Comprehensive Analysis of MeGRAS Family Genes in Cassava and their Genome Collinearity Relationship with Arabidopsis and Populus Genome

Senthilkumar K Muthusamy, Amina A. T., Vivek Hegde, Krishna Radhika N., Koundinya A. V. V., Visalakashi Chandra C., Sheela M. N.

Abstract


GRAS transcription factor family genes play diverse role in plant growth and development and often have a role as integrators of multiple development regulatory and environmental signals. Functional characterization and understanding of GRAS transcription factor family genes will help to breed, high yielding improved cassava genotypes. In this study, a genome wide analysis led to identification of 78 MeGRAS genes in cassava. The genes are distributed in all the chromosomes of cassava except chromosome no. 16. The identified cassava MeGRAS family members localized in different subcellular compartments including the nucleus, cytoplasm, chloroplast and mitochondria suggest a wider cellular localization and diverse role of MeGRAS family members in cassava. Occurrence of tissue-specific (biotic, abiotic, light-responsive, circadian and cell cycle-responsive) /cis-regulatory elements in the promoter regions of the MeGRAS family showed the potential role of MeGRAS family in plant growth, plant development and stress tolerance in cassava. Genome collinearity analysis with Arabidopsis and Populus genome showed the evolution of the MeGRAS family members through duplication and divergence in cassava. This comprehensive analysis contributes for a better understanding of the complexity of MeGRAS family members in cassava, and also provide further basis to dissect their potential role in development and stress response of cassava


Keywords


GRAS, transcription factor, genome-wide, cassava, collinearity, Populus, cis elements

References


Bredeson, J.V., Lyons, J.B., Prochnik, S.E., Wu, G.A., Ha, C.M., Edsinger-Gonzales, E., Grimwood, J., Schmutz, J., Rabbi, I.Y., Egesi, C. and Nauluvula, P. 2016. Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity. Nat. Biotechnol., 34(5): 562-570.

Burns, A., Gleadow, R., Cliff, J., Zacarias, A. and Cavagnaro, T., 2010. Cassava: the drought, war and famine crop in a changing world. Sustainability, 2(11): 3572-3607.

Chen, Y., Zhu, P., Wu, S., Lu, Y., Sun, J., Cao, Q., Li, Z. and Xu, T. 2019. Identification and expression analysis of GRAS transcription factors in the wild relative of sweet potato Ipomoea trifida. BMC genomics, 20: 911.

Fan, W., Hai, M., Guo, Y., Ding, Z., Tie, W., Ding, X., Yan, Y., Wei, Y., Liu, Y., Wu, C. and Shi, H. 2016. The ERF transcription factor family in cassava: genome-wide characterization and expression analyses against drought stress. Sci. Rep., 6: 37379.

Heckmann, A.B., Lombardo, F., Miwa, H., Perry, J.A., Bunnewell, S., Parniske, M., Wang, T.L. and Downie, J.A. 2006. Lotus japonicus nodulation requires two GRAS domain regulators, one of which is functionally conserved in a non-legume. Plant physiol., 142(4): 1739-1750.

Hirsch, S. and Oldroyd, G.E., 2009. GRAS-domain transcription factors that regulate plant development. Plant Signal. Behav., 4(8): 698-700.

Katiyar, A., Smita, S., Muthusamy, S.K., Chinnusamy, V., Pandey, D.M. and Bansal, K.C. 2015. Identification of novel drought responsive microRNAs and trans-acting siRNAs from Sorghum bicolor (L.) Moench by high-throughput sequencing analysis. Front. Plant Sci., 6: 506.

Lee, M.H., Kim, B., Song, S.K., Heo, J.O., Yu, N.I., Lee, S.A., Kim, M., Kim, D.G., Sohn, S.O., Lim, C.E. and Chang, K.S. 2008. Large-scale analysis of the GRAS gene family in Arabidopsis thaliana. Plant Mol. Biol., 67(6): 659-670.

Lenka, S.K., Singh, A.K., Muthusamy, S.K., Smita, S., Chinnusamy, V. and Bansal, K.C. 2019. Heterologous expression of rice RNAbinding glycine-rich (RBG) gene OsRBGD3 in transgenic Arabidopsis thaliana confers cold stress tolerance. Funct. Plant Biol., 46(5): 482-491.

Lescot, M., Déhais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., Rouzé, P. and Rombauts, S. 2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res., 30(1): 325-327.

Letunic, I. and Bork, P. 2018. 20 years of the SMART protein domain annotation resource. Nucleic Acids Res., 46(1): 493-496.

Liu, X. and Widmer, A. 2014. Genome-wide comparative analysis of the GRAS gene family in Populus, Arabidopsis and rice. Plant Mol. Biol. Rep., 32(6): 1129-1145.

Lozano, R., Hamblin, M.T., Prochnik, S. and Jannink, J.L. 2015. Identification and distribution of the NBS-LRR gene family in the Cassava genome. BMC genomics, 16(1): 360.

Muthusamy, S.K., Dalal, M., Chinnusamy, V. and Bansal, K.C. 2016. Differential regulation of genes coding for organelle and cytosolic ClpATPases under biotic and abiotic stresses in wheat. Front. Plant Sci., 7: 929.

Muthusamy, S.K., Dalal, M., Chinnusamy, V. and Bansal, K.C. 2017. Genome-wide identification and analysis of biotic and abiotic stress regulation of small heat shock protein (HSP20) family genes in bread wheat. J. plant physiol., 211: 100-113.

Muthusamy, S.K., Lenka, S.K., Katiyar, A., Chinnusamy, V., Singh, A.K. and Bansal, K.C. 2019. Genome-wide identification and analysis of biotic and abiotic stress regulation of C4 photosynthetic pathway genes in rice. Appl. Biochem. Biotechnol., 187(1): 221-238.

Pysh, L.D., Wysocka Diller, J.W., Camilleri, C., Bouchez, D. and Benfey, P.N. 1999. The GRAS gene family in Arabidopsis: Sequence characterization and basic expression analysis of the SCARECROW LIKE genes. Plant J., 18(1):111-119.

Raju, S. Roy, S., Ravi, V., Neelakantan, S.M., Makasana, J. and Chakrabarti, S.K. 2015. Evaluation of postharvest physiological deterioration in storage roots of cassava (Manihot esculenta) genotypes. Indian J. Agric. Sci., 85(10): 1279-1284.

Ravi, V., Aked, J. and Balagopalan, C. 1996. Review on tropical root and tuber crops I. Storage methods and quality changes. Crit. Rev. Food Sci. Nutr., 36(7): 661-709.

Tian, C., Wan, P., Sun, S., Li, J. and Chen, M. 2004. Genome-wide analysis of the GRAS gene family in rice and Arabidopsis. Plant Mol. Biol., 54(4): 519-532.

Wang, Y., Tang, H., DeBarr y, J.D., Tan, X., Li, J., Wang, X., Lee, T.H., Jin, H., Marler, B., Guo, H. and Kissinger, J.C. 2012. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res., 40(7): e49.

Xu, W., Chen, Z., Ahmed, N., Han, B., Cui, Q. and Liu, A. 2016. Genome-wide identification, evolutionary analysis, and stress responses of the GRAS gene family in castor beans. Int. J. Mol. Sci., 17(7): 1004.


Full Text: PDF

Refbacks

  • There are currently no refbacks.