Genome-wide analysis of cotton C2H2-zinc finger transcription factor family and their expression analysis during fiber development

Salih et al. BMC Plant Biology (2019) 19:400 https://doi.org/10.1186/s12870-019-2003-8 RESEARCH ARTICLE Open Access Genome-wide analysis of cotton C2H2-zinc finger transcription factor family and their expression analysis during fiber development Haron Salih1,2,3, Magwanga Richard Odongo2, Wenfang Gong2, Shoupu He2 and Xiongming Du2* Abstract Background: C2H2-zinc finger protein family is commonly found in the plant, and it is known as the key actors in the regulation of transcription and vital component of chromatin structure. A large number of the C2H2-zinc finger gene members have not been well characterized based on their functions and structure in cotton. However, in other plants, only a few C2H2-zinc finger genes have been studied. Results: In this work, we performed a comprehensive analysis and identified 386, 196 and 195 C2H2-zinc finger genes in Gossypium hirsutum (upland cotton), Gossypium arboreum and Gossypium raimondii, respectively. Phylogenetic tree analysis of the C2H2-zinc finger proteins encoding the C2H2-zinc finger genes were classified into seven (7) subgroups. Moreover, the C2H2-zinc finger gene members were distributed in all cotton chromosomes though with asymmetrical distribution patterns. All the orthologous genes were detected between tetraploid and the diploid cotton, with 154 orthologous genes pair detected between upland cotton and Gossypium arboreum while 165 orthologous genes were found between upland cotton and Gossypium raimondii. Synonymous (Ks) and non-synonymous (Ka) nucleotide substitution rates (Ka/Ks) analysis indicated that the cotton C2H2-zinc finger genes were highly influenced mainly by negative selection, which maintained their protein levels after the duplication events. RNA-seq data and RT-qPCR validation of the RNA seq result revealed differential expression pattern of some the C2H2-zinc finger genes at different stages of cotton fiber development, an indication that the C2H2-zinc finger genes play an important role in initiating and regulating fiber development in cotton. Conclusions: This study provides a strong foundation for future practical genome research on C2H2-zinc finger genes in upland cotton. The expression levels of C2H2-zinc finger genes family is a pointer of their involvement in various biochemical and physiological functions which are directly related to cotton fiber development during initiation and elongation stages. This work not only provides a basis for determining the nominal role of the C2H2zinc finger genes in fiber development but also provide valuable information for characterization of potential candidate genes involved in regulation of cotton fiber development. Keywords: Comparative genomics analysis, C2H2-zinc finger family, Cotton, Fiber development, Phylogenetic * Correspondence: 2 State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China Full list of author information is available at the end of the article © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Salih et al. BMC Plant Biology (2019) 19:400 Background Zinc finger protein family is one of the most abundant transcription factors found in higher plants [1]. Furthermore, the zinc finger protein is a unique type of protein domain in which a zinc ion is bounded by cysteine and histidine residues [2], and mainly categorized into different types, namely C2H2, C2HC, C2HC5, C2C2, CCCH, C3HC4, C4, C4HC3, C6, and C8 based on the position and number of histidine and cysteine residues [3]. C2H2-zinc finger proteins, also referred as TFIIIA-type finger proteins with the general formula of X2CX2– 4CX12HX2–8H, where X represents the amino acid, C represents cysteine while H represents histidine, form one of zinc finger proteins family which has been wellcharacterized in various plants species [4], with a wide distribution within the plant kingdom [3, 5]. The C2H2zinc finger proteins were first discovered in Petunia [6]. To date, there are 176, 189 and 124 C2H2-zinc finger genes so far identified in Arabidopsis, rice and foxtail millet, respectively [3], 109 in Populus trichocarpa [7] and 211 in maize [8]. In previous studies of the C2H2zinc finger transcription factor proteins, they have been found to be vital in promoting plant growth and development [9]. C2H2-zinc finger proteins form a major portion of proteins in higher organism genomes [10]. They play different functions, which includes recognition of DNA, packaging of RNA, activation of transcriptional, apoptosis regulation, assembly and folding protein and also in binding of lipids [11]. In addition, C2H2-zinc finger transcription factor proteins are broadly involved in various processes such as biotic and abiotic stress [12], leaf trichome initiation [13], floral organelles [14], seed germination and primary microRNA biogenesis in Arabidopsis [15]. In rice, soybean and poplar, C2H2-zinc finger proteins do enhance adaptation to cold and drought stress [16–18]. It has been reported that C2H2zinc finger gene do promoted pathogen defense in Capsicum annuum [19]. Moreover, a novel gene, AtGIS from arabidopsis, was found to promote trichome development in Transgenic tobacco [20]. In cotton, C2H2zinc finger protein family was down-regulated at the fiber initiation stage in fuzz-less and lint-less (fl) mutant [21] and it was found that several C2H2-zinc finger genes were down-regulated in Ligon-lintless-1 and upregulated in wild-type during cotton fiber elongation stage [22]. Recently, C2H2-zinc finger genes have been suggested as the candidate genes controlling cotton fiber development in the Ligon-lintless-2 mutant compared to the wild-type [23]. Cotton is largely planted for both natural fiber and seed oil production [24] in more than 80 countries throughout the world [25]. Advancement in spinning technology has created the demand for high fiber quality in terms of length and fineness, moreover, cotton fiber developmental process occurs through four Page 2 of 17 overlapping stages, namely, initiation, elongation, secondary cell wall formation and maturation [25] Fiber initiation, elongation and secondary cell wall have a great impact on the number, length and fineness of fibers, which are the main factors determining lint quality and quantity of yield [25]. Elongation stage of cotton fiber starts immediately after initiation stage and continues for 3 w (...truncated)