Evolutionary and expression analysis of CAMTA gene family in Nicotiana tabacum yielded insights into their origin, expansion and stress responses

Kaleem U Kakar,Kaleem U Kakar,Kaleem U Kakar,Kaleem U Kakar,Kaleem U Kakar,Zarqa Nawaz,Zarqa Nawaz,Xueliang Ren,Qingyao Shu,Qingyao Shu,Xueliang Ren,Jingjing Jin,Jingjing Jin,Peijian Cao,Peijian Cao,Zhouqi Cui

doi:10.1038/s41598-018-28148-9

Abstract

Calmodulin-binding transcription activators (CAMTAs) represent the novel gene family of transcriptional regulators, which play important biological functions. Though, the first ever plant CAMTA gene was evidenced in Nicotiana tabacum in 2002. But, the systematic identification, origin and function of this gene family has not been performed due to the lack of reference genome information until now. Here, we identified 29 CAMTA genes in four Nicotiana species, including thirteen NtabCAMTAs, six NsylCAMTAs, and five NtomCAMTAs and NbenCAMTAs. These CAMTA families were classified into five phylogenetic groups (I-V), among which, the group-IV CAMTAs probably emerged the earliest. The NtabCAMTA family genes have diverse structures, and are randomly localized on five chromosomes and scaffolds. N. tabacum acquired 11 copies of homolog CAMATA genes from the parental genomes of N. tomentosiformis and N. sylvestris, followed by expansion through polyploidization and duplication. The NtabCAMTA genes were differentially expressed in different plant parts, and showed sensitivity towards different abiotic and biotic stresses. Co-expression network analysis revealed that some NtabCAMTA subunits interact with each other, and co-expressed. The current study is the first report presenting a comprehensive overview of Nicotiana CAMTA families, and opens a new avenue for the improvement of the cultivated tobacco.

Highlights

Calmodulin-binding transcription activators (CAMTAs) represent the novel gene family of transcriptional regulators, which play important biological functions
Thirty-five candidate protein sequences were analyzed for the presence of CAMTA-specific conserved domains
Twenty-nine full length CAMTA genes having essential domains were identified from four Nicotiana species, including thirteen from N. tabacum, six from N. sylvestris, and five genes from N. tomentosiformis and N. benthamiana, respectively

Summary

Introduction

Calmodulin-binding transcription activators (CAMTAs) represent the novel gene family of transcriptional regulators, which play important biological functions. Because of its complexity and larger size, the fully annotated reference genome sequence of N. tabacum was not available until now, which left behind large gaps in studying important biological pathways and gene families of tobacco including CAMTA. Edwards et al.[27] and China tobacco (Ren et al unpublished), we used comprehensive bioinformatics and experimental approaches to perform genome-wide identification and characterization of CAMTA gene family in N. tabacum, N. sylvestris, N. tomentosiformis and N. benthaminana species. Using the available RNA-seq data and Real-time quantitative PCR analysis, we quantified and analyzed the expression profiles of NtabCAMTA family genes during plant growth and development, and stress responses to different biotic and abiotic factors. This study will help to identify novel CAMTA genes for future breeding to improve plant production, quality and stress resistance, and open a new avenue for further elucidation for their roles underlying the signal transduction in tobacco

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Conclusion