Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: novel insights into synteny, structures, and transcript profiles

BMC Genomics

Research Article

Abdulwareth A. Almoneafy¹  Khadija Kakar²  Raqeeb Ullah³  Xue-liang Ren⁴  Zarqa Nawaz⁵  Essa Ali⁶  Qing-Yao Shu⁷  Kaleem U. Kakar⁸ 

[1] Department of Biological sciences, College of Education and Science, Albaydaa University, Rada’a, Yemen;Department of Biotechnology, BUITEMS, Quetta, Pakistan;Department of Environmental Sciences, Quaid –i- Azam University, Islamabad, Pakistan;Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, 550081, Guiyang, China;Guizhou Academy of Tobacco Science, Longtanba Road No. 29, Guanshanhu District, (550081), Guiyang, Guizhou, People’s Republic of China;Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, 550081, Guiyang, China;Wuxi Hupper Bioseed Technology Academy Ltd., 214000, Wuxi, China;State Key Laboratory of Rice Biology, Institute of Crop Science, Zhejiang University, 310058, Hangzhou, China;State Key Laboratory of Rice Biology, Institute of Crop Science, Zhejiang University, 310058, Hangzhou, China;Institute of Crop Sciences, Zhejiang University, 866 Yuhangtang Road, 310029, Hangzhou, China;State Key Laboratory of Rice Biology, Institute of Crop Science, Zhejiang University, 310058, Hangzhou, China;Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, 550081, Guiyang, China;

关键词: Abiotic and biotic stress;    Ion channels;    CNGC;    Expression pattern;    Brassica oleracea;    Evolution;    RNA-seq;    qRT-PCR analysis;   

DOI  :  10.1186/s12864-017-4244-y

 received in 2017-07-12, accepted in 2017-10-31,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe cyclic nucleotide-gated ion channel (CNGC) family affects the uptake of cations, growth, pathogen defence, and thermotolerance in plants. However, the systematic identification, origin and function of this gene family has not been performed in Brassica oleracea, an important vegetable crop and genomic model organism.ResultsIn present study, we identified 26 CNGC genes in B. oleracea genome, which are non-randomly localized on eight chromosomes, and classified into four major (I-IV) and two sub-groups (i.e., IV-a and IV-b). The BoCNGC family is asymmetrically fractioned into the following three sub-genomes: least fractionated (14 genes), most fractionated-I (10), and most fractionated-II (2). The syntenic map of BoCNGC genes exhibited strong relationships with the model Arabidopsis thaliana and B. rapa CNGC genes and provided markers for defining the regions of conserved synteny among the three genomes. Both whole-genome triplication along with segmental and tandem duplications contributed to the expansion of this gene family. We predicted the characteristics of BoCNGCs regarding exon-intron organisations, motif compositions and post-translational modifications, which diversified their structures and functions. Using orthologous Arabidopsis CNGCs as a reference, we found that most CNGCs were associated with various protein–protein interaction networks involving CNGCs and other signalling and stress related proteins. We revealed that five microRNAs (i.e., bol-miR5021, bol-miR838d, bol-miR414b, bol-miR4234, and bol-miR_new2) have target sites in nine BoCNGC genes. The BoCNGC genes were differentially expressed in seven B. oleracea tissues including leaf, stem, callus, silique, bud, root and flower. The transcript abundance levels quantified by qRT-PCR assays revealed that BoCNGC genes from phylogenetic Groups I and IV were particularly sensitive to cold stress and infections with bacterial pathogen Xanthomonas campestris pv. campestris, suggesting their importance in abiotic and biotic stress responses.ConclusionOur comprehensive genome-wide analysis represents a rich data resource for studying new plant gene families. Our data may also be useful for breeding new B. oleracea cultivars with improved productivity, quality, and stress resistance.

【 授权许可】

CC BY   
© The Author(s). 2017