of other proteins to DNA, resulting in synergistic or an-
tagonistic regulation of gene transcription [3, 4] . Among
the several histone modifications, histone acetylation is a
reversible process that plays essential roles in epigenetic
regulation. The acetyla tion of core histones is catalyzed
by histone acetyltransferases (HATs) to promote tran-
scriptional activation, whereas deacetylation is regulated
by histone deacetylases (HDACs) that drive the tran-
scriptional suppression [5]. HDACs deacetylate the ly-
sine residues of N-terminal histone tails, resulting in the
repression of gene expression [6].
HDACs are involved in a large amount of biological
processes associated with plant growth and development
[7–9]. Based on sequence homology to yeas t HDACs,
HDACs in plants are divided into three main categories:
reduced potassium dependency 3 / histone deacetylase 1
(RPD3/HDA1), histone deacetylase 2 (HD2), and silent
information regulator 2 (SIR2)[7, 10, 11]. RPD3/HDA1-
type histone deacetylases, which are homologous to
yeast RPD3 and HDA-1, belong to a large family, and
they require zinc ions to catalyze activity; the HDAC in-
hibitor trichostatin A (TSA) or sodium butyrate can in-
hibit their enzymatic activities [7]. The Arabidopsis
RPD3/HDA1 gene family is further classified into three
groups. Class I includes HDA6, HDA7, HDA9, and
HDA19; class II includes HDA5, HDA15, and HDA18;
and HDA2 is the only member of class III [7 , 8]. The
other genes of PRD3/HDA1 family are unclassified in
Arabidopsis.
Over the past 20 years, RPD3/HDA1-type HDACs (call
RPD3 for short below) have been studied extensively as
global regulatory factors playing essential roles in a
series of plant growth and development processes and
the response to various environmental stresses [8, 12–
14]. In Arabidopsis, it has been reported that AtHDA19
was involved in various developmental processes, includ-
ing flowering time, circadian clocks functions, and seed
development [15,
16]. Additionally, AtHDA19 might
regulate gene expression related to jasmonic acid and
ethylene signaling pathways in response to wounding
and path ogen infection [17]. In maize, the expression
patterns of the three ZmPRD3 genes ZmRpd3/101,
ZmRpd3/102, and ZmRpd3/108 showed widespread ex-
pression in all investigated corn organs. Furthermore,
the gene products could be detected in all cellular parts
at specific stages such as kernel, shoot, and anther devel-
opmental periods [18]. In rice, HDA705 responded to
ABA and abiotic stresses, and its expression was induced
by JA. In addition, the expression of HDA702 and
HDA704 was significantly induced by SA, JA, or ABA
[19, 20]. These findings indicate that the RPD3 members
play an important regulatory role in plant development
and in the response to various stresses and plant
hormones.
Cotton is one of the most important economic crops
in China with an essential role in the national economy.
Early maturity and stress resistance are vital target traits
of cotton breeding. Over the past two decades, the RPD3
genes have been intensively studied, and some progress
has been made in Arabidopsis and some other crops.
However, there is a lack of systematic research on the
RPD3 gene family in cotton. Thus, it is necessary to ex-
plore the potential functions of RPD3 genes in cotton. In
our study, the protein seq uences of cotton RPD3-type
HDACs were predicted by genome-wide identification
and the phylogenetic tree, gene structure, conserved
motif, protein do main, expression profiles, and prelimin -
ary functions were comprehensively analyzed. The infor-
mation gained for GhRPD3 provides a reference for
further exploration of the possible functions of RPD3
genes in cotton growth and development.
Results
Identification of RPD3 genes in nine species
In this study, a total of 108 RPD3 protein sequences
from nine species were identified after eliminating re-
dundant sequences, and they are named by the pos-
ition on the chromosome. The corresponding
relationship be tween gene ID n umber and gene name
is shown in Additional file 1:TableS1.Atotalof18
genes (GhHDA1-GhHDA18) containing Hist_deacetyl
(PF00850) domains w ere identified from G. hirsutum;
9 genes were located on the A t genome, and 9 genes
were mapped on the Dt genome. Furthermore, 18
genes (GbHDA1-GbHDA18)fromG. barbadense,9
genes (GaHDA1-GaHDA9)fromG. aboreum,and9
genes ( GrHDA1-GrHDA 9)fromG. raimondii were
detected. Tetraploid c otton possessed twice as many
RPD3 genes as diploid cotton, indicating that no
RPD3 cotton gene was lost in t he process of poly-
ploidy. The numbers of RPD3 genes in the other five
species were 10 (Arabidopsi s), 14 (Oryza sativa L.),
11 (Populus trichocarpa), 8 (Theobroma cacao), and
11 (Zea mays L.). The GhRPD3 protein length ranged
from 232 to 635 aa with an a verage o f 459 aa. The
physicochemical parameters showed that the isoelec-
tricpoint(pl)ofGhRPD3 proteins varied from 4.47
to 8.65 with an average value of 5.68, and the mo-
lecular w eight of GhRPD3 proteins varied f rom 25.79
to 73.01 kDa with an avera ge value of 51.21 k Da. The
subcellular localization results indicated that most of
the GhRPD3 genes were located in cytoplasmic (10)
or nuclear (8), suggesting that GhRPD3 genes might
possess multiple regulatory functions (Table 1). The
predicted length, pI, MW and subcellular localization
of the RPD3 p roteins in other eight species are shown
in Additional file 1: Table S1.
Zhang et al. BMC Genomics (2020) 21:643 Page 2 of 16