Genome-wide identification and gene expression analysis of clade A protein phosphatase 2C family genes in Brassica juncea var. tumida

Abscisic acid (ABA) plays crucial roles in plant response to environmental stresses and development. The clade A phosphatases (PP2Cs) play a crucial role in ABA signaling. However, little is known about the details regarding clade A PP2Cs family genes in Brassica juncea var. tumida . Here, 20 clade A PP2Cs family genes were identified in tuber mustard genome, including BjuABI1s , BjuABI2s , BjuAHG1s , BjuAHG3s , BjuHAB1 , BjuHAB2s , BjuHAI1s , BjuHAI2s and BjuHAI3 . The promoters of clade A BjuPP2Cs family genes contained various of cis-acting elements, such as ABRE, GT1GMSCAM4, ARFAT and MYB1AT. We also analyzed the expression patterns of clade A BjuPP2Cs under abiotic stresses (low temperature, NaCl and ABA) treatment, pathogen Plasmodiophora brassicae treatment and different stages of stem swollen. The results suggested that clade A BjuPP2Cs regulated tuber mustard response to P. brassicae to mediate the formation of clubroot and might play roles in stem swelling and response to abiotic stresses. This study provides valuable information for further functional investigations of clade A PP2Cs family genes in B. juncea var. tumida .

Culture-independent analysis of the bacterial communities in Chinese fermented vegetables and genomic analysis of lactic acid bacteria

Six different fermented vegetables were collected from Zhejiang Province, China, to explore the associated bacterial communities using a high-throughput sequencing platform. A total of 24 phyla, 274 families and 569 genera were identified from six samples. Firmicutes and Proteobacteria were the main phyla in all of samples. Meanwhile, Brevibacterium was the major genus in Xiaoshan pickled radish. Lactobacillus-related genera and Vibrio were the major genera in fermented potherb mustard and its brine. Enterobacter and Cobetia were the major genera in fermented radish and its brine. Chromohalobacter was the major genus in the tuber mustard. These results indicated there were clear differences between the bacterial genera present in Xiaoshan pickled radish, fermented potherb mustard, fermented radish, and tuber mustard. This demonstrated the possible influences of raw materials and manufacturing processes. Furthermore, a large number of lactic acid bacteria were isolated and identified by culture-dependent and 16S rRNA gene sequence analysis, which accounted for more than 68% of all the isolates. In addition, whole genome analysis of Lactobacillus suantsaii, Lactobacillus sakei subsp. sakei, and Weissella cibaria showed they had large numbers of genes associated with carbohydrate metabolism. This may explain why these three bacterial strains can grow in fermented vegetable environments.

Maxent modelling for predicting climate change effects on the potential planting area of tuber mustard in China

Potential planting area for tuber mustard was simulated using the Maxent model under current and future conditions based on 591 coordinates and 22 environmental layers. Model accuracy was excellent, with area under the receiving operator curve values of 0.967 and 0.958 for model training and testing, respectively. Dominant factors were mean diurnal range, mean temperature of the coldest quarter, annual mean temperature and minimum temperature of the coldest month, with thresholds of 6.5–7.5, 5.5–9, 16–19 and 2.0–6.5 °C, respectively. Under current conditions, suitable habitat areas (2.16% of total land in China) were concentrated mainly in Central, Southwest and East China, which can be defined as three occurrence and diffusion centres. In the 2050s and 2070s, suitable habitat areas are predicted to change to 3.72 and 3.92%, and 3.60 and 3.73% under scenarios RCP4.5 and RCP6.0, respectively, indicating that suitable habitat areas will increase slightly. However, future distribution of tuber mustard was predicted to differ among provinces or cities, i.e. predicted suitable habitat areas in Sichuan Province increased up to the 2050s but remained relatively unchanged between the 2050s and 2070s; in Chongqing city they first increased and then decreased; in Hunan, Anhui, Jiangsu, Zhejiang and Fujian Provinces they increased continuously; and in Guizhou, Hubei, Jiangxi Provinces and Shanghai city they first decreased, and then increased. The results from the current study provide useful information for management decisions of tuber mustard.

Variations in the glucosinolates of the individual edible parts of three stem mustards ( Brassica juncea )

The composition and content of glucosinolates were investigated in the edible parts (petioles, peel and flesh) of tuber mustard, bamboo shoots mustard and baby mustard by high-performance liquid chromatography to reveal the association between the different cooking methods and their glucosinolate profiles. Eight glucosinolates were identified from tuber mustard and baby mustard, including three aliphatic glucosinolates, four indole glucosinolates and one aromatic glucosinolate. Only six of the eight glucosinolates were detected in bamboo shoots mustard. The results show that the distribution and content of glucosinolates varied widely among the different tissues and species. The highest contents of glucosinolates in tuber mustard, bamboo shoots mustard and baby mustard were found in flesh, petioles and peel, respectively. The content of total glucosinolates ranged from 5.21 µmol g –1 dry weight in bamboo shoots mustard flesh to 25.64 µmol g −1 dry weight in baby mustard peel. Aliphatic glucosinolates were predominant in the three stem mustards, followed by indole and aromatic glucosinolates. Sinigrin was the predominant glucosinolate in the three stem mustards. Sinigrin content in tuber mustard was slightly higher than that in baby mustard and much higher than that in bamboo shoots mustard, suggesting that the pungent-tasting stem mustards contained more sinigrin. In addition, a principal components analysis showed that bamboo shoots mustard was distinguishable from the other two stem mustards. A variance analysis indicated that the glucosinolates were primarily influenced by a species × tissue interaction. The correlations among glucosinolates were also analysed.

A tuber mustard AP2/ERF transcription factor gene, BjABR1, functioning in abscisic acid and abiotic stress responses, and evolutionary trajectory of the ABR1 homologous genes in Brassica species

The AP2/ERF superfamily of transcription factors is one of the largest transcription factor families in plants and plays an important role in plant development processes and stress responses. In this study, BjABR1, an AP2/ERF superfamily gene, from tuber mustard (Brassica juncea var. tumida Tsen et Lee), sharing high amino acid sequence similarity with the AtABR1 (Arabidopsis thaliana AP2-like abscisic acid repressor 1) gene, were performed functional research, and the ABR1 homologous genes in Brassica species were identified and performed phylogenetic analysis. The promoter sequence of BjABR1 contained many phytohormone- and stress-related cis-elements; ABA (abscisic acid) and abiotic stresses can induce BjABR1 expression in tuber mustard; overexpression of BjABR1 in Arabidopsis can alleviate plant sensitivity to ABA and salt and osmotic stresses, and the alleviation may be due to changes in stress/ABA-induced gene expression. These results indicated that BjABR1 functions in ABA and abiotic stress responses. By BLAST searches against the genome database of five Brassica species (three diploids, B. rapa, B. nigra, and B. oleracea, and two allotetraploid, B. juncea and B. napus) using the protein sequence of AtABR1, 3, 3, 3, 6, and 5 ABR1 homologous genes in B. nigra, B. rapa, B. oleracea, B. juncea, and B. napus were identified, respectively, and they shared high sequence similarity. By sequence analysis, annotation mistakes of the protein-coding regions of two ABR1 homologous genes, GSBRNA2T00134741001 and BjuB007684, were found and corrected. Then, the evolution analysis of these ABR1 homologous genes showed that the ancestor of the three diploid species had three ABR1 homologous genes and each diploid inherited all the three genes from their ancestor; then, allotetraploid B. juncea inherited all the six genes from B. rapa and B. nigra with no gene lost, while allotetraploid B. napus inherited all the three genes from B. oleracea and two genes from B. rapa with one gene lost, indicating that ABR1 homologous genes possessed greater hereditary conservation in Brassica species. The ABR1 homologous genes between B. rapa and B. oleracea shared much higher sequence similarity compared to that of B. nigra in diploid species, indicating that ABR1 homologous genes in B. nigra had experienced more rapid evolution, and B. rapa and B. oleracea may share closer relationship compared to B. nigra. Moreover, the spatial and temporal expression analysis of six ABR1 homologous genes of tuber mustard showed that they possessed different expression models. These results imply that ABR1 homologous genes are important to Brassica plants, and they may possess similar function in ABA and abiotic stress responses but play a role in different tissues and growing stages of plant. This study will provide the foundation to the functional research of ABR1 homologous genes in the Brassica species and help to reveal and understand the evolution mechanisms of Brassica species.