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Genome-wide identification and expression pattern analysis of lipoxygenase gene family in banana.

ABSTRACT: The LOX genes have been identified and characterized in many plant species, but studies on the banana LOX genes are very limited. In this study, we respectively identified 18 MaLOX, 11 MbLOX, and 12 MiLOX genes from the Musa acuminata, M. balbisiana and M. itinerans genome data, investigated their gene structures and characterized the physicochemical properties of their encoded proteins. Banana LOXs showed a preference for using and ending with G/C and their encoded proteins can be classified into 9-LOX, Type I 13-LOX and Type II 13-LOX subfamilies. The expansion of the MaLOXs might result from the combined actions of genome-wide, tandem, and segmental duplications. However, tandem and segmental duplications contribute to the expansion of MbLOXs. Transcriptome data based gene expression analysis showed that MaLOX1, 4, and 7 were highly expressed in fruit and their expression levels were significantly regulated by ethylene. And 11, 12 and 7 MaLOXs were found to be low temperature-, high temperature-, and Fusarium oxysporum f. sp. Cubense tropical race 4 (FocTR4)-responsive, respectively. MaLOX8, 9 and 13 are responsive to all the three stresses, MaLOX4 and MaLOX12 are high temperature- and FocTR4-responsive; MaLOX6 and MaLOX17 are significantly induced by low temperature and FocTR4; and the expression of MaLOX7 and MaLOX16 are only affected by high temperature. Quantitative real-time PCR (qRT-PCR) analysis revealed that the expression levels of several MaLOXs are regulated by MeJA and FocTR4, indicating that they can increase the resistance of banana by regulating the JA pathway. Additionally, the weighted gene co-expression network analysis (WGCNA) of MaLOXs revealed 3 models respectively for 5 (MaLOX7-11), 3 (MaLOX6, 13, and 17), and 1 (MaLOX12) MaLOX genes. Our findings can provide valuable information for the characterization, evolution, diversity and functionality of MaLOX, MbLOX and MiLOX genes and are helpful for understanding the roles of LOXs in banana growth and development and adaptations to different stresses.

SUBMITTER: Liu F

PROVIDER: S-EPMC8113564 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Turnip (Brassica rapa L. subsp. rapa) is an important crop with edible and medicinal values, and various stresses, especially salt stress and drought stress, seriously threaten the yield of turnips. LOXs play important roles in regulating plant growth and development, signal transduction, and biotic and abiotic stress responses through secondary metabolites produced by the oxylipin metabolic pathway, and although the turnip genome has been published, however, the role of LOX family genes in various abiotic stress responses has not been systematically studied in turnips. In this study, a total of 15 LOX genes (BrrLOX) were identified in turnip, distributed on six chromosomes. Phylogenetic tree analysis classified these LOX genes into two classes: three 9-LOX proteins and 12 13-LOX type II proteins. Gene duplication analysis showed that tandem and segmental duplication were the main pathways for the expansion of the BrrLOX gene family. The Ka and Ks values of the duplicated genes indicate that the BrrLOX gene underwent strong purifying selection. Further analysis of the cis-acting elements of the promoters suggested that the expression of the BrrLOX gene may be influenced by stress and phytohormones. Transcriptome data analysis showed that 13 BrrLOX genes were expressed at one or more stages of turnip tuber development, suggesting that LOX genes may be involved in the formation of turnip fleshy roots. The qRT-PCR analysis showed that four stresses (salt stress, drought stress, cold stress, and heat stress) and three hormone treatments (methyl jasmonate, salicylic acid, and abscisic acid) affected the expression levels of BrrLOX genes and that different BrrLOX genes responded differently to these stresses. In addition, weighted gene co-expression network analysis (WGCNA) of BrrLOX revealed seven co-expression modules, and the genes in these co-expression modules are collectively involved in plant growth and development and stress response processes. Thus, our results provide valuable information for the functional identification and regulatory mechanisms of BrrLOX in turnip growth and development and stress response.

Project description:ATP-binding cassette (ABC) transporter genes act as transporters for different molecules across biological membranes and are involved in a diverse range of biological processes. In this study, we performed a genome-wide identification and expression analysis of genes encoding ABC transporter proteins in three Capsicum species, i.e., Capsicum annuum, Capsicum baccatum and Capsicum chinense. Capsicum is a valuable horticultural crop worldwide as an important constituent of many foods while containing several medicinal compounds including capsaicin and dihydrocapsaicin. Our results identified the presence of a total of 200, 185 and 187 ABC transporter genes in C. annuum, C. baccatum and C. chinense genomes, respectively. Capsaicin and dihydrocapsaicin content were determined in green pepper fruits (16 dpa). Additionally, we conducted different bioinformatics analyses including ABC genes classification, gene chromosomal location, Cis elements, conserved motifs identification and gene ontology classification, as well as profile expression of selected genes. Based on phylogenetic analysis and domain organization, the Capsicum ABC gene family was grouped into eight subfamilies. Among them, members within the ABCG, ABCB and ABCC subfamilies were the most abundant, while ABCD and ABCE subfamilies were less abundant throughout all species. ABC members within the same subfamily showed similar motif composition. Furthermore, common cis-elements involved in the transcriptional regulation were also identified in the promoter regions of all Capsicum ABC genes. Gene expression data from RNAseq and reverse transcription-semi-quantitative PCR analysis revealed development-specific stage expression profiles in placenta tissues. It suggests that ABC transporters, specifically the ABCC and ABCG subfamilies, may be playing important roles in the transport of secondary metabolites such as capsaicin and dihydrocapsaicin to the placenta vacuoles, effecting on their content in pepper fruits. Our results provide a more comprehensive understanding of ABC transporter gene family in different Capsicum species while allowing the identification of important candidate genes related to capsaicin content for subsequent functional validation.

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Genome-wide identification and expression pattern analysis of lipoxygenase gene family in banana.

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