| Literature DB >> 34925390 |
Kangtai Sun1, Hui Fang1, Yu Chen2, Zhimin Zhuang1, Qi Chen1, Tingyu Shan1, Muhammad Kashif Riaz Khan3, Jun Zhang2, Baohua Wang1.
Abstract
Plant cytochrome P450 (P450) participates in a wide range of biosynthetic reactions and targets a variety of biological molecules. These reactions lead to various fatty acid conjugates, plant hormones, secondary metabolites, lignin, and various defensive compounds. In our previous research, transcriptome analysis was performed on the salt-tolerant upland cotton "Tongyan No. 1." Many differentially expressed genes (DEGs) belong to the P450 family, and their domains occur widely in plants. In this current research, P450 genes were identified in Gossypium hirsutum with the aid of bioinformatics methods for investigating phylogenetic relations, gene structure, cis-elements, chromosomal localization, and collinearity within a genome. qRT-PCR was conducted to analyze P450 gene expression patterns under salt stress. The molecular weights of the 156 P450 genes were in the range of 5,949.6-245,576.3 Da, and the length of the encoded amino acids for all the identified P450 genes ranged from 51 to 2,144. P450 proteins are divided into four different subfamilies based on phylogenetic relationship, gene structure, and chromosomal localization of gene replication. The length of P450 genes in upland cotton differs greatly, ranging from 1,500 to 13,000 bp. The number of exons in the P450 family genes ranged from 1 to 9, while the number of introns ranged from 0 to 8, and there were similar trends within clusters. A total of 31 cis-acting elements were identified by analyzing 1,500 bp promoter sequences. Differences were found in cis-acting elements among genes. The consistency between qRT-PCR and previous transcriptome analysis of salt tolerance DEGs indicated that they were likely to be involved in the salt tolerance of cotton seedlings. Our results provide valuable information on the evolutionary relationships of genes and functional characteristics of the gene family, which is beneficial for further study of the cotton P450 gene family.Entities:
Keywords: P450; cotton; differentially expressed genes; gene family; salt tolerance
Year: 2021 PMID: 34925390 PMCID: PMC8674417 DOI: 10.3389/fpls.2021.685054
Source DB: PubMed Journal: Front Plant Sci ISSN: 1664-462X Impact factor: 5.753
Primers of qRT-PCR for candidate genes.
| Gene ID | Forward primer | Reverse primer |
| Gh_D04G1016 | TGTCGTTCAAGCCAGAGA | GGTGAAGCAATGAGCCTAA |
| Gh_D05G0425 | GTTCAGCAACGACATCCT | ACCTCCTATCTCCACTTCTT |
| Gh_D12G0534 | CTACACTTATCTCCTCGTCTT | CTTCATTCGTCACTTCATCC |
| Gh_A09G0463 | AAGTCCAAGTGCTACAATCA | GCTCCTGCCAAGTTAGTAA |
| Gh_D04G1716 | GTGACTTAGCAACCAACATT | CATCAAGCCAACCGAGAA |
| Gh_A10G2124 | GCCACATCATACCTTCACT | ACCGACTCACTTCTTCATC |
FIGURE 1Phylogenetic tree of the P450 family protein sequences in upland cotton.
FIGURE 2Gene structure diagram of the P450 family in upland cotton. The three columns in the diagram are phylogenetic tree, motif, and exon in order from left to right.
FIGURE 3Upstream cis-acting elements of the P450 family genes in upland cotton.
Annotation of cis-acting elements at the 5′ end of P450 gene.
| Regulatory element | Core sequence | Element function |
| AAGAA-motif | GAAAGAA | Conserved sequence |
| ABRE | ACGTG | |
| AE-box | AGAAACTT | Part of a module for light response |
| AP-1 | TGAGTTAG | Conserved sequence |
| ATCT-motif | AATCTAATCC | Part of a conserved DNA module involved in light responsiveness |
| ABRE | ACGTG | |
| AT∼TATA-box | TATATA | Conserved sequence |
| CAAT-box | CCAAT | Common |
| CAG-motif | CAG-motif | Part of a light response element |
| CTAG-motif | ACTAGCAGAA | |
| CAT-box | GCCACT | |
| DRE | ||
| MYC | CATGTG | |
| TATA | TATAAAAT | |
| G-box | TACGTG | |
| GA-motif | ATAGATAA | Part of a light responsive element |
| GATA-motif | AAGGATAAGG | Part of a light responsive element |
| GT1-motif | GGTTAA | Light responsive element |
| Gap-box | CAAATGAA(A/G)A | Part of a light responsive element |
| HD-Zip 1 | CAAT(A/T)ATTG | Element involved in differentiation of the palisade mesophyll cells |
| MBS | CAACTG | MYB binding site involved in drought-inducibility |
| Myb | CAACTG | |
| MYB-like | TAACCA | |
| STRE | AGGGG | |
| Box II | ACACGTAGA | Part of a light responsive element |
| TATA-box | TATATTTATATTT | Core promoter element around -30 of transcription start |
| TCT-motif | TCTTAC | Part of a light responsive element |
| W box | TTGACC | |
| as-1 | TGACG | |
| box S | AGCCACC |
FIGURE 4Locations of the P450 genes on upland cotton chromosomes.
FIGURE 5Collinearity analysis of the whole upland cotton genome and P450 family genes.
FIGURE 6Expression patterns of the P450 family genes in the salt-tolerant transcriptome of upland cotton “Tongyan No. 1”.
FIGURE 7The relative expression levels of six candidate genes in upland cotton under salt stress. A asterisk on the bars indicate significant difference at 0.05 probability level by t test. **P ≤ 0.01, ****P ≤ 0.0001 in t-test.