Genome-wide identification of MAPK family in papaya (Carica papaya) and their involvement in fruit postharvest ripening

Abstract

Background: Papaya (Carica papaya) is an economically important fruit cultivated in the tropical and subtropical regions of China. However, the rapid softening rate after postharvest leads to a short shelf-life and considerable economic losses. Accordingly, understanding the mechanisms underlying fruit postharvest softening will be a reasonable way to maintain fruit quality and extend its shelf-life.

Results: Mitogen-activated protein kinases (MAPKs) are conserved and play essential roles in response to biotic and abiotic stresses. However, the MAPK family remain poorly studied in papaya. Here, a total of nine putative CpMAPK members were identified within papaya genome, and a comprehensive genome-wide characterization of the CpMAPKs was performed, including evolutionary relationships, conserved domains, gene structures, chromosomal locations, cis-regulatory elements and expression profiles in response to phytohormone and antioxidant organic compound treatments during fruit postharvest ripening. Our findings showed that nearly all CpMAPKs harbored the conserved P-loop, C-loop and activation loop domains. Phylogenetic analysis showed that CpMAPK members could be categorized into four groups (A-D), with the members within the same groups displaying high similarity in protein domains and intron-exon organizations. Moreover, a number of cis-acting elements related to hormone signaling, circadian rhythm, or low-temperature stresses were identified in the promoters of CpMAPKs. Notably, gene expression profiles demonstrated that CpMAPKs exhibited various responses to 2-chloroethylphosphonic acid (ethephon), 1-methylcyclopropene (1-MCP) and the combined ascorbic acid (AsA) and chitosan (CTS) treatments during papaya postharvest ripening. Among them, both CpMAPK9 and CpMAPK20 displayed significant induction in papaya flesh by ethephon treatment, and were pronounced inhibition after AsA and CTS treatments at 16 d compared to those of natural ripening control, suggesting that they potentially involve in fruit postharvest ripening through ethylene signaling pathway or modulating cell wall metabolism.

Conclusion: This study will provide some valuable insights into future functional characterization of CpMAPKs, and hold great potential for further understanding the molecular mechanisms underlying papaya fruit postharvest ripening.

Keywords: 1-methylcyclopropene (1-MCP); Ethephon; Fruit ripening; Gene expression; Genome-wide analysis; Mitogen-activated protein kinase (MAPK); Papaya.

Fig. 1

Multiple sequence alignment of the conserved kinase domains of CpMAPKs. The multiple alignment is conducted using ClustalX, and is presented using GeneDoc. The eleven conserved kinase domains that have been found among plant MAPKs are indicated by Roman numerals (I to XI). The conserved loop domains, including P-loop, C-loop, activation loop and CD-domain, are shown in red boxes. The first two letters of each MAPK indicate the abbreviated species name. At: Arabidopsis thaliana; Zm: Zea mays; Os: Oryza sativa; Cp: Carica papaya

Fig. 2

Phylogenetic analysis of MAPK proteins in plants. The phylogenetic tree was constructed using MEGA 11 program with the neighbor-joining method, and bootstrap value is set to 1000, which is indicated as percentages for the branches. The first two letters of each MAPK indicate the abbreviated species name. Zm: Zea mays; At: Arabidopsis thaliana; Bd: Brachypodium distachyon; Ma: Musa acuminata; Md: Malus domestica; Br: Brassica rapa; Cp: Carica papaya. The members of CpMAPK family are separately indicated by red stars

Fig. 3

Analysis of gene structures and protein structures of CpMAPKs in papaya. A Gene structure analysis of CpMAPKs. The exons of CpMAPKs were indicated by the yellow boxes, and the introns were indicated by the middle lines. B Conserved motif and domain analysis of CpMAPKs. C Analysis of conserved amino acids of motifs. The upper case in the left panel indicated the different subgroups of CpMAPKs in phylogenetic tree

Fig. 4

The Cis-regulatory elements analysis of CpMAPK genes. A The distribution of cis-elements of CpMAPKs. B The number of cis-elements of CpMAPKs. ABRE: abscisic acid-responsive element; CGTCA/TGACG-motif: MeJA-responsive elements; MYB/MBS/MBSI: MYB transcription factor binding sites; MYC: MYC transcription factors binding sites; TATC-box/GARE-motif/P-box: gibberellin-responsive element; TCA-element: salicylic acid-responsive element; TGA-box: auxin-responsive element; LTR: low-temperature-responsive element; MSA-like: cell cycle regulation; ERE: ethylene-responsive element; Circadian: circadian control

Fig. 5

Effects of 1-MCP and ethephon on fruit firmness, respiration rate and ethylene production during papaya fruit postharvest ripening. A Appearance of papaya fruits during natural, 1-MCP-delayed and ethephon-induced ripening. B Changes in firmness. C Respiration rate. D Ethylene production rate. The green-mature papaya fruits were harvested, and then separately treated with 0.5 g/L ethephon for 5 min, and 0.5 μL/L 1-MCP for 2 h. The untreated fruits were used as a control. Each experiment was conducted with three biological replicates, and each replicate with three fruits. The red asterisks indicate significant differences between CK and 1-MCP treatments, and black asterisks indicate significant differences between CK and ethephon treatments by Student’s t-test: * P < 0.05; ** P < 0.01; *** P < 0.001, respectively

Fig. 6

The expression levels of CpMAPKs in fruit flesh in response to ethephon (ETH) and 1-MCP treatment. The papaya flesh tissues were sampled at 0, 3, 6 and 9 d after being subjected to ethephon and 1-MCP treatment. The relative expression levels were determined by qRT-PCR, and calculated by ΔΔC_t method. The red asterisks indicate significant differences between CK and 1-MCP treatments, and black asterisks indicate significant differences between CK and ethephon treatments by Student’s t-test: * P < 0.05; ** P < 0.01, respectively

Fig. 7

The expression levels of CpMAPKs in papaya flesh in response to the combined treatment of AsA and chitosan. The papaya fruit tissues were sampled at 0, 8 and 16 d after being subjected to AsA and CTS treatment. Untreated fruits were used as a control. The relative expression levels were determined by qRT-PCR, and calculated by ΔΔC_t method. The asterisks indicate significant differences between CK and AsA + CTS combined treatments by Student’s t-test: * P < 0.05; ** P < 0.01, respectively