zhang J, Cai B, Zhang Z, Gao F, Zhu B, Fu X-Y, Jin X-F, Chen J-M, Qiao Y-S, Xiong A-S, Yao Q-H (2009) Genome-wide analysis of the putative AP2/ERF family genes in Vitis vinifera. Sci Hortic 123:73–81CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Ji-Yu Zhang
    • 1
  • Sheng-Nan Huang
    • 1
  • Zheng-Hai Mo
    • 1
  • Ji-Ping Xuan
    • 1
  • Xiao-Dong Jia
    • 1
  • Gang Wang
    • 1
  • Zhong-Ren Guo
    • 1
  1. 1.Institute of BotanyJiangsu Province and Chinese Academy of SciencesNanjingChina

Personalised recommendations