Catalase (CAT) Gene Family in Rapeseed (Brassica napus L.): Genome-Wide Analysis, Identification, and Expression Pattern in Response to Multiple Hormones and Abiotic Stress Conditions

Abstract

Catalase (CAT) is an antioxidant enzyme expressed by the CAT gene family and exists in almost all aerobic organisms. Environmental stresses induce the generation of reactive oxygen species (ROS) that eventually hinder plant growth and development. The CAT enzyme translates the hydrogen peroxide (H2O2) to water (H2O) and reduce the ROS levels to shelter the cells' death. So far, the CAT gene family has not been reported in rapeseed (Brassica napus L.). Therefore, a genome-wide comprehensive analysis was conducted to classify the CAT genes in the rapeseed genome. The current study identified 14 BnCAT genes in the rapeseed genome. Based on phylogenetic and synteny analysis, the BnCATs belong to four groups (Groups I–IV). A gene structure and conserved motif analysis showed that Group I, Group II, and Group IV possess almost the same intron/exon pattern, and an equal number of motifs, while Group III contains diverse structures and contain 15 motifs. By analyzing the cis-elements in the promoters, we identified five hormone-correlated responsive elements and four stress-related responsive elements. Further, six putative bna-miRNAs were also identified, targeting three genes (BnCAT4, BnCAT6, and BnCAT8). Gene ontology (GO) enrichment analysis showed that the BnCAT genes were largely related to cellular organelles, ROS response, stimulus response, stress response, and antioxidant enzymes. Almost 10 BnCAT genes showed higher expression levels in different tissues, i.e., root, leaf, stem, and silique. The expression analysis showed that BnCAT1–BnCAT3 and BnCAT11–BnCAT13 were significantly upregulated by cold, salinity, abscisic acid (ABA), and gibberellic acid (GA) treatment, but not by drought and methyl jasmonate (MeJA). Notably, most of the genes were upregulated by waterlogging stress, except BnCAT6, BnCAT9, and BnCAT10. Our results opened new windows for future investigations and provided insights into the CAT family genes in rapeseed.

Genome-Wide Characterization of Glutathione Peroxidase (GPX) Gene Family in Rapeseed (Brassica napus L.) Revealed Their Role in Multiple Abiotic Stress Response and Hormone Signaling

“…For tissue-specific expression profiling, we downloaded RNA-seq data (BioProject ID: PRJCA001495, accessed on 1 July 2021) of rapeseed from the National Genomics Data Center. The complete method was described in a recent work [ 28 ]. Mainly, cuffquant and Cuffnorm were employed to create normalized counts in transcripts per million (TPM) values.…”

“…The seeds of the ZS11 genotype were obtained from Wuhan Zhongyou Seed Technology Co., Ltd., Wuhan, China. The stress treatments were performed as designated in previous work [ 28 ]. Briefly, the vigorous seeds were carefully chosen and sterilized with 10% hypochlorous acid solution for 5 min.…”

“…The BnACTIN was used as an internal control. The qRT-PCR reaction was performed as follows: 94 °C for 10 min, followed by 40 cycles of 94 °C for 15 s, 60 °C for 30 s, and 72 °C for 10 s. Each qRT-PCR reaction was carried out with three biological triplicates, and the data were observed using the 2 −ΔΔCT method [ 28 , 46 ]. All the primers used in this experiment are listed in Table S1 .…”

“…As defined in recent reports [28,29], two methods were employed to classify GPX genes in the Brassica napus genome, including BLASTP and the Hidden Markov Model (HMM) [28]. The sequence of Brassica napus genome was downloaded from the BnPIR database (http://cbi.hzau.edu.cn/bnapus/index.php, accessed on 1 July 2021) [30].…”

Genome-wide analysis and expression patterns of lipid phospholipid phospholipase gene family in Brassica napus L.

“…β-actin was used as an internal control, and all the primers used in the present study are listed in Additional file 1 . The qRT-PCR procedure was performed as follows: 94 °C for 10 min, followed by 40 cycles of 94 °C for 15 s, 60 °C for 30 s, 72 °C for 10 s. Each qRT-PCR reaction was carried out with three biological triplicates, and the data were examined using the 2 −△△CT method as described previously [ 54 , 55 ]. For tissue-specific expression profiling, we followed the same method as described earlier.…”