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Genome-wide survey and expression analysis of the calcium-dependent protein kinase gene family in cassava

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Abstract

Calcium-dependent protein kinases (CPKs) play important roles in regulating plant tolerance to abiotic stress and signal transduction; however, no data are currently available regarding the CPK family in cassava. Herein, we identified 27 CPK genes from cassava based on our previous genome sequencing data. Phylogenetic analysis showed that cassava CPKs could be clustered into three groups, which was further supported by gene structure and conserved protein motif analyses. Global expression analysis suggested that MeCPK genes showed distinct expression patterns in different tissues between wild subspecies and cultivated varieties, indicating their involvement in the functional diversity of different varieties. Transcriptomics, interaction networks, and co-expression assays revealed a broad transcriptional response of cassava CPKs and CPK-mediated networks to drought stress and their differential expression profiles in different varieties, implying their contribution to drought stress tolerance in cassava. Expression analysis of eight MeCPK genes suggested a comprehensive response to osmotic stress, salt, cold, abscisic acid, and H2O2, which indicated that cassava CPKs might be convergence points for different signaling pathways. This study provides a basis for crop improvements and understanding of abiotic stress responses and signal transduction mediated by CPKs in cassava.

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References

  • Asano T, Kunieda N, Omura Y, Ibe H, Kawasaki T, Takano M, Sato M, Furuhashi H, Mujin T, Takaiwa F, Wu Cy CY, Tada Y, Satozawa T, Sakamoto M, Shimada H (2002) Rice SPK, a calmodulin-like domain protein kinase, is required for storage product accumulation during seed development: phosphorylation of sucrose synthase is a possible factor. Plant Cell 14:619–628

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Asano T, Tanaka N, Yang G, Hayashi N, Komatsu S (2005) Genome-wide identification of the rice calcium-dependent protein kinase and its closely related kinase gene families: comprehensive analysis of the CDPKs gene family in rice. Plant Cell Physiol 46:356–366

    Article  PubMed  CAS  Google Scholar 

  • Asano T, Hakata M, Nakamura H, Aoki N, Komatsu S, Ichikawa H, Hirochika H, Ohsugi R (2011) Functional characterisation of OsCPK21, a calcium-dependent protein kinase that confers salt tolerance in rice. Plant Mol Biol 75:179–191

    Article  PubMed  CAS  Google Scholar 

  • Asano T, Hayashi N, Kobayashi M (2012) A rice calcium-dependent protein kinase OsCPK12 oppositely modulates salt-stress tolerance and blast disease resistance. Plant J 69:26–36

    Article  PubMed  CAS  Google Scholar 

  • Cheng SH, Willmann MR, Chen HC, Sheen J (2002) Calcium signaling through protein kinases. The Arabidopsis calcium-dependent protein kinase gene family. Plant Physiol 129:469–485

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Choi HI, Park HJ, Park JH, Kim S, Im MY, Seo HH, Kim YW, Hwang I, Kim SY (2005) Arabidopsis calcium-dependent protein kinase AtCPK32 interacts with ABF4, a transcriptional regulator of abscisic acid-responsive gene expression, and modulates its activity. Plant Physiol 139:1750–1761

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39:29–37

    Article  Google Scholar 

  • Franz S, Ehlert B, Liese A, Kurth J, Cazale AC, Romeis T (2011) Calcium-dependent protein kinase CPK21 functions in abiotic stress response in Arabidopsis thaliana. Mol Plant 4:83–96

    Article  PubMed  CAS  Google Scholar 

  • Harmon AC, Gribskov M, Harper JF (2000) CDPKs-a kinase for every Ca2+ signal? Trends Plant Sci 5:154–159

    Article  PubMed  CAS  Google Scholar 

  • Harper JF (2001) Dissecting calcium oscillators in plant cells. Trends Plant Sci 6:395–397

    Article  PubMed  CAS  Google Scholar 

  • Harper JF, Sussman MR, Schaller GE, Putnam-Evans C, Charbonneau H, Harmon AC (1991) A calcium-dependent protein kinase with a regulatory domain similar to calmodulin. Science 252:951–954

    Article  PubMed  CAS  Google Scholar 

  • Hirayama T, Shinozaki K (2010) Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J 61:1041–1052

    Article  PubMed  CAS  Google Scholar 

  • Ho SL, Huang LF, Lu CA, He SL, Wang CC, Yu SP, Chen J, Yu SM (2013) Sugar starvation- and GA-inducible calcium-dependent protein kinase 1 feedback regulates GA biosynthesis and activates a 14-3-3 protein to confer drought tolerance in rice seedlings. Plant Mol Biol 81:347–361

    Article  PubMed  CAS  Google Scholar 

  • Knight H, Knight MR (2001) Abiotic stress signalling pathways: specificity and cross-talk. Trends Plant Sci 6:262–267

    Article  PubMed  CAS  Google Scholar 

  • Komatsu S, Yang G, Khan M, Onodera H, Toki S, Yamaguchi M (2007) Over-expression of calcium-dependent protein kinase 13 and calreticulin interacting protein 1 confers cold tolerance on rice plants. Mol Genet Genomics 277:713–723

    Article  PubMed  CAS  Google Scholar 

  • Kong X, Lv W, Jiang S, Zhang D, Cai G, Pan J, Li D (2013) Genome-wide identification and expression analysis of calcium-dependent protein kinase in maize. BMC Genom 14:433

    Article  CAS  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace F, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    Article  PubMed  CAS  Google Scholar 

  • Li AL, Zhu YF, Tan XM, Wang X, Wei B, Guo HZ, Zhang ZL, Chen XB, Zhao GY, Kong XY, Jia JZ, Mao L (2008) Evolutionary and functional study of the CDPK gene family in wheat (Triticum aestivum L). Plant Mol Biol 66:429–443

    Article  PubMed  CAS  Google Scholar 

  • Liu W, Li W, He Q, Daud MK, Chen J, Zhu S (2014) Genome-wide survey and expression analysis of calcium-dependent protein kinase in Gossypium raimondii. PLoS One 9:e98189

    Article  PubMed  PubMed Central  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCt method. Methods 25:402–408

    Article  PubMed  CAS  Google Scholar 

  • Ma SY, Wu WH (2007) AtCPK23 functions in Arabidopsis responses to drought and salt stresses. Plant Mol Biol 65:511–518

    Article  PubMed  CAS  Google Scholar 

  • Mehlmer N, Wurzinger B, Stael S, Hofmann-Rodrigues D, Csaszar E, Pfister B, Bayer R, Teige M (2010) The Ca2+-dependent protein kinase CPK3 is required for MAPK-independent salt-stress acclimation in Arabidopsis. Plant J 63:484–498

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Mori IC, Murata Y, Yang Y, Munemasa S, Wang YF, Andreoli S, Tiriac H, Alonso JM, Harper JF, Ecker JR, Kwak JM, Schroeder JI (2006) CDPKs CPK6 and CPK3 function in ABA regulation of guard cell S-type anion- and Ca2+-permeable channels and stomatal closure. PLoS Biol 4:1749–1762

    Article  CAS  Google Scholar 

  • Okogbenin E, Setter TL, Ferguson M, Mutegi R, Ceballos H, Olasanmi B (2013) Phenotypic approaches to drought in cassava: review. Front Physiol 4:93

    Article  PubMed  PubMed Central  Google Scholar 

  • Ray S, Agarwal P, Arora R, Kapoor S, Tyagi AK (2007) Expression analysis of calcium-dependent protein kinase gene family during reproductive development and abiotic stress conditions in rice (Oryza sativa L ssp Indica). Mol Genet Genomics 278:493–505

    Article  PubMed  CAS  Google Scholar 

  • Saijo Y, Hata S, Kyozuka J, Shimamoto K, Izui K (2000) Over-expression of a single Ca2+-dependent protein kinase confers both cold and salt/drought tolerance on rice plants. Plant J 23:319–327

    Article  PubMed  CAS  Google Scholar 

  • Salcedo A, Zambrana C, Siritunga D (2014) Comparative expression analysis of reference genes in field-grown cassava. Tropical Plant Biol 7:53–64

    Article  CAS  Google Scholar 

  • Sanders D, Brownlee C, Harper JF (1999) Communicating with calcium. Plant Cell 11:691–706

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Tao P, Zhong X, Li B, Wang W, Yue Z, Lei J, Guo W, Huang X (2014) Genome-wide identification and characterization of aquaporin genes (AQPs) in Chinese cabbage (Brassica rapa ssp. pekinensis). Mol Genet Genomics 289:1131–1145

    Article  PubMed  CAS  Google Scholar 

  • Tohge T, Fernie AR (2010) Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. Nat Protoc 5:1210–1227

    Article  PubMed  CAS  Google Scholar 

  • Utsumi Y, Tanaka M, Morosawa T, Kurotani A, Yoshida T, Mochida K, Matsui A, Umemura Y, Ishitani M, Shinozaki K, Sakurai T, Seki M (2012) Transcriptome analysis using a high-density oligomicroarray under drought stress in various genotypes of cassava: an important tropical crop. DNA Res 19:335–345

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Wang W, Feng B, Xiao J, Xia Z, Zhou X, Li P, Zhang W, Wang Y, Møller BL, Zhang P, Luo MC, Xiao G, Liu J, Yang J, Chen S, Rabinowicz PD, Chen X, Zhang HB, Ceballos H, Lou Q, Zou M, Carvalho LJ, Zeng C, Xia J, Sun S, Fu Y, Wang H, Lu C, Ruan M, Zhou S, Wu Z, Liu H, Kannangara RM, Jørgensen K, Neale RL, Bonde M, Heinz N, Zhu W, Wang S, Zhang Y, Pan K, Wen M, Ma PA, Li Z, Hu M, Liao W, Hu W, Zhang S, Pei J, Guo A, Guo J, Zhang J, Zhang Z, Ye J, Ou W, Ma Y, Liu X, Tallon LJ, Galens K, Ott S, Huang J, Xue J, An F, Yao Q, Lu X, Fregene M, López-Lavalle LA, Wu J, You FM, Chen M, Hu S, Wu G, Zhong S, Ling P, Chen Y, Wang Q, Liu G, Liu B, Li K, Peng M (2014) Cassava genome from a wild ancestor to cultivated varieties. Nat Commun 5:5110

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Wei S, Hu W, Deng X, Zhang Y, Liu X, Zhao X, Luo Q, Jin Z, Li Y, Zhou S, Sun T, Wang L, Yang G, He G (2014) A rice calcium-dependent protein kinase OsCPK9 positively regulates drought stress tolerance and spikelet fertility. BMC Plant Biol 14:133

    Article  PubMed  PubMed Central  Google Scholar 

  • Xiong L, Schumaker KS, Zhu JK (2002) Cell signaling during cold, drought, and salt stress. Plant Cell 14:S165–S183

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Xu J, Tian YS, Peng RH, Xiong AS, Zhu B, Jin XF, Gao F, Fu XY, Hou XL, Yao QH (2010) AtCPK6, a functionally redundant and positive regulator involved in salt/drought stress tolerance in Arabidopsis. Planta 231:1251–1260

    Article  PubMed  CAS  Google Scholar 

  • Xu J, Duan X, Yang J, Beeching JR, Zhang P (2013) Enhanced reactive oxygen species scavenging by overproduction of superoxide dismutase and catalase delays postharvest physiological deterioration of cassava storage roots. Plant Physiol 161:1517–1528

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Zhang P, Wang WQ, Zhang GL, Kaminek M, Dobrev P, Xu J, Gruissem W (2010) Senescence-inducible expression of isopentenyl transferase extends leaf life, increases drought stress resistance and alters cytokinin metabolism in cassava. J Integr Plant Biol 52:653–669

    PubMed  CAS  Google Scholar 

  • Zhang H, Liu WZ, Zhang Y, Deng M, Niu F, Yang B, Wang X, Wang B, Liang W, Deyholos MK, Jiang YQ (2014) Identification, expression and interaction analyses of calcium-dependent protein kinase (CPK) genes in canola (Brassica napus L.). BMC Genom 15:211

    Article  Google Scholar 

  • Zhao R, Sun HL, Mei C, Wang XJ, Yan L, Liu R, Zhang XF, Wang XF, Zhang DP (2011) The Arabidopsis Ca2+-dependent protein kinase CPK12 negatively regulates abscisic acid signaling in seed germination and post-germination growth. New Phytol 192:61–73

    Article  PubMed  CAS  Google Scholar 

  • Zhao P, Liu P, Shao J, Li C, Wang B, Guo X, Yan B, Xia Y, Peng M (2014) Analysis of different strategies adapted by two cassava cultivars in response to drought stress: ensuring survival or continuing growth. J Exp Bot. doi:10.1093/jxb/eru507

    Google Scholar 

  • Zhu SY, Yu XC, Wang XJ, Zhao R, Li Y, Fan RC, Shang Y, Du SY, Wang XF, Wu FQ, Xu YH, Zhang XY, Zhang DP (2007) Two calcium-dependent protein kinases, CPK4 and CPK11, regulate abscisic acid signal transduction in Arabidopsis. Plant Cell 19:3019–3036

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Zidenga T, Leyva-Guerrero E, Moon H, Siritunga D, Sayre R (2012) Extending cassava root shelf life via reduction of reactive oxygen species production. Plant Physiol 159:1396–1407

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Zou JJ, Wei FJ, Wang C, Wu JJ, Ratnasekera D, Liu WX, Wu WH (2010) Arabidopsis calcium-dependent protein kinase CPK10 functions in abscisic acid- and Ca2+-mediated stomatal regulation in response to drought stress. Plant Physiol 154:1232–1243

    Article  PubMed  CAS  PubMed Central  Google Scholar 

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    Authors and Affiliations

    1. Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, People’s Republic of China

      Wei Hu, Xiaowan Hou, Zhiqiang Xia, Yan Yan, Yunxie Wei, Meiling Zou, Cheng Lu, Wenquan Wang & Ming Peng

    2. College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, 467000, Henan, People’s Republic of China

      Lianzhe Wang

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    1. Wei Hu
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    2. Xiaowan Hou
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    3. Zhiqiang Xia
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    4. Yan Yan
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    10. Ming Peng
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    Corresponding authors

    Correspondence to Wei Hu, Wenquan Wang or Ming Peng.

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    Funding

    This study was funded by the ‘973’ Program of the Ministry of Science and Technology of China (2010CB126600), the ‘863’ Program of the Ministry of Science and Technology of China (2012AA101204-2), the Natural Science Foundation of Hainan Province (314122, 20153048), the National Nonprofit Institute Research Grant of CATAS-ITBB (ITBB2015ZD04), the Major Technology Project of Hainan (ZDZX2013023-1), the International Science and Technology Cooperation Program of China (2013DFA32020), and the International Science and Technology Cooperation Plan (2011DFB31690).

    Conflict of interest

    The authors declare that they have no conflict of interest.

    Ethical approval

    This article does not contain any studies with human participants or animals performed by any of the authors.

    Additional information

    Communicated by S. Hohmann.

    W. Hu, X. Hou, Z. Xia contributed equally to this work.

    The cassava CPK genes identified in this study were submitted to GenBank (http://www.ncbi.nlm.nih.gov/genbank/genbank) (accession number: KP675743-KP675769).

    Electronic supplementary material

    Below is the link to the electronic supplementary material.

    Supplementary material 1 Table S1. Primers used in qRT-PCR analysis. (XLS 25 kb)

    Supplementary material 2 Table S2. Characteristics of CPKs in cassava. (XLS 25 kb)

    Supplementary material 3 Table S3. The accession numbers of CPKs in cassava, Arabidopsis and rice. (XLS 36 kb)

    438_2015_1103_MOESM4_ESM.xlsx

    Supplementary material 4 Table S4. The expression profiles (log2-based values) of the cassava CPK genes in different tissues. (XLSX 15 kb)

    438_2015_1103_MOESM5_ESM.xls

    Supplementary material 5 Table S5. The expression profiles (log2-based values) of the cassava CPK genes after drought treatment. (XLS 32 kb)

    438_2015_1103_MOESM6_ESM.xls

    Supplementary material 6 Table S6. Annotation summary of genes involved in the CPK family interaction network. (XLS 29 kb)

    438_2015_1103_MOESM7_ESM.xls

    Supplementary material 7 Table S7. Expression patterns of the genes involved in CPK-mediate interaction networks responding to drought in cassava. (XLS 29 kb)

    438_2015_1103_MOESM8_ESM.tif

    Supplementary material 8 Fig.S1. The phylogenetic relationship and exon–intron structure analyses of cassava CPKs. The Neighbor-joining tree was created using ClustalX 2.0 and MEGA5 with amino acid sequences of MeCPKs. Three clusters labeled as I, II, and III are indicated with different color backgrounds. Exon–intron structure analyses were conducted using GSDS database. Lengths of exons and introns of each MeCPK gene were exhibited proportionally. (TIFF 2183 kb)

    Supplementary material 9 Fig.S2. Motifs annotation of CPKs in cassava. (TIFF 2006 kb)

    438_2015_1103_MOESM10_ESM.tif

    Supplementary material 10 Fig.S3. Motif analyses of cassava CPKs according to the phylogenetic relationship. All motifs were identified by MEME database with the complete amino acid sequences of MeCPKs. Lengths of motifs for each MeCPK protein were exhibited proportionally. (TIFF 2182 kb)

    Supplementary material 11 Fig.S4. Interaction network of AtCPKs by STRING. (TIFF 13568 kb)

    438_2015_1103_MOESM12_ESM.tif

    Supplementary material 12 Fig.S5. Expression profiles of CPK genes in leaves of cassava in response to salt stress. The mRNA fold differences of each gene are relative to that of leaf samples at 0 h. Data are mean ± SD of n = 3 biological replicates. Statistic analyses are conducted between treated and control samples at each time point. Means denoted by the same letter do not significantly differ at P < 0.05 as determined by Duncan’s multiple range test. (TIFF 382 kb)

    438_2015_1103_MOESM13_ESM.tif

    Supplementary material 13 Fig.S6. Expression profiles of CPK genes in leaves of cassava in response to osmotic stress. The mRNA fold differences of each gene are relative to that of leaf samples at 0 h. Data are mean ± SD of n = 3 biological replicates. Statistic analyses are conducted between treated and control samples at each time point. Means denoted by the same letter do not significantly differ at P < 0.05 as determined by Duncan’s multiple range test. (TIFF 350 kb)

    438_2015_1103_MOESM14_ESM.tif

    Supplementary material 14 Fig.S7. Expression profiles of CPK genes in leaves of cassava in response to cold stress. R7d and R14d represent recovery for 7 and 14 days, respectively. The mRNA fold differences of each gene are relative to that of leaf samples at 0 h. Data are mean ± SD of n = 3 biological replicates. Statistic analyses are conducted between treated and control samples at each time point. Means denoted by the same letter do not significantly differ at P < 0.05 as determined by Duncan’s multiple range test. (TIFF 343 kb)

    438_2015_1103_MOESM15_ESM.tif

    Supplementary material 15 Fig.S8. Expression profiles of CPK genes in leaves of cassava in response to ABA. The mRNA fold differences of each gene are relative to that of leaf samples at 0 h. Data are mean ± SD of n = 3 biological replicates. Statistic analyses are conducted between treated and control samples at each time point. Means denoted by the same letter do not significantly differ at P < 0.05 as determined by Duncan’s multiple range test. (TIFF 358 kb)

    438_2015_1103_MOESM16_ESM.tif

    Supplementary material 16 Fig.S9. Expression profiles of CPK genes in leaves of cassava in response to H2O2. The mRNA fold differences of each gene are relative to that of leaf samples at 0 h. Data are mean ± SD of n = 3 biological replicates. Statistic analyses are conducted between treated and control samples at each time point. Means denoted by the same letter do not significantly differ at P < 0.05 as determined by Duncan’s multiple range test. (TIFF 365 kb)

    438_2015_1103_MOESM17_ESM.tif

    Supplementary material 17 Fig. S10. Photos of different varieties of cassava after 12 days drought treatment. (TIFF 8592 kb)

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    Hu, W., Hou, X., Xia, Z. et al. Genome-wide survey and expression analysis of the calcium-dependent protein kinase gene family in cassava. Mol Genet Genomics 291, 241–253 (2016). https://doi.org/10.1007/s00438-015-1103-x

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