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Article

Gene Expression Correlation Analysis Reveals MYC-NAC Regulatory Network in Cotton Pigment Gland Development

by
Hailiang Cheng
1,
Xiaoxu Feng
1,2,
Dongyun Zuo
1,
Youping Zhang
1,
Qiaolian Wang
1,
Limin Lv
1,
Chaofeng Wu
1,
Shuyan Li
1,
Yuanli Dai
1,
Da Qu
1,
Man He
1,
Shang Liu
1 and
Guoli Song
1,*
1
State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
2
Plant Genetics, Gembloux Agro Bio-Tech, University of Liège, 5030 Gembloux, Belgium
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2021, 22(9), 5007; https://doi.org/10.3390/ijms22095007
Submission received: 1 April 2021 / Revised: 21 April 2021 / Accepted: 28 April 2021 / Published: 8 May 2021
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding)
Browse Figures
Versions Notes

Abstract

:
Plant NAC (NAM, ATAF1/2, and CUC2) family is involved in various development processes including Programmed Cell Death (PCD) associated development. However, the relationship between NAC family and PCD-associated cotton pigment gland development is largely unknown. In this study, we identified 150, 153 and 299 NAC genes in newly updated genome sequences of G. arboreum, G. raimondii and G. hirsutum, respectively. All NAC genes were divided into 8 groups by the phylogenetic analysis and most of them were conserved during cotton evolution. Using the vital regulator of gland formation GhMYC2-like as bait, expression correlation analysis screened out 6 NAC genes which were low-expressed in glandless cotton and high-expressed in glanded cotton. These 6 NAC genes acted downstream of GhMYC2-like and were induced by MeJA. Silencing CGF1 (Cotton Gland Formation1), another MYC-coding gene, caused almost glandless phenotype and down-regulated expression of GhMYC2-like and the 6 NAC genes, indicating a MYC-NAC regulatory network in gland development. In addition, predicted regulatory mechanism showed that the 6 NAC genes were possibly regulated by light, various phytohormones and transcription factors as well as miRNAs. The interaction network and DNA binding sites of the 6 NAC transcription factors were also predicted. These results laid the foundation for further study of gland-related genes and gland development regulatory network.

1. Introduction

Cotton is an important economic crop providing natural fiber resource and potential nutrition resource. For example, global cottonseed production, if being fully utilized, could provide sufficient protein consumption for 500 million people one year [1]. Nevertheless, presence of toxic gossypol in pigment gland limited the use of the cottonseed production due to its toxicity for human and monogastric animals [2,3]. Besides, gossypol is phytoalexin providing plant resistance to various insects and pathogens [4,5,6,7]. It is significant for improving cotton economic value to breed cotton cultivars with high gossypol in plant and low gossypol in seed. In 2006, Sunikumar et al. created low-gossypol cotton using RNAi technology to suppress specially the expression of δ-cadinene synthase genes in cottonseed, which are key factors in gossypol biosynthesis [8,9,10,11]. The transgenic cotton showed reduced gossypol content in seed and normal in foliage and floral parts [10,12].
Pigment glands or gossypol glands are the specific organ of Gossypium spp. The gland is a cavity structure formed by lysigenous intercellular space generated by programmed cell death (PCD) [13,14]. As the main storage of gossypol, mature glands contain plenty of gossypol and various terpenoid aldehydes [11,15]. Gossypol content was reported to be closely related to pigment gland number in cotton [16,17,18]. However, compared with gossypol biosynthesis, little is known about the mechanism underlying pigment gland organogenesis. Up to now, six independent gene loci, named Gl1, Gl2, Gl3, Gl4, Gl5 and Gl6, were identified to be involved in gland formation. The first reported one is recessive gene gl1, which controlling phenotype of glanded cotyledon and leaf, and glandless hypocotyls, petiole, boll shell and stem [19]. Then, homozygous recessive gl2gl2gl3gl3 were reported to confer completely glandless phenotype of upland cotton plant [20,21]. Allele gl4 and gl5 contribute to reducing gland density and gl6 is similar to gl1 with weaker function [22,23]. One dominant gene Gl2e is allele of Gl2 and responsible for whole-plant glandless phenotype of mutant ‘Bahtim 110′ from radiation mutagenesis of ‘Giza45′ (G. barbadense L.) [24,25]. Since then, many efforts were made to isolate the genes relate to gland formation. In 2016, Gl2e was mapped to a 15 kb region on chromosome A12 and a basic helix-loop-helix (bHLH) transcription factor GhMYC2-like was identified and supposed to be involved in gland formation because of an amino acid substitution in conserved domain and low expression level in glandless cotton [26]. The transcription factor was functionally confirmed by virus induced gene silencing (VIGS) and named Gossypium Pigment Gland Formation (GoPGF). The gene on chromosome A12 and D12 were identified as Gl2 and Gl3, and gl2 and gl3 were revealed to be derived from the premature truncated Gl2 and Gl3, respectively [27]. Then, three Cotton Gland Formation (CGF) genes were identified by transcriptome analysis of glanded and glandless cotton embryos. Silencing CGF1 and CGF3 (synonym GoPGF) dramatically suppressed gland formation and the critical role of CGF3 in gland formation was further confirmed by CRISPR/Cas9-mediated knockout of the gene. CGF2 encoding NAC transcription factors have a mild regulating effect on gland formation [28]. Although many efforts were made recently [29,30], the molecular mechanism of gland development was still unclear.
NAC (NAM, ATAF1/2, CUC2) transcription factors are plant-specific proteins and belong to one of the largest transcription factor families [31]. There are a highly conserved DNA-binding domain and a variable transcriptional regulatory region at N-terminal and C-terminal of NAC transcription factors, respectively [32]. The first NAC gene was identified in Petunia, which controlling development of shoot apical meristem (SAM) [33]. Then, NAC genes were identified in various plants, including Arabidopsis thaliana [34], Oryza sativa [35], Vitis vinifera [36] and Gossypium spp. [37,38,39,40,41]. Increasing evidences indicate NACs involved in plant abiotic and biotic response and development regulation [42,43,44,45,46]. It is worth mentioning that NACs participate in PCD-associated vegetative development [47]. For example, a XYLEM NAC DOMAIN 1 (XND1) negatively regulated lignocellulose synthesis and PCD in xylem [48], VASCULAR-RELATED NAC DOMAIN 6 (VND6) and VND7 can activate PCD in xylem vessel element differentiation and VND7 directly bind the promoter of XND1 to regulate its expression [49,50]. In leaf senescence process, NAC transcription factor ORE1 directly targets senescence-induced BIFUNCTIONAL NUCLEASE1 (BFN1) to regulate PCD in Arabidopsis [51]. ANAC033/SOMBRERO controls the PCD in lateral root cap differentiation [52]. Recently, ANAC087 and ANAC046 were also reported to regulate PCD in the columella and lateral root cap [53].
Gland formation is a PCD-associated development process and one pair of NAC genes (CGF2) are reported to affect gland density. NAC genes form one large gene family and previous studies focus on functions of NAC family members in stress responses and fiber development in cotton [37,38,39,40,41]. It is unknown whether other NAC genes participate in gland development regulation. In this study, genome-wide identification and expression correlation analysis of NAC genes in cotton were performed and 6 NAC genes were screened out to be supposed to involve in gland formation. Further analysis revealed that they acted downstream of GhMYC2-like and were induced by MeJA. Besides, Another MYC transcription factor CGF1 influenced gland formation by regulating GhMYC2-like and these 6 NAC genes. These results delineated a MYC-NAC regulatory network in gland development. In addition, the regulatory mechanism of 6 NAC genes was predicted. This study laid the foundation for further analysis of gland-related NAC genes and gland development regulatory network.

2. Results

2.1. Identification and Phylogenetic Analysis of NAC Genes Family in Cotton

To identify the NAC genes, recently updated genome reference sequences of gossypium spp. were downloaded from database (https://www.cottongen.org/, accessed on 20 June 2020). Total 299, 150 and 153 NAC proteins were obtained in G. hirsutum, G. arboreum and G. raimondii respectively using hmmsearch and blastp search. Then, the conserved domain in NAC proteins were confirmed using online software PfamScan (https://www.ebi.ac.uk/Tools/pfa/pfamscan/, accessed on 20 June 2020). The NAC proteins in 3 cotton genomes were named Gh_NAC1-Gh_NAC299, Ga_NAC1-Ga_NAC150 and Gr_NAC1-Gr_NAC153, respectively. The characteristics of NAC proteins were analyzed. For example, the range of length of NAC proteins were from 87 (Gh_NAC100) to 860 (Gh_NAC140) amino acids, 66 (Ga_NAC5) to 1133 (Ga_NAC18) amino acids and 123 (Gr_NAC131) to 859 (Gr_NAC100) amino acids. The range of isoelectric point of NAC proteins were from 4.102 (Gh_NAC160) to 10.281 (Gh_NAC111), 4.445 (Ga_NAC68) to 10.14 (Ga_NAC121) and 4.381 (Gr_NAC117) to 10.65 (Gr_NAC144). The grand average of hydropathy of NAC proteins were range from −1.001 (Gh_NAC259) to −0.187 (Gh_NAC189), −0.956 (Ga_NAC55) to −0.335 (Ga_NAC9) and −0.977 (Gr_NAC119) to −0.293 (Gr_NAC131). Subcellular localization prediction showed that about 3/4 NAC proteins located in nucleus and 1/4 were extracellular, except for Ga_NAC3 (membrane), Ga_NAC97 (chloroplast) and Gr_NAC69 (chloroplast). Detail information of each NAC protein was listed in Tables S2–S4.
A maximum likehood (ML) tree was constructed to uncover the phylogenetic relationship of the NAC proteins in G. hirsutum, G. arboreum and G. raimondii (Figure 1). The 602 NAC proteins were divided into 8 groups (I–VIII). Almost all NAC genes in G. arboreum and G. raimondii, which are genome progenitors of G. hirsutum, have the orthologous genes in G. hirsutum. There were some exceptions, such as Ga_NAC5, Ga_NAC19, Ga_NAC49, Ga_NAC62, Ga_NAC129, Gr_NAC1, Gr_NAC49, Gr_NAC55, Gr_NAC125, Gr_NAC131, Gr_NAC133 and Gr_NAC146 without orthologs in G. hirsutum, which indicating the gene loss in allotetraploid or gene gain in diploid cotton. Gene gain was also observed during evolution of G. hirsutum, such as Gh_NAC255/Gh_NAC256, Gh_NAC106/Gh_NAC107 and Gh_NAC188/Gh_NAC189 share one ortholog in G. raimondii, respectively.

2.2. Gene Chromosomal Location, Duplication and Synteny Analysis of NACs in Cotton

Total 298 out of 299 Gh_NACs were distributed on all chromosomes with number range from 7 to 17 and the other one located on scaffold (Figure S1A,B). Ga_NACs and Gr_NACs distributed on corresponding chromosomes with similar pattern (Figure S1C,D). Gene duplication analysis revealed that 231, 18 and 10 duplicated gene pairs of NAC genes derived from segmental duplication in G. hirsutum, G. arboreum and G. raimondii, respectively (Table S5 and Figures S2–S4). Most Gh_NAC gene duplications were derived from allotetraploid formation (duplicated gene pairs from A and D subgenome). Several NACs had more than one duplicated genes implying their contribution to NAC gene family expansion. Meanwhile, tandem duplication of NACs were also detected (Table S5), such as Gh_NAC85/Gh_NAC86/Gh_NAC87, Gh_100/Gh_NAC101, Ga_NAC25/Ga_NAC26, Ga_NAC83/Ga_NAC84/Ga_NAC85, Gr_NAC41/Gr_NAC42/Gr_NAC43, Gr_NAC54/Gr_NAC55. Ka/Ks ratio of each pair of NAC genes was calculated to explore the selective pressure in evolution. As shown in Table S5, most duplicated NAC gene pairs had a Ka/Ks ratio < 1, which undergoing purifying selection. Seven pairs with Ka/Ks ratio > 1 were subjected to positive selection, including Gh_NAC14/Gh_NAC164, Gh_NAC33/Gh_NAC200, Gh_NAC89/Gh_NAC239, Gh_NAC122/Gh_NAC271, Gh_NAC81/Gh_NAC231, Gh_NAC28/Gh_NAC170 and Gh_NAC72/Gh_NAC222.
To investigate the synteny relationship of NAC genes, total 114, 100 and 74 NAC genes were identified in Arabidopsis thaliana, Theobroma cacao and Vitis vinifera. Synteny analysis showed that NAC genes had high collinear relationship in three cotton genomes, as well as between diploid cotton and A. thaliana, T. cacao and V. vinifera, respectively (Figure 2 and Figure 3 and Table S6). Total 115/124, 109/114 and 96/104 orthologous NAC gene pairs were detected between G. arboreum/G. raimondii and A. thaliana, T. cacao and V. vinifera, respectively (Table S7). Among them, orthologous genes of 55 Ga_NACs and 65 Gr_NACs were detected in all three plants suggesting that they were generated before the species divergence and highly conserved during species differentiation (Figure 3). Besides, we explored the occurrence time of NACs tandem duplication. Corresponding tandem duplications of Ga_NAC114/Ga_NAC115, Gr_NAC80/Gr_NAC81, Gh_NAC121/Gh_NAC122 and Gh_NAC270/Gh_NAC271 were observed in cacao indicating that the duplication occurred at 33 million years ago (mya), which is divergence time of cotton ancestor and cacao [54]. Another tandem duplication event Ga_NAC49/Ga_NAC50 was detected in cacao but not in G. raimondii and G. hirsutum, suggesting that the duplication occurred at 33 mya and lost in G. raimondii and G. hirsutum after species differentiation. Some tandem duplications only existed in cotton implying that they were generated at 5–10 mya before G. arboreum and G. raimondii diverged from the common ancestor. These duplications were also retained in G. hirsutum, including Ga_NAC83/Ga_NAC84/Ga_NAC85, Gr_NAC41/Gr_NAC42/Gr_NAC43, Ga_NAC97/Ga_NAC98 and Gr_NAC69/Gr_NAC70 (Table S6). Other tandem duplications of NAC genes generated and evolved independently in each cotton species in recent 1–2 Mya after the allotetraploid formation. These results suggested NAC gene family experienced complex gene gain and loss during Gossypium evolution.

2.3. Identification of Gland Formation Associated NAC Genes in G. hirsutum

The transcription factor GhMYC2-like (synonym GoPGF) was identified as a vital regulator in pigment gland development [26,27,28]. To identify the NAC genes involved in pigment gland development, spatiotemporal expression analysis of all Gh_NAC genes and GhMYC2-like were conducted using the public RNA-seq data. Expression correlation of GhMYC2-like and each NAC gene was calculated and 7 NAC genes were identified as being co-expressed with GhMYC2-like (correlation > 0.5) (Figure 4A). Among of them, Gh_NAC120 belonged to group V and other Six (3 pair of alleles including 2 duplicated gene pairs) were from group VII (Figure 1 and Table S5). Notably, as shown in Figure 4B, the 7 NAC genes showed low expression level in ovule before 10 dpa and high expression level after 20 dpa, which in line with gland development time that starting at 14–16 dpa [28]. The result suggested that these genes were likely to participate in gland development regulation.
To confirm whether 7 NAC genes were relative to glandless phenotype, the genes expression were checked in glanded cotton CCRI12 (China Cotton Research Institute 12), Liao7, CCRI17, dominant glandless (Dgl) cotton Dgl-CCRI12, Dgl-Liao7 and recessive glandless (Rgl) cotton Rgl-CCRI12 and Rgl-CCRI17, as well as stem-glandless line T582. According to our RNA sequencing data, except for Gh_NAC120, the expression of other 6 NAC genes and GhMYC2-like were lower in leaves or stems of glandless cotton than that in glanded cotton (Figure 5A). Meanwhile, qRT-PCR was employed to verify the expression pattern of 7 NAC genes and GhMYC2-like in leaves and stems of all these cotton lines. Previous studies revealed stable reference gene expression is important for accurate quantification of gene expression [55,56]. In this study, we used 3 reference genes (actin, ubiquitin and histone) for qRT-PCR analysis. As shown in Figure 5B, Gh_NAC120 was highly expressed in all stems of materials regardless of gland phenotype suggesting that it was not associated to gland formation. The other 6 NAC genes and GhMYC2-like were at low expression level in all glandless materials in accord with the RNA-seq results. There were similar results by using 3 reference genes as internal controls, suggesting the expression analysis was relatively accurate and each reference gene was available for qPCR analysis (Figure S5). Among of 6 genes, the function of Gh_NAC5/Gh_NAC153 (assigned as CGF2) was verified in gland formation by gene knockout [28]. These results indicated GhMYC2-like probably functioned together with these 6 NAC genes in gland development.

2.4. The Gland-Related NACs Function Downstream of GhMYC2-Like

Normal expression of GhMYC2-like was essential for gland development suggesting that it may be at the heart of the regulatory network controlling the gland-related genes expression. To investigate the relationship of GhMYC2-like and 6 NACs, RNAi transgenic plants were generated to interfere the transcript accumulation of GhMYC2-like in glanded cotton CCRI24. The gland development was repressed completely in all organs of RNAi plants (Figure S6). Expression analysis indicated that the transcript level of GhMYC2-like was suppressed extremely. Similarly, other 6 NACs were also down-regulated dramatically in RNAi plants suggesting that they functioned downstream of GhMYC2-like. In addition, unsurprisingly, transcript accumulation of Gh_NAC120 was not interrupted (Figure 6 and Figure S7).
In previous reports, it was reviewed that MYC2 acted as a master regulator in jasmonate (JA) signaling pathway in Arabidopsis [57]. To analyze whether JA signaling pathway also involved in gland development, expression change of GhMYC2-like and 6 NAC genes were detected at different time in cotton seedling which were subjected to MeJA treatment. As a result, all GhMYC2-like and 6 NAC genes were induced by MeJA and expression level reached the peak at 4 h or 8 h after treatment (Figure 7 and Figure S8). Among of them, Gh_NAC85 and Gh_NAC235 were highest sensitive to MeJA treatment and showed about 15 times of expression level at peak than 0 h stage. These results suggested the 6 NACs functioned downstream of GhMYC2-like and JA signaling pathway might be involved in gland development.

2.5. Silencing Gland-Related NACs Inffluences Gland Development

To check the function of gland-related NACs, virus induced gene silencing (VIGS) was performed to silencing the transcripts of the NACs. In previous report, silencing CGF2(Gh_NAC5/Gh_NAC153) reduced the number of gland by microscopic analysis [28]. In view of the high sequence similarity between CGF2 and the other 4 NAC genes (about 70%) and between the 4 NACs each other (more than 87%), the target sequence for VIGS was selected by sequence alignment (Figure S9). A 257 bp fragment was selected with low similarity between CGF2 and the other 4 NACs for silencing the 4 NAC genes specifically. Besides, the phytoene desaturase (PDS) gene was silenced with the NACs as a phenotypic marker for VIGS. As shown in Figure 8, silencing the 4 NAC genes reduced gland number greatly. Accompany with dramatic silencing of 4 NAC genes, the expression of Gh_NAC5/Gh_NAC153 was also suppressed appreciably, which might also contribute to the reduction of gland number (Figure 8 and Figure S10). These results suggested that the NAC genes may be involved in gland development with functional redundancy.

2.6. CGF1 Influences Gland Formation by Regulating GhMYC2-Like and GLAND-Related NACs

In the previous report, another MYC transcription factor CGF1 could influence gland formation significantly [28]. To explore how it functioned in gland formation, virus induced gene silencing (VIGS) was employed to knockdown CGF1 expression in glanded cotton CCRI12. As shown in Figure 9, the gland number decreased observably in VIGS plants compared with control plants indicating important roles of CGF1 in gland development (Figure 9A). Along with suppressed expression of CGF1, GhMYC2-like was also down-regulated dramatically (Figure 9B and Figure S11). Besides, the expression of CGF1 was not influenced in RNAi-GhMYC2-like plants, indicating that CGF1 functioned upstream of GhMYC2-like (Figure S11). Therefore, it is reasonable to conclude that CGF1 participated in gland development process by regulating GhMYC2-like. In addition, as expected, the expression of 6 gland-related NAC genes was also reduced remarkably in VIGS-CGF1 plants (Figure 9B and Figure S12). To check if CGF1 influenced specifically gland-related NAC genes, other 9 NACs close to 6 gland-related NACs in phylogenetic tree were selected for qRT-PCR analysis. As shown in Figure S13, expression of eight genes was unaffected in VIGS-CGF1 plants, except for one (Gh_NAC87) with a little reduced expression. We speculated that CGF1 might specifically affect gland-related NACs expression by regulating GhMYC2-like.

2.7. Expression Profiling of 6 Gland-Related NAC Genes under Various Stresses

In previous studies, NAC family members were reported to be relative to stress responses [42]. To explore whether these 6 NAC genes also have relation to stress response, dynamic expression of them were obtained from public RNA-seq data after various treatments, including cold, hot, salinity and polyethylene glycol (PEG). It can be seen in Figure 10, Gh_NAC5, Gh_NAC85, Gh_NAC153 and Gh_NAC235 were not sensitive to all treatments. Gh_NAC86 and Gh_NAC236 could response to the stress treatments and Gh_NAC236 was more sensitive. Among of the treatments, hot and cold stresses caused opposite expression pattern of the genes. Along with the increase of the cold treatment time, expression of Gh_NAC86 and Gh_NAC236 were induced at 1 h and dramatic decline until 12 h back to initial state. On the contrast, they were still up-regulated extremely at 12 h after hot treatment. These results suggested that Gh_NAC86 and Gh_NAC236 also play roles in abiotic stress responses.

2.8. Predicted Regulatory Mechanism of the 6 NAC Genes

To explore possible regulatory mechanism of the 6 NAC genes, analysis of cis-elements and transcription factor binding sites (TFBS) were conducted in the 1500 bp promoter regions upstream of initiation codon. The results showed, except for common elements of CAAT-box and TATA-box, many cis-elements involved in light response were identified in all 6 NAC promoters. Plant hormone response elements were observed in different NAC promoters, including Methyl jasmonate (MeJA) response elements in Gh_NAC5, Gh_NAC153, Gh_NAC235 and Gh_NAC236, auxin response elements in Gh_NAC85, Gh_NAC86, Gh_NAC235 and Gh_NAC236, absence acid (ABA) response elements in Gh_NAC5, Gh_NAC85, Gh_NAC153 and Gh_NAC235. In addition, unsurprising, defense and stress response elements were found only in promoter regions of Gh_NAC86 and Gh_NAC236, whose expression was influenced by stress treatments (Figure 11A).
TFBS analysis showed that there were 33 transcription factors of 20 families which were predicted to bind to the promoter regions of 5 NAC genes except for Gh_NAC85 (Figure S14 and Table S8). The TFs included members of Dof, GATA, HD-ZIP, MIKC_MADS, TCP, bHLH, MYB, ERF and C2H2, which were related to various development regulation and environmental stimuli. The CGF1 and GhMYC2-like were not included in the 33 transcription factors, which indicating that they probably indirectly regulated expression of the NACs through other factors.
Many evidences showed that miRNAs play important roles in plant development regulation [58]. To check whether miRNA also participated in gland development regulation, these 6 NAC gene sequences were used to scan potential miRNA targets in online software psRNATarget with all upland cotton miRNA sequences [59]. The result revealed that Gh_NAC5 and Gh_NAC153 might be targeted by ghr-miR482a/b and ghr-miR7506, as well as Gh_NAC85 and Gh_NAC235 by ghr-miR156a/b/d (Figure S15, Table S9).
To predict the interaction network of 6 NACs, the orthologs of each NAC were identified by using blastp search in protein database of The Arabidopsis Information Resource (TAIR) according to the score and E-value. The best match one was consider as the ortholog of each NAC and the 6 NACs share one common ortholog (AT2G43000) in Arabidopsis. AT2G43000 was used to screen the STRING database for interaction network prediction. As shown in Figure 11B, the NAC protein was likely to interact with different proteins to participate in different biological processes, such as biotic stress responses (CYP71A12, PAD3, AT1G26380 and AT5G38900), abiotic stress responses (GAI, DREB2A and AT1G07440) and signal transduction (AT1G74360). Besides, we conducted interaction network prediction of CGF1 and GhMYC2-like using their orthologs(AT5G46830 and AT4G17880)in STRING, respectively. One interaction network including CGF1 and GhMYC2-like could be constructed which mainly consist of members of JA signalling pathway, such as JAZs, COI and NINJA (Figure S16). This was consistent with the results above that JA signalling pathway could play important roles in pigment gland development. But, there was no overlap between the MYC-included and NAC-included interaction networks. These results suggested that the 6 NAC genes might be involved in light and phytohormone signaling pathways and various biological processes regulated by different transcription factors or miRNAs. In addition, we predicted the binding sites of these 6 NAC proteins in footprintDB database by using protein sequence search in Arabidopsis database. The result showed that the NACs might bind two putative binding motifs to regulate downstream genes (Figure 11C).

3. Discussion

3.1. Identification and Phylogenetic Analysis of NAC Genes in Cotton

Plant-specific NAC protein family is one of the biggest transcription factor families, whose members participate in various stress responses and development regulation including PCD-associated development [47]. Although NAC genes have been identified in cotton [37,38,39,40,41], there is no report of integrated analysis of NAC members related to PCD-associated pigment gland development in cotton. With the development of new generation of sequencing technology, more accurate genomic information has been obtained, which lays a foundation for more accurate identification and analysis of gene functions [60,61]. In this study, we identified 150, 153 and 299 NAC genes in G. arboreum, G. raimondii and G. hirsutum. The numbers are larger than that reported before, which may be due to the better genome assembly [37,38]. Analysis of protein feature reveals that all NAC proteins are hydrophilic and most of them are predicted to be located in nucleus which conforms to the characteristics of transcription factors. However, unintelligibly, some NAC transcription factors are putative secreted proteins (extracellular proteins), which presumably do not act as transcription factors.
The phylogenetic tree shows that NAC proteins are divided into 8 groups in three cotton species. Almost all Ga_NACs and Gr_NACs appear with corresponding Gh_NACs in the phylogenetic tree branches, indicating their high conservation in 3 cotton genomes. But, some exceptions reflect the evolution divergence of NACs [38]. Gene duplication is the main force of gene family expansion [62]. In three cotton genomes, both segmental and tandem NAC gene duplications are identified contributing to family expansion (Table S5). Selective pressure analysis shows almost all NAC gene duplications are under purifying selection which consistent with previous reports [38,39]. Synteny analysis shows that plenty of NAC genes in cotton have corresponding orthologs in grape, Arabidopsis and cacao. These genes are relatively conserved during plants evolution implying their important roles in plant growth. Some NAC genes are only generated or retained in cotton suggesting that they are responsible for the unique characteristics of cotton, such as Ga_NAC2/Gh_NAC2, Gr_NAC12/Gh_NAC151, Ga_NAC79/Gh_NAC81, Gr_NAC37/Gh_NAC231, etc.

3.2. Expression Analysis and Potential Roles of NAC Genes in Pigment Gland Development

Pigment glands are the main storage of gossypol and gland number has a close relation with gossypol content [16,17,18]. It is of great meaning to study gland-related genes for low-gossypol cotton breeding. In previous studies, GhMYC2-like (synonym GoPGF or CGF3) was confirmed to be the vital regulator of pigment gland development [26,27,28]. As a transcription factor, GhMYC2-like works by regulating other genes, but the regulatory network is still unclear now. Here, we conduct expression correlation analysis using GhMYC2-like gene as bait to screen co-expressed NAC genes using cotton RNA-seq data. Seven NAC genes are screened out with pearson correlation coefficient >0.5. It is notable that these 7 NAC genes are at low level expression before gland formation and turn into high level when gland development is starting in ovules. Then, it is further verified that 6 NAC genes among of them are low-expressed in all glandless materials suggesting they are involved in gland development. Meanwhile, Knockdown of GhMYC2-like causes extremely down-regulated expression of these 6 NAC genes, indicating they act downstream of GhMYC2-like. In the previous study, it is reported that knockout of CGF2 (Gh_NAC5/Gh_NAC153) could reduce gland density but not stop gland formation [28]. In this study, we selected a small fragment with low similarity between CGF2 and the other 4 NAC genes to silencing the latter specifically. Silencing the 4 NAC genes could also lead to reduction of gland number greatly. But, the expression of CGF2 was also supressed appreciably, which might contribute to the low gland density as well. Therefore, we speculate that other 4 NAC genes (two pairs of tandem duplicated genes) may act together with Gh_NAC5/Gh_NAC153 with functional redundancy in gland development and respective effect is weak. In addition, Silencing CGF1 (another MYC transcription factor) could cause down-regulated expression of GhMYC2-like and NACs, leading to dramatic decreased gland number. It can be concluded that CGF1 acts as a regulator of GhMYC2-like to participate in gland development process. These results delineate a primary MYC-NAC transcription factors regulatory network in gland development in which GhMYC2-like acts as a key factor and downstream NAC genes or other factors lead to PCD to generate gland finally (Figure 12).

3.3. Putative Molecular Regulatory Mechanisms of Gland-Related NAC Genes

Phytohormone JA and its derivatives are key regulators in biotic stress responses [63]. In this study, GhMYC2-like and 6 NAC genes are induced by MeJA, indicating JA signaling pathway may be associated to gland development and the genes are likely to be involved in biotic stress responses. Perhaps they also contribute to the resistance of glanded cotton to some insects and pathogens. Gh_NAC86 and Gh_NAC236 can be also induced by abiotic stresses suggesting their potential function in abiotic stress responses (Figure 10). Gh_NAC85 and Gh_NAC235 are duplicated genes of Gh_NAC86 and Gh_NAC236 respectively, but they do not response to abiotic stresses, possibly due to lack of defense and stress response elements. This suggests the gene functional divergence may not only derive from coding sequence changes but also regulation region changes. Predicted regulatory mechanism of 6 NAC genes indicates that they might be regulated by light, various phytohormones and transcription factors, as well as miRNAs (Figure 12). Interaction network prediction suggests the 6 NAC proteins possibly enrich its functions by interacting with different proteins. Although need further confirmation, it implies their rich functionality and complex regulation network.

4. Materials and Methods

4.1. Identification and Phylogenetic Analysis of NAC Proteins

Newly published genome and protein sequences of G. hirsutum L. (ZJU version) [64], G. arboreum L. (CRI version) [65] and G. raimondii Ulbrich (JGI version) [66] were downloaded from CottonGen (https://www.cottongen.org, accessed on 20 June 2020). Genome and protein sequences of Arabidopsis, Theobroma cacao and Vitis vinifera were downloaded from EnsemblGenomes database (http://plants.ensembl.org/index.html, accessed on 20 June 2020). To identify NAC proteins, BLASTP and the hidden Markov model (HMM) search program were employed to search all protein sequences using the conserved No Apical Mristem (NAM) domain as bait as described before [40]. The domains of candidate NAC proteins were confirmed by online tool PfamScan (https://www.ebi.ac.uk/Tools/pfa/pfamscan/, accessed on 20 June 2020) [67]. The information of NAC proteins were obtained from cottonFGD (https://cottonfgd.org/, accessed on 20 June 2020) [68]. Subcellular localization analysis was made using ProtComp tool (http://linux1.softberry.com/, accessed on 20 June 2020). All NAC protein sequences were aligned using MAFFT and clustered by FastTree and phylogenetic tree was constructed using maximum likelihood (ML) method on cottonFGD (https://cottonfgd.org/, accessed on 20 June 2020) [68]. The phylogenetic tree was visualized in EvolView program (https://www.evolgenius.info//evolview/, accessed on 20 June 2020) [69].

4.2. Gene Chromosomal Location, Duplication and Synteny Analysis of NACs in Cotton

Chromosomal location of NAC genes were determined based on the genome annotation information and illuminated with TBtools [70]. The gene duplication analysis of three cotton species were conducted using MCScanX software by criterion of sequence coverage and similarity of aligned sequence both more than 80% [71]. The synonymous substitution (Ks) and nonsynonymous substitution (Ka) of each duplicated gene pairs were calculated in TBtools with default parameters [70]. Synteny analysis was carried out using JCVI python package (https://github.com/tanghaibao/jcvi/, accessed on 20 June 2020) [72]. Gene duplication and synteny relationship were visualized by TBtools [70].

4.3. Gene Expression and Correlation Analysis of GhMYC2-Like and NAC Genes

RNA-seq data (accession: PRJNA248163) was downloaded from European Nucleotide Archive (ENA) database. The samples included different development stages of root and ovlue and various tissues of G. hirsutum TM-1. Salmon tool was employed to quantify the gene expression by Transcripts Per Million (TPM) [73]. All gene expression levels were normalized by log2 (TPM+1) and pearson correlation analysis was performed using R package psych. The heatmaps of genes expression were made with R package pheatmap.

4.4. Plant Materials and MeJA Treatment

To verify the NAC genes relative to gland phenotype, genes expression were analyzed by qRT-PCR in various cotton lines, including glanded cotton CCRI12, Liao7, CCRI17, Dominant glandless (Dgl) cotton Dgl-CCRI12 (with Gl2e), Dgl-Liao7 (with Gl2e) and Recessive glandless (Rgl) cotton Rgl-CCRI12 (with gl2 and gl3), Rgl-CCRI17 (with gl2 and gl3), as well as stem-glandless line T582 (with gl1). All the plant materials were from National Medium-term Gene Bank of Cotton (Anyang, China) and maintained by selfing in our lab. RNAi transgenic plants were generated by agrobacterium-mediated genetic transformation to interfere accumulation of GhMYC2-like transcripts. For MeJA treatment, Liao7 plants grew in green house with 27 °C (16 h light/8 h dark) and the leaves at three-leaf stage were treated by 100 μM MeJA. The treated leaves were collected at 0 h, 2 h, 4 h, 8 h and 12 h after treatment, respectively.

4.5. Virus Induced Gene Silencing (VIGS)

A 628-bp specific fragment of CGF1 gene was amplified and inserted to pTRV2, a tobacco rattle virus vector. For VIGS of the NAC genes and PDS gene simultaneously, the fragments of two genes were inserted to pTRV2 in tendam. Silencing PDS gene could lead to plant bleaching, which was used as phenotypic marker for VIGS. The pTRV2-CGF1, pTRV2 and pTRV1 were transferred into Agrobacterium tumefaciens GV3101, respectively. The CCRI12 plants grew in illumination incubator with 16 h/8 h light/dark at 25 °C. The VIGS procedure was performed according to the method reported before [74]. Three weeks later, the gland phenotype was recorded and leaves of VIGS plants were collected for RNA extraction and qRT-PCR.

4.6. RNA Extraction and QRT-PCR Analysis

The stem or leaf tissues of the plant materials were collected and put in liquid nitrogen immediately. Total RNA was extracted using RNAprep Pure Plant Kit (Tiangen, Beijing, China) according to the instructions. The first cDNA strand synthesis was made using PrimeScript II 1st Strand cDNA Synthesis Kit (TAKARA, Dalian, China). The qRT-PCRs were performed on ABI QuantStudio5 RT-PCR system (Applied Biosystems, Foster City, CA, USA) with three replicates using TB Green Premix Ex Taq Kit (TAKARA, Dalian, China). PCR reaction conditions were as follows: 95 °C for 30 s; 40 cycles at 95 °C for 5 s and 60 °C for 30 s; followed by 95 °C for 15 s, 60 °C for 1 min, 95 °C for 15 s. ACTIN (Genbank id AY305733), ubiquitin (Genbank id EU604080) and histone (Genbank id AF024716) were employed as internal controls. Relative gene expression was calculated using the 2−ΔΔCT method. All primers information was listed in Table S1.

4.7. Predictions of Cis-Elements, TFBS, miRNA Targets, Interaction Network and Binding Sites

The 1.5 kb promoter sequences of NAC genes were extracted upstream of initiation codon. All sequences were submitted to PlantCARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/, accessed on 20 June 2020) to search putative cis-elements. TFBS predications were performed using Binding Site Prediction tool in PlantTFDB database (http://planttfdb.cbi.pku.edu.cn/, accessed on 20 June 2020) with p value < 1 × 10−6. For miRNA targets prediction, NAC genes sequences were submitted to psRNATarget server to check the possible target sites by miRNAs of upland cotton with default parameters. Because of the well-studied interaction network in Arabidopsis, interaction network prediction of the 6 NAC proteins were performed in STRING database (http://string-db.org/cgi/input.pl, accessed on 20 June 2020) using their orthologs in Arabidopsis. To obtain the putative binding sites, the 6 NAC proteins sequences were submitted to footprintDB database (http://floresta.eead.csic.es/footprintdb/index.php, accessed on 20 June 2020) to search putative binding sites.

Supplementary Materials

The following are available online at https://www.mdpi.com/article/10.3390/ijms22095007/s1, Figure S1 Chromosomal location of cotton NACs. (A) and (B) Chromosomal location of NACs from A subgenome and D subgenome of G. hirsutum, respectively. (C) and (D) Chromosomal location of NACs from G. arboreum and G. raimondii, respectively. Numbers on the left indicate the length of chromosome. Black lines indicate the tandem duplication relationship. Ga: Gossypium arboreum, Gr: Gossypium raimondii, A/D: A/D subgenome of Gossypium hirsutum. The numbers indicate chromosome number. Figure S2 Synteny analysis of NACs in G. hirsutum. Red lines indicate the collinear relationship. Blue and purple blocks indicate chromosomes of A subgenome and D subgenome. A/D: A/D subgenome of Gossypium hirsutum. The numbers indicate chromosome number. Figure S3 Synteny analysis of NACs in G. arboreum. Red lines indicate the collinear relationship. Ga: Gossypium arboreum, the numbers indicate chromosome number. Figure S4 Synteny analysis of NACs in G. raimondii. Red lines indicate the collinear relationship. Gr: Gossypium raimondii. The numbers indicate chromosome number. Figure S5 Expression analysis of GhMYC2-like and 7 NAC genes in glanded and glandless cotton. Reference gene: ubiquitin (A) and histone (B). CCRI: China Cotton Research Institute, Dgl: dominant glandless, Rgl: recessive glandless, L7: Liaomian7. Figure S6 Phenotype of RNAi plants interferencing the expression of GhMYC2-like. (A–C) indicate the glandless leaf, seed and hypocotyl of RNAi plants. (D–F) indicate the glanded leaf, seed and hypocotyl of CCRI24 plants. Figure S7 QRT-PCR analysis of GhMYC2-like and 7 NAC genes in CCRI24 and RNAi plants. Reference gene: ubiquitin (A) and histone (B). Figure S8 Dynamic expression analysis of GhMYC2-like and 7 NAC genes after MeJA treatment by qRT-PCR. Reference gene: ubiquitin (A) and histone (B). Figure S9 6 NAC gene sequences alignment. The red boxes indicate target region for VIGS. Figure S10 Silencing gland-related NAC genes causes reduction of gland number. (A) Phenotype of VIGS plants. (B)and(C) QRT-PCR analysis of genes expression in VIGS plants. Reference gene: ubiquitin (B) and histone (C). Figure S11 Expression analysis of CGF1 in RNAi-GhMYC2-like plants. Reference gene: actin (A), ubiquitin (B) and histone (C). Figure S12 Silencing CGF1 causes glandless phenotype and down-regulated expression of GhMYC2-like and 6 NAC genes. Reference gene: ubiquitin (A) and histone (B). Figure S13 Expression analysis of 9 NAC genes with close relation to the 6 gland-related NAC genes in CGF1-VIGS plants. Reference gene: actin (A), ubiquitin (B) and histone (C). Figure S14 TFBS analysis of 6 NAC gene promoters. The numbers indicate the distance (in base pairs) upstream (−) or downstream (+) of the translation initiation codon ATG. Figure S15 miRNA targets prediction of 6 NAC genes. Blue blocks indicate the NAM conserved domain. Red blocks indicate the target sits of miRNAs. Figure S16 Interaction network of GhMYC2-like and CGF1. Table S1 All primers information in this study. Table S2 Gh_NAC genes information. Table S3 Ga_NAC genes information. Table S4 Gr_NAC genes information. Table S5 NAC gene duplications information in three cotton genomes. Table S6 Orthologious NAC genes of three cotton genomes. Table S7 Orthologious NAC genes between cotton and A. thaliana, T. cacao and V. vinifera. Table S8 Predicted TFBS information. Table S9 Information of predicted miRNA targets of 6 NAC genes.

Author Contributions

Conceptualization, H.C. and G.S.; methodology, H.C., X.F., D.Z., Y.Z., L.L. and S.L. (Shuyan Li); software, H.C., D.Z. and Y.Z.; investigation, Y.D., D.Q. and M.H.; resources, C.W. and S.L. (Shang Liu); writing—original draft preparation, H.C.; writing—review and editing, X.F., D.Z. and G.S.; supervision, Q.W. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Key R&D Program of China (2018YFD0100402); the National Natural Science Foundation of China (31901581); Central Public-interest Scientific Institution Basal Research Fund (1610162020040906 and 1610162020010305); and Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Not applicable.

Conflicts of Interest

The authors declare no conflict of interest.

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Figure 1. Phylogenetic analysis of NAC proteins from three cotton genomes. The labels in color indicate NAC proteins form G. hirsutum (red), G. arboreum (blue) and G. raimondii (green), respectively.
Figure 1. Phylogenetic analysis of NAC proteins from three cotton genomes. The labels in color indicate NAC proteins form G. hirsutum (red), G. arboreum (blue) and G. raimondii (green), respectively.
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Figure 2. Synteny analysis of NACs in cotton. The grey lines indicate NACs collinear relationship in three genomes and color lines indicate that only in two genomes. Ga: Gossypium arboreum, Gr: Gossypium raimondii, A/D: A/D subgenome of Gossypium hirsutum. The numbers indicate chromosome number. Tig means contig.
Figure 2. Synteny analysis of NACs in cotton. The grey lines indicate NACs collinear relationship in three genomes and color lines indicate that only in two genomes. Ga: Gossypium arboreum, Gr: Gossypium raimondii, A/D: A/D subgenome of Gossypium hirsutum. The numbers indicate chromosome number. Tig means contig.
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Figure 3. Synteny analysis of NACs between diploid cotton and Arabidopsis, cacao and grape. Blue, green, purple, yellow (A) and grey (B) blocks indicate the chromosomes of cacao, Arabidopsis, grape, G. arboreum (A) and G. raimondii (B), respectively. The gene labels and red lines indicate collinear relationship of genes with high conservation.
Figure 3. Synteny analysis of NACs between diploid cotton and Arabidopsis, cacao and grape. Blue, green, purple, yellow (A) and grey (B) blocks indicate the chromosomes of cacao, Arabidopsis, grape, G. arboreum (A) and G. raimondii (B), respectively. The gene labels and red lines indicate collinear relationship of genes with high conservation.
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Figure 4. Expression correlation analysis of GhMYC2-like and NAC genes. (A) Distribution of expression correlation. The red dots indicate genes. Black arrows indicate the genes co-expressed with GhMYC2-like (B) Relative expression levels of GhMYC2-like and 7 NAC genes in different tissues and development stages of TM-1. Dpa: Day Post Anthesis.
Figure 4. Expression correlation analysis of GhMYC2-like and NAC genes. (A) Distribution of expression correlation. The red dots indicate genes. Black arrows indicate the genes co-expressed with GhMYC2-like (B) Relative expression levels of GhMYC2-like and 7 NAC genes in different tissues and development stages of TM-1. Dpa: Day Post Anthesis.
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Figure 5. Expression analysis of GhMYC2-like and 7 NAC genes in glanded and glandless cotton (reference gene: actin). (A) Relative expression levels of GhMYC2-like and 7 NAC genes in glanded and glandless cotton. (B) QRT-PCR analysis of GhMYC2-like and 7 NAC genes in glanded and glandless cotton. CCRI: China Cotton Research Institute, Dgl: dominant glandless, Rgl: recessive glandless, L7: Liaomian7.
Figure 5. Expression analysis of GhMYC2-like and 7 NAC genes in glanded and glandless cotton (reference gene: actin). (A) Relative expression levels of GhMYC2-like and 7 NAC genes in glanded and glandless cotton. (B) QRT-PCR analysis of GhMYC2-like and 7 NAC genes in glanded and glandless cotton. CCRI: China Cotton Research Institute, Dgl: dominant glandless, Rgl: recessive glandless, L7: Liaomian7.
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Figure 6. QRT-PCR analysis of GhMYC2-like and 7 NAC genes in CCRI24 and RNAi plants (reference gene: actin).
Figure 6. QRT-PCR analysis of GhMYC2-like and 7 NAC genes in CCRI24 and RNAi plants (reference gene: actin).
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Figure 7. Dynamic expression analysis of GhMYC2-like and 7 NAC genes after MeJA treatment by qRT-PCR (reference gene: actin).
Figure 7. Dynamic expression analysis of GhMYC2-like and 7 NAC genes after MeJA treatment by qRT-PCR (reference gene: actin).
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Figure 8. Silencing gland-related NAC genes causes reduction of gland number. (A) Microscopic images of VIGS plant leaf by stereomicroscope (Olympus SZX10). The number indicates gland number per cm2. (B) QRT-PCR analysis of genes expression in VIGS plants (reference gene: actin).
Figure 8. Silencing gland-related NAC genes causes reduction of gland number. (A) Microscopic images of VIGS plant leaf by stereomicroscope (Olympus SZX10). The number indicates gland number per cm2. (B) QRT-PCR analysis of genes expression in VIGS plants (reference gene: actin).
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Figure 9. Silencing CGF1 causes glandless phenotype and down-regulated expression of GhMYC2-like and 6 NAC genes (reference gene: actin). (A) Phenotype of VIGS plants. (B) Expression analysis of CGF1, GhMYC2-like and 6 NAC genes by qRT-PCR. CGF1_At: CGF1 from A subgenome, CGF1_Dt: CGF1 from D subgenome.
Figure 9. Silencing CGF1 causes glandless phenotype and down-regulated expression of GhMYC2-like and 6 NAC genes (reference gene: actin). (A) Phenotype of VIGS plants. (B) Expression analysis of CGF1, GhMYC2-like and 6 NAC genes by qRT-PCR. CGF1_At: CGF1 from A subgenome, CGF1_Dt: CGF1 from D subgenome.
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Figure 10. Expression changes of 6 NAC genes after different stress treatments.
Figure 10. Expression changes of 6 NAC genes after different stress treatments.
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Figure 11. Predicted regulatory mechanism of 6 NAC genes. (A) Cis-elements analysis of 6 NAC gene promoters. (B) Predicted interaction network of 6 NAC proteins. (C) Putative binding motifs of 6 NAC proteins.
Figure 11. Predicted regulatory mechanism of 6 NAC genes. (A) Cis-elements analysis of 6 NAC gene promoters. (B) Predicted interaction network of 6 NAC proteins. (C) Putative binding motifs of 6 NAC proteins.
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Figure 12. Putative MYC-NAC regulatory network in pigment gland formation.
Figure 12. Putative MYC-NAC regulatory network in pigment gland formation.
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Cheng, H.; Feng, X.; Zuo, D.; Zhang, Y.; Wang, Q.; Lv, L.; Wu, C.; Li, S.; Dai, Y.; Qu, D.; et al. Gene Expression Correlation Analysis Reveals MYC-NAC Regulatory Network in Cotton Pigment Gland Development. Int. J. Mol. Sci. 2021, 22, 5007. https://doi.org/10.3390/ijms22095007

AMA Style

Cheng H, Feng X, Zuo D, Zhang Y, Wang Q, Lv L, Wu C, Li S, Dai Y, Qu D, et al. Gene Expression Correlation Analysis Reveals MYC-NAC Regulatory Network in Cotton Pigment Gland Development. International Journal of Molecular Sciences. 2021; 22(9):5007. https://doi.org/10.3390/ijms22095007

Chicago/Turabian Style

Cheng, Hailiang, Xiaoxu Feng, Dongyun Zuo, Youping Zhang, Qiaolian Wang, Limin Lv, Chaofeng Wu, Shuyan Li, Yuanli Dai, Da Qu, and et al. 2021. "Gene Expression Correlation Analysis Reveals MYC-NAC Regulatory Network in Cotton Pigment Gland Development" International Journal of Molecular Sciences 22, no. 9: 5007. https://doi.org/10.3390/ijms22095007

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