Genome-wide identification of the DUF668 gene family in cotton and expression profiling analysis of GhDUF668 in Gossypium hirsutum under adverse stress

- Genome-wide identification of the DUF668 gene family in cotton and expression.
- However, our knowledge of the function of the DUF668 gene family is limited..
- Gene structure and motif analyses revealed that the members of the DUF668 gene family can be clustered in G.
- Among them, the expression levels of Gh_DUF668–08 and Gh_DUF668–23 increased sharply at 6 h and reached a maximum at 12 h under biotic and abiotic stress, which showed that they might be involved in the process of adverse stress resistance in cotton..
- This study provides an important theoretical basis for further research on the function of the DUF668 gene family and the molecular mechanism of adverse stress resistance in cotton..
- Overexpression of the salt-inducing gene TaSRHP (con- taining the DUF581 domain) in wild-type Arabidopsis can enhance its resistance to salt and drought stress [21].
- Although some members of the DUF gene family have been identified, a great number of DUF members are still unknown, especially in cotton.
- At present, all of the major cotton areas worldwide are threatened by varying degrees of salt, al- kali, drought, cold damage and disease [26–30].
- In this study, members of the DUF668 family were system- atically identified, and bioinformatic analyses were per- formed based on cotton genome data.
- Chromosome distribution, gene replication, promoter cis-acting ele- ments, and expression profiles of the GhDUF668 gene were analyzed in different tissues and under various stresses.
- The results will further broaden our under- standing of the roles of DUF668 genes in plants, provid- ing a basis for further research on the functions of these genes in cotton under adverse stresses and laying a foun- dation for the subsequent analysis of their functions..
- Identification of the DUF668 gene family from cotton To investigate the copy number variation in the DUF668 genes during cotton evolution, a comprehen- sive search was conducted for DUF668 genes across cotton lineages, including G.
- The results were verified in the NCBI-CDD database (Figure S1).
- In the end, there were and 33 sequences in G.
- The DUF668 fam- ily genes in two diploid cotton species are basically half of the number in two tetraploid cotton species, which conforms to the known evolutionary.
- relationship of cotton [24, 25], indicating that the DUF668 family is conserved in the evolution of cot- ton.
- Gh_DUF668–01 ~ Gh_DUF668–32 were named according to the position of the 32 sequences on the chromosome (Table 1) in G.
- The open reading frame (ORF) of the DUF668 family genes in G.
- Each of the family members.
- The number of GhDUF668 genes in subge- nome A was consistent with the number of GaDUF668 genes, and two of the DUF668 genes were missing from subgenome D compared to the number of GrDUF668 genes.
- This result showed that the DUF668 genes might have been lost and duplicated in the process of evolution.
- Phylogenetic analysis of the DUF668 gene family in cotton.
- To explore the phylogenetic relationship of the cotton DUF668 genes, a phylogenetic tree was constructed..
- All of the DUF668 proteins can be divided into 4 subgroups (Fig.
- This was consistent with the results of the previous analysis and conforms to the evolutionary rela- tionship in cotton.
- 1 Chromosome locations of the G.
- Except for the Gh_DUF668–30 gene, one sequence for the DUF668 family genes in the subgenome D in G.
- analytical results of the DUF668 family genes in the A subgroup.
- 2 Phylogenic tree of the DUF668 family members in G.
- Motif 1 and 9 are specific elements of the fourth branch, motif 2 and 4 are specific sequences in addition to the fourth branch.
- Phylogenic tree, motif and gene structure of the DUF6688 genes in G.
- The phylogenetic tree, gene structure and motif were analyzed according to the full-length coding sequence (CDS) and protein sequence of the GhDUF668 genes (Fig.
- the rest of the members had the same motif .
- The difference between the structures of GhDUF and 32 in the same group might be due to changes in the function of the gene or errors in genome annotation.
- Cis-acting element analysis of the DUF668 gene in G..
- The 2000 bp promoter region upstream of the GhDUF668 genes was extensively analyzed.
- Our analysis of the expression patterns of the GhDUF668 gene in roots, stems, leaves, pistils, stamens, calyxes, petals and receptacles in cotton showed that most of the selected 32 GhDUF668 genes had tissue expression specificity (Fig.
- The rest were classified as the third expression pattern, and the expression level of the eight tissues in this pattern was.
- The gene expression of the GhDUF668 genes was specific and contained more complex functions..
- Expression analysis of the DUF668 gene in G.
- The expression analysis of the GhDUF668 genes after cold, heat, drought and salt treatment showed that the expression patterns of the GhDUF668 genes can be divided into three categories (Fig.
- These genes might play a corresponding role in the response to cold stress in G.
- Although most of the genes had obvious expression changes and reached their maximum at 12 h, RNA-seq measurement was performed at only 12 h..
- In summary, the expression levels of approxi- mately half of the GhDUF668 genes significantly changed with higher tissue-specific expression levels under abiotic stress conditions.
- genes might play a role in the abiotic stress response of G..
- 7 Expression analysis of the DUF668 genes from G.
- 8 Expression analysis of the DUF668 genes from G.
- dah- liae treatment in the early stage of cotton.
- Response of the DUF668 gene in G.
- Our previous analysis showed that most of the expression of the GhDUF668 genes undergoes sig- nificant changes under stress treatment conditions..
- We selected KK 1543 (drought-resist- ant), Xinluzao 26 (drought-susceptible), Zhongzhimian 2 (disease-resistant) [28] and Simian 3 (disease-suscep- tible) (unpublished) to determine whether these genes were involved in the response to adverse stress.
- Thus, the expression levels were significantly increased, suggesting that these genes might participate in the process of responding to the in- vasion of V991 in cotton.
- Minor changes in the expression levels of the other three genes were observed.
- In summary, these five genes might play a role in the process of responding to the invasion of V.
- 9 Expression profiling of the GhDUF668 genes in root tissue under drought and Verticillium wilt conditions.
- In summary, these 5 genes might have a role in the drought stress response in cotton.
- This implied that the expression of these genes was regulated by adverse stresses and might play a certain role in the process of responding to adverse stress in G.
- The expression levels of GhDUF668–08 and GhDUF668–23 were significantly upregulated among the five genes in the same period.
- This further shows that GhDUF668–08 and GhDUF668–23 might play certain roles in the response to biotic and abiotic stress in cotton..
- Tissue-specific expression analysis of the DUF668 gene in G.
- The first part of the plants to sense the response to drought stress and pathogen invasion is the root.
- 08 and GhDUF668–23 genes changed significantly in the roots.
- This result showed that the increased expression of the GhDUF668 genes in the roots was likely to en- hance cotton resistance.
- 10 Tissue-specific expression analysis of the GhDUF668 genes under drought and Verticillium wilt stress.
- the certain role of the GhDUF668 genes in stress resistance..
- This study further deepens the knowledge of cotton genomics and genetics, providing the possibility to discover members of the DUF668 gene family in cotton and their phylogenetic re- lationships.
- This might contribute to the double duplication of the cotton genome, or it might be that more genes were an- notated in cotton than in other species .
- Although the second broad group contains the same number of CDS and motif except for Gh_DUF668–06, from the perspective of the full length of genes, the number and length of similar CDS have different gene lengths, indicating that the intron length has a larger difference.
- These results indicate that this gene family plays a more important role in the growth and development of cotton..
- Moreover, analysis of the gene expression in different tissues and the molecular.
- However, minor changes in the stems and leaves were observed.
- DUF668–08 and Gh_DUF668–23 had the most obvi- ous changes in the roots..
- The results indi- cate that Gh_DUF668–08 and Gh_DUF668–23 play leading roles in the response to biotic and abiotic stresses in cotton..
- In this study, cotton DUF668 genes were identified in the whole genome.
- Thirty-two DUF668 genes were observed in the G.
- 08 and GhDUF668–23 , which might play leading roles in the response of biotic and abiotic stress in cotton..
- The middle and lower parts of the pot were cut with a small knife in the two-leaf stage to ensure that the roots were damaged, then V.
- The root tissues of the two treatments were collected at and 72 h..
- Identification and bioinformatics analysis of the cotton DUF668 gene.
- The number of amino acid residues, relative molecular mass, and theoret- ical isoelectric point of the GhDUF668 protein were calcu- lated by ExPASy software (http://cn.expasy.org/tools) [58]..
- Subcellular localization of the GhDUF668 protein was predicted by EuLoc online software (http://euloc.mbc..
- Phylogeny and collinearity analysis of the cotton DUF668 gene family.
- A phylogenetic tree was constructed based on the results of the sequence align- ment by using neighbor-joining (NJ), and the bootstrap value setting was 1000 [60].
- The chromosomal posi- tions and collinearity of the DUF668 genes in cotton were visualized through Circos (http://circos.ca/)..
- Chromosome location, gene structure and motif analysis of the DUF668 gene family in G.
- hirsutum genome annotation file, and the chromosome location map of the GhDUF668 gene was redrawn with Mapchart software [62].
- The phylogenetic tree of the GhDUF668 genes was constructed, and the nwk file was obtained through MEGA7 software.
- Analysis of upstream cis-acting elements of the DUF668 gene.
- The upstream DNA sequences (2000 bp) of the GhDUF668 genes were obtained.
- The ex- pression data were analyzed by standard analysis of the transcriptome on the raw data [66–68].
- According to the cDNA information of the GhDUF668 genes, primers in the specific region were designed at.
- the 5′ end or 3′ end of the gene sequence with Primer 5.0 software (Table S4).
- The relative RNA transcript levels of the candidate genes were calculated ac- cording to the 2 −ΔΔ CT method [69]..
- Then, the homologous genes of Gossypium hirsutum were screened out by a comparison of the interaction genes from Arabidopsis in COTTONGEN (http://www..
- Distribution of the DUF668 domain in the DUF668 proteins of cotton..
- The funding agencies played no role in the design of the study, data collection or analysis, or interpretation or writing of the manuscript..
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- Genome-wide identification of cyclophilin gene family in cotton and expression analysis of the fibre development in Gossypium barbadense .
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