Biologia plantarum 2018, 62:269-276 | DOI: 10.1007/s10535-018-0778-3

Identification of putative CONSTANS-like genes from the de novo assembled transcriptome of leek

C. Liu1, Q. Tang1, C. Cheng1, Y. Xu1, Z. Yang1, Z. Dai1, J. Su1,*
1 Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, P.R. China

Leek is an economically important vegetable. In model plants, the CONSTANS (CO) and CONSTANS-like (COL) genes play central roles in plant flowering modulation. However, none of leek CO homolog has been identified, because of limited gene resources obtained in this crop. Here, we reported the transcriptome analysis of leek, along with the identification of putative leek CONSTANS-like (COL) (ApCOL) genes. A total of 189 713 non-redundant transcripts were de novo assembled by using about 128.9 million clean sequence reads, of which, 48 621 were achieved for functional annotation. Thereafter, the search for putative ApCOL genes against the assembled transcripts was performed, and 17 genes were identified. The 17 putative ApCOL proteins, together with 16 function-known COL proteins published for other species, were subjected to phylogenetic analysis and divided into four groups. Some putative ApCOL members showed high sequence similarity with published COL proteins involved in flowering regulation. Expression analysis revealed that, among the 17 putative ApCOL genes, eight, two, and three genes showed higher expression in leaves, cauloids, and roots, respectively. The discovery of putative ApCOL genes and the characterization of their expression patterns will provide a basis for future clarification of their functions in leek growth and development.

Keywords: Allium porrum; expression analysis; flowering regulation; phylogenetic tree
Subjects: CONSTANS; transcriptome analysis; flowering; phylogenetic tree; gene epression
Species: Allium porum

Received: April 1, 2017; Revised: August 23, 2017; Accepted: August 30, 2017; Published: June 1, 2018Show citation

ACS AIP APA ASA Harvard Chicago IEEE ISO690 MLA NLM Turabian Vancouver
Liu, C., Tang, Q., Cheng, C., Xu, Y., Yang, Z., Dai, Z., & Su, J. (2018). Identification of putative CONSTANS-like genes from the de novo assembled transcriptome of leek. Biologia plantarum, 62(2), 269-276. doi: 10.1007/s10535-018-0778-3.
Download citation
  • BibTeX (.bib)
  • Bookends (.ris)
  • EasyBib (.ris)
  • EndNote (.enw)
  • EndNote 8 (.xml)
  • ISI WoS (.isi)
  • Medlars (.medlars)
  • Mendeley (.ris)
  • MODS (.xml)
  • Papers (.ris)
  • RefWorks (.txt)
  • RefManager (.ris)
  • RIS (.ris)
  • MS Word (.xml)
  • Zotero (.ris)

    • Open full article

    Supplementary files

    Download filebpl-201802-0008_S1.pdf

    File size: 692.11 kB

    References

    1. An, H., Roussot, C., Suárez-López, P., Corbesier, L., Vincent, C., Piñeiro, M., Hepworth, S., Mouradov, A., Justin, S., Turnbull, C., Coupland, G.: CONSTANS acts in the phloem to regulate a systemic signal that induces photoperiodic flowering of Arabidopsis. - Development 131: 3615-3626, 2004. Go to original source...
    2. Campoli, C., Drosse, B., Searle, I., Coupland, G., Von Korff, M.: Functional characterisation of HvCO1, the barley (Hordeum vulgare) flowering time ortholog of CONSTANS. - Plant J. 69: 868-880, 2012. Go to original source...
    3. Cheng, X., Wang, Z.: Overexpression of COL9, a CONSTANSLIKE gene, delays flowering by reducing expression of CO and FT in Arabidopsis thaliana. - Plant J. 43: 758-768, 2005. Go to original source...
    4. Chou, M., Shih, M., Chan, M., Liao, S., Hsu, C., Haung, Y., Chen, J., Liao, D., Wu, F., Lin, C.: Global transcriptome analysis and identification of a CONSTANS-like gene family in the orchid Erycina pusilla. - Planta 237: 1425-1441, 2013. Go to original source...
    5. Conesa, A., Gotz, S., García-Gómez, J., Terol, J., Talón, M., Robles, M.: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. - Bioinformatics 21: 3674-3676, 2005. Go to original source...
    6. De Clercq, H., Baert, J., Van Bockstaele, E.: Breeding potential of Belgian landraces of leek (Allium ampeloprasum L. var, porrum). - Euphytica 106: 101-109, 1999. Go to original source...
    7. Finn, R., Clements, J., Eddy, S.: HMMER web server: interactive sequence similarity searching. - Nucl. Acids Res. 39 (Suppl. 2): W29-W37, 2011. Go to original source...
    8. Fu, L., Niu, B., Zhu, Z., Wu, S., Li, W.: CD-HIT: accelerated for clustering the next-generation sequencing data. - Bioinformatics 28: 3150-3152, 2012. Go to original source...
    9. Grabherr, M., Haas, B., Yassour, M., Levin, J., Thompson, D., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zengm, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., Di Palma, F., Birren, B., Nusbaum, C., Lindblad-Toh, K., Friedman, N., Regev, A.: Full length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29: 644-652, 2011. Go to original source...
    10. Griffiths, S., Dunford, R., Coupland, G., Laurie, D.: The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis. - Plant Physiol. 131: 1855-1867, 2003.
    11. Hassidim, M., Harir, Y., Yakir, E., Kron, I., Green, R.: Overexpression of CONSTANS-LIKE 5 can induce flowering in short-day grown Arabidopsis. - Planta 230: 481-491, 2009. Go to original source...
    12. Hayama, R., Coupland, G.: The molecular basis of diversity in the photoperiodic flowering responses of Arabidopsis and rice. - Plant Physiol. 135: 677-684, 2004. Go to original source...
    13. Imaizumi, T.: Arabidopsis circadian clock and photoperiodism: time to think about location. - Curr. Opin. Plant Biol. 13: 83-89, 2010. Go to original source...
    14. Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., Madden, T., NCBI BLAST: a better web interface. - Nucl. Acids Res. 36: W5-W9 2008. Go to original source...
    15. Kikuchi, R., Kawahigashi, H., Oshima, M., Ando, T., Handa, H.: The differential expression of HvCO9, a member of the CONSTANS-like gene family, contributes to the control of flowering under short-day conditions in barley. - J. exp. Bot. 63: 773-784, 2012. Go to original source...
    16. Kim, S., Yun, C., Lee, J., Jang, Y., Park, H., Kim, J.: OsCO3, a CONSTANS-LIKE gene, controls flowering by negatively regulating the expression of FT-like genes under SD conditions in rice. - Planta 228: 355-365, 2008. Go to original source...
    17. Kitts, P., Church, D., Thibaud-Nissen, F., Choi, J., Hem, V., Sapojnikov, V., Smith, R., Tatusova, T., Xiang, C., Zherikov, A., Di Cuccio, M., Murphy, T., Pruitt, K., Kimchi, A.: Assembly: a resource for assembled genomes at NCBI. - Nucl. Acids Res. 44: D73-D80 2016. Go to original source...
    18. Kumar, S., Stecher, G., Tamura, K.: MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. - Mol. Biol. Evol. 33: 1870-1874, 2016.
    19. Lee, Y., Jeong, D., Lee, D., Yi, J., Ryu, C., Kim, S., Jeong, H., Choi, S., Jin, P., Yang, J., Cho, L., Choi, H., An, G.: OsCOL4 is a constitutive flowering repressor upstream of Ehd1 and downstream of OsphyB. - Plant J. 63: 18-30, 2010. Go to original source...
    20. Liu, T., Liu, H., Zhang, H., Xing, Y.: Validation and characterization of Ghd7.1, a major QTL with pleiotropic effects on spikelets per panicle, plant height, and heading date in rice (Oryza sativa L.). - J. Integr. Plant Biol. 55: 917-927, 2013c. Go to original source...
    21. Liu, T., Tang, S., Zhu, S., Tang, Q., Zheng, X.: Transcriptome comparison reveals the patterns of selection in domesticated and wild ramie (Boehmeria nivea L. Gaud). - Plant mol. Biol. 86: 85-92, 2014a. Go to original source...
    22. Liu, T., Zeng, L., Zhu, S., Chen, X., Tang, Q., Mei, S., Tang, S.: Large-scale development of expressed sequence tag-derived simple sequence repeat markers by deep transcriptome sequencing in garlic (Allium sativum L.). - Mol. Breed. 35: 204, 2015b. Go to original source...
    23. Liu, T., Zhang, Y., Zhang, H., Xing, Y.: Quantitative trait loci for the number of grains per panicle dependent on or independent of heading date in rice (Oryza Sativa L.). - Breed. Sci. 61: 142-150, 2011. Go to original source...
    24. Liu, T., Zhu, S., Tang, Q., Chen, P., Yu, Y., Tang, S.: De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud). - BMC Genomics 14: 125, 2013a. Go to original source...
    25. Liu, T., Zhu, S., Tang, Q., Tang, S.: Identification of 32 fulllength NAC transcription factors in ramie (Boehmeria nivea L. Gaud) and characterization of the expression pattern of these genes. - Mol. Genet. Genomics 289: 675-684, 2014b. Go to original source...
    26. Liu, T., Zhu, S., Tang, Q., Tang, S.: Genome-wide transcriptomic profiling of ramie (Boehmeria nivea L. Gaud) in response to cadmium stress. - Gene 558: 131-137, 2015a. Go to original source...
    27. Liu, T., Zhu, S., Tang, Q., Tang, S.: Identification of a CONSTANS homologous gene with distinct diurnal expression patterns in varied photoperiods in ramie (Boehmeria nivea L. Gaud). - Gene 560: 63-70, 2015c. Go to original source...
    28. Liu, T., Zhu, S., Tang, Q., Yu, Y., Tang, S.: Identification of drought stress-responsive transcription factor in ramie (Boehmeria nivea L. Gaud). - BMC Plant Biol. 13: 130, 2013b. Go to original source...
    29. Livak, K., Schmittgen, T.: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. - Methods 25: 402-408, 2001. Go to original source...
    30. Martin, J., Storgaard, M., Andersen, C., Nielsen, K.: Photoperiodic regulation of flowering in perennial ryegrass involving a CONSTANS like homolog. - Plant mol. Biol. 56: 159-169, 2004. Go to original source...
    31. Mei, S., Liu, T., Wang, Z.: Comparative transcriptome profile of the cytoplasmic male sterile and fertile floral buds of radish (Raphanus sativus L.). - Int. J. mol. Sci. 17: 42, 2016. Go to original source...
    32. Metzker, M.: Sequencing technologies-the next generation. - Natur. Rev. Genet. 11: 31-46, 2010. Go to original source...
    33. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A., Kanehisa, M.: KAAS: an automatic genome annotation and pathway reconstruction server. - Nucl. Acids Res. 35: W182-W185 2007. Go to original source...
    34. Mutz, K., Heilkenbrinker, A., Lonne, M., Walter, J., Stahl, F.: Transcriptome analysis using next-generation sequencing. - Curr. Opin. Biotechnol. 24: 22-30, 2013. Go to original source...
    35. Parcy, F.: Flowering: a time for integration. - Int. J. Dev. Biol. 49: 585-593, 2005. Go to original source...
    36. Ricroch, A., Yockteng, R., Brown, S., Nadot, S.: Evolution of genome size across some cultivated Allium species. - Genome 48: 51-520, 2005. Go to original source...
    37. Robson, F., Costa, M., Hepworth, S., Vizir, I., Pineiro, M., Reeves, P., Putterill, J., Coupland, G.: Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants. - Plant J. 28: 619-631, 2001. Go to original source...
    38. Sato, Y., Antonio, B.A., Namiki, N., Takehisa, H., Minami, H., Kamatsuki, K., Sugimoto, K., Shimizu, Y., Hirochika, H., Nagamura, Y., RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions. - Nucl. Acids Res. 39: D1141-D1148 2010.
    39. Soininen, T., Jukarainen, N., Soininen, P., Auriola, S., Julkunen-Tiitto, R., Oleszek, W., Stochmal, A., Karjalainen, R., Vepsäläinen, J.: Metabolite profiling of leek (Allium porrum L) cultivars by 1H NMR and HPLC-MS. - Phytochem. Anal. 25: 220-228, 2014. Go to original source...
    40. Suarez-Lopez, P., Wheatley, K., Robson, F., Onouchi, H., Valverde, F., Coupland, G.: CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. - Nature 40: 1116-1120, 2001. Go to original source...
    41. Sun, X., Yu, X., Zhou, S., Liu, S.: De novo assembly and characterization of the Welsh onion (Allium fistulosum L.) transcriptome using Illumina technology. - Mol. Genet. Genomics 291: 647, 2016. Go to original source...
    42. Takase, T., Kakikubo, Y., Nakasone, A., Nishiyama, Y., Yasuhara, M., Kiyosue, Y.: Characterization and transgenic study of CONSTANS-LIKE8 (COL8) gene in Arabidopsis thaliana 35S:COL8 delays flowering under long-day conditions. - Plant Biotechnol. 28: 439-446, 2011. Go to original source...
    43. Thompson, J., Gibson, T., Plewniak, F., Jeanmougin, F., Higgins, D.: The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. - Nucl. Acids Res. 25: 4876-4882, 1997. Go to original source...
    44. Tsuji, H., Taoka, K., Shimamoto, K.: Regulation of flowering in rice: two florigen genes, a complex gene network, and natural variation. - Curr. Opin. Plant Biol. 14: 45-52, 2011. Go to original source...
    45. Turck, F., Fornara, F., Coupland, G.: Regulation and Identity of florigen: FLOWERING LOCUS T moves center stage. - Annu. Rev. Plant Biol. 59: 573-594, 2008. Go to original source...
    46. Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Roy, N., Paepe, A., Speleman, F.: Accurate normalization of realtime quantitative RT-PCR data by geometric averaging of multiple internal control genes. - Genome Biol. 3: research0034.1-0034.11 2012.
    47. Wu, W., Zheng, X., Lu, G., Zhong, Z., Gao, H., Chen, L., Wu, C., Wang, H., Wang, Q., Zhou, K., Wang, J., Wu, F., Zhang, X., Guo, X., Cheng, Z., Lei, C., Lin, Q., Jiang, L., Wang, H., Ge, S., Wan, J.: Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cultivation in Asia. - Proc. nat. Acad. Sci. USA 110: 2775-2780, 2013. Go to original source...
    48. Yan, W., Liu, H., Zhou, X., Li, Q., Zhang, J., Lu, L., Liu, T., Liu, H., Zhang, C., Zhang, Z., Shen, G., Yao, W., Chen, H., Yu, S., Xie, W., Xing, Y.: Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice. - Cell Res. 23: 969-971, 2013. Go to original source...
    49. Yano, M., Katayose, Y., Ashikari, M., Yamanouchi, U., Monna, L., Fuse, T., Baba, T., Yamamoto, K., Umehara, Y., Nagamura, Y., Sasaki, T.: Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. - Plant Cell 12: 2473-2484, 2000. Go to original source...
    50. Yu, Y., Zeng, L., Yan, Z., Liu, T., Sun, K., Zhu, T., Zhu, A.: Identification of ramie genes in response to Pratylenchus coffeae infection challenge by digital gene expression analysis. - Int. J. mol. Sci. 16: 21989-22007, 2015. Go to original source...
    51. Zeng, L., Shen, A., Chen, J., Yan, Z., Liu, T., Xue, Z., Yu, Y.: Transcriptome analysis of ramie (Boehmeria nivea L. Gaud.) in response to ramie moth (Cocytodes coerulea Guenée) infestation. - BioMed Res. Int. 2016: 3702789, 2016.
    52. Zhang, L., Li, Q., Dong, H., He, Q., Liang, L., Tan, C., Han, Z., Yao, W., Li, G., Zhao, H., et al.: Three CCT domaincontaining genes were identified to regulate heading date by candidate gene-based association mapping and transformation in rice. - Sci. Rep. 5: 7663, 2015. Go to original source...
    53. Zheng, J., Yu, C., Chen, P., Wang, Y., Liu, T., Xiong, H.: Identification and expression analysis of glutamine synthetase genes in ramie (Boehmeria nivea L. Gaud). - Open Life Sci. 10: 299-309, 2015.
    54. Zheng, X., Tang, S., Zhu, S., Dai, Q., Liu, T.: Identification of an NAC transcription factor family by deep transcriptome sequencing in onion (Allium cepa L.). - PLoS ONE 11: e0157871, 2016b. Go to original source...
    55. Zheng, X., Zhu, S., Tang, S., Liu, T.: Identification of drought, cadmium and root-lesion nematode infection stressresponsive transcription factors in ramie. - Open Life Sci. 11: 191-199, 2016a.
    56. Zhou, S., Chen, L., Liu, S., Wang, X., Sun, X.: De novo assembly and annotation of the Chinese chive (Allium tuberosum Rottler ex Spr.) transcriptome using the Illumina platform. - PLoS ONE 10: e0133312, 2015. Go to original source...
    57. Zhu, S., Tang, S., Tan, Z., Yu, Y., Dai, Q., Liu, T.: Comparative transcriptomics provide insight into the morphogenesis and evolution of fistular leaves in Allium. - BMC Genomics 18: 60, 2017. Go to original source...
    58. Zhu, S., Tang, S., Tang, Q., Liu, T.: Genome-wide transcriptional changes of ramie (Boehmeria nivea L. Gaud) in response to root-lesion nematode infection. - Gene 552: 67-74, 2014. Go to original source...
    59. Zhu, S., Zheng, X., Dai, Q., Tang, S., Liu, T.: Identification of quantitative trait loci for flowering time traits in ramie (Boehmeria nivea L. Gaud). - Euphytica 210: 367-374, 2016. Go to original source...

    Return to the content