**1. Introduction**

Transcription factors are essential for the control of gene expression. Gene expression can be regulated by transcription factors that either activate or repress transcription, so they are vital for many cell biological process [1]. The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (TCP) gene family is a small group of transcription factors exclusive to higher plants [2]. This class of transcription factors has many functions in regulating diverse plant growth and development processes by controlling cell proliferation [3]. They are characterized by a highly conserved 59-amino-acid basic helix–loop–helix (bHLH) motif at the N-terminus designated as the TCP domain [4]. This domain is responsible for DNA binding, nuclear targeting, and is involved in protein–protein interactions [5]. Based on variation in the TCP domain, TCP family members can be classified into two classes: Class I (also known as the PCF or TCP-P class) and class II (also known as the TCP-C class) [6,7]. Class II is further subdivided into the CINCINNATA (CIN) and CYC/TB1 subgroups. In addition to the TCP domain, several class II members possess an 18–20-residue arginine-rich motif [8]. This so-called R domain was predicted to form a hydrophilic α-helix or a coiled-coil structure that mediates protein–protein interactions [2].

It has been reported that many TCP transcription factors participate in the regulation of diverse physiological and biological processes, such as phytohormone biosynthesis and signal transduction, branching, leaf morphogenesis flower development and senescence, pollen development, and regulation of the circadian clock in various plants [9–11]. In *Arabidopsis thaliana* seeds, *TCP14* was expressed in the vascular tissues of embryos. It promotes germination through antagonism of abscisic acid signaling [12]. *TCP1* is expressed in restricted areas of the flower meristem, leaf vasculature, and at the junctions of roots and hypocotyls. It mediates the expression of a key brassinosteroid (BR) biosynthetic gene by directly associating with the two GGNCCC motifs in the promoter region of *DWARF4* (*DWF4*) [13]. *DWF4* encodes a 22-hydroxylase and is responsible for multiple 22-hydroxylation steps during BR biosynthesis [14]. The expression levels of *DWF4* were positively correlated with *TCP1* abundance in *planta*. In Arabidopsis flowers, the gynoecium and silique development was modulated by *TCP15* through partly regulating auxin biosynthesis. The ectopic expression of Arabidopsis *TCP15* represses style and stigma development, thus producing gynoecia with decreased stigmatic tissue and/or carpel fusion defects in apical parts [15]. TCP17 and its two closely related homologs, TCP5 and TCP13, play an important role in mediating shade-induced hypocotyl elongation by up-regulating auxin biosynthesis via a PHYTOCHROME INTERACTING FACTORS (PIF)-dependent and a PIF-independent pathway [16]. In rice (*Oryza sativa*), *OsTCP19* was upregulated under salt and water-deficit stress. Overexpression of *OsTCP19* in Arabidopsis caused upregulation of *INDOLE-3-ACETIC ACID3*(*IAA3*), *ABSCISIC ACID INSENSITIVE 3*(*ABI3*), and *ABI4,* and downregulation of *LIPOXYGENASE2* (*LOX2*), thus leading to developmental abnormalities, such as less lateral roots [17]. MicroRNAs (miRNAs) are a class of smallnon-coding RNAs generated from single-strand hairpin RNA precursors. They regulate gene expression by binding to complementary sequences within target mRNAs [18]. Considerable progress has been made in identifying the targets of plant miRNAs. In Arabidopsis, five CIN-like *TCP* genes (*TCP2*, *TCP3*, *TCP4*, *TCP10*, and *TCP24*) were targeted by miR319 and have been implicated in regulating leaf morphogenesis [19]. Knockdown of a subset of Class II TCP transcription factors by overexpression of miR319 increases tolerance to dehydration and salinity stress in bentgrass (*Agrostis stolonifera*) [20]. Accumulated functional characterization of TCPs indicated their diverse function in a developmental-, tissue-, and signal-dependent context. In addition to their importance as transcriptional regulators of cell-cycle genes, TCPs have other functions with comparable impact on plant development. Characterization of TCPs and their signaling pathway will be beneficial to unravel their exact role in the control of plant development and evolution.

Allotetraploid upland cotton (*Gossypiumhirsutum* L.) accounts for more than 90% of cultivated cotton worldwide, is the main source of renewable textile fibers, and is also grown to produce oilseed. It has proven to be difficult to sequence, owing to its complex allotetraploid (AtDt) genome [21]. Recently, its whole genome was sequenced by integrating whole-genome shotgun reads, bacterial artificial chromosome-end sequences, and genotype-by-sequencing genetic maps [22,23]. Repeated sequences account for 67.2% of the AtD<sup>t</sup> genome, and transposable elements originating from D<sup>t</sup> were more active than those from A<sup>t</sup> [23]. Availability of the genome information can provide a great opportunity to identify and characterize TCP genes in this plant species for the first time. In this study, we identified and characterized 73 non-redundant TCP transcription factors in the *G. hirsutum* genome. Detailed information regarding their genomic structures, chromosomal locations, and a phylogenetic tree were also provided. Using RNA-seq data, we investigated their transcript profiles in different tissues, including different developmental stages of ovule and fiber, as well as their response to heat, drought, and salt stress. Furthermore, the miR319-targeted TCP genes were characterized.
