Genome-Wide Analysis of the Peroxidase Gene Family and Verification of Lignin Synthesis-Related Genes in Watermelon

Abstract

Watermelon (Citrullus lanatus) is an important horticultural crop worldwide, but peel cracking caused by peel hardness severely decreases its quality. Lignification is one of the important functions of class III peroxidase (PRX), and its accumulation in the plant cell wall leads to cell thickening and wood hardening. For in-depth physiological and genetical understanding, we studied the relationship between peel hardness and lignin accumulation and the role of PRXs affecting peel lignin biosynthesis using genome-wide bioinformatics analysis. The obtained results showed that lignin accumulation gradually increased to form the peel stone cell structure, and tissue lignification led to peel hardness. A total of 79 ClPRXs (class III) were identified using bioinformatics analysis, which were widely distributed on 11 chromosomes. The constructed phylogenetics indicated that ClPRXs were divided into seven groups and eleven subclasses, and gene members of each group had highly conserved intron structures. Repeated pattern analysis showed that deletion and replication events occurred during the process of ClPRX amplification. However, in the whole-protein sequence alignment analysis, high homology was not observed, although all contained four conserved functional sites. Repeated pattern analysis showed that deletion and replication events occurred during ClPRXs’ amplification process. The prediction of the promoter cis-acting element and qRT-PCR analysis in four tissues (leaf, petiole, stem, and peel) showed different expression patterns for tissue specificity, abiotic stress, and hormone response by providing a genetic basis of the ClPRX gene family involved in a variety of physiological processes in plants. To our knowledge, we for the first time report the key roles of two ClPRXs in watermelon peel lignin synthesis. In conclusion, the extensive data collected in this study can be used for additional functional analysis of ClPRXs in watermelon growth and development and hormone and abiotic stress response.

Genome-Wide Identification and Analysis of the Class III Peroxidase Gene Family in Tobacco (Nicotiana tabacum)

“…Based on phylogenetic relationships, the NtPOD family was categorized into six subgroups. Notably, subgroup VI was characterized by multiple exons and different motifs from the other five subgroups, which was consistent with previous studies in cassava ( Wu et al, 2019 ), Chinese pear ( Cao et al, 2016 ), and watermelon ( Yang et al, 2022 ). Therefore, we inferred that POD subgroup VI may have similar origins with other plants and have some specific functions in plants.…”

Development of Whole Genome SNP-CAPS Markers and Preliminary QTL Mapping of Fruit Pedicel Traits in Watermelon

“…In China, fresh and premium-grade marketable cucumbers should account for <14% of the total fruit length (1/7 part) (Zhou et al, 2005 ). Further, mature lengthy pedicel with more diameter can grasp the large and heavy weighted fruits (Solomon et al, 2021 ) because endogenous lignification gradually modifies the cell tissue structure which led to stem hardness (Yang et al, 2022 ). In cucumbers, the key to efficient mechanical harvesting depends upon the differentiation between mature FPS, leaves, and main stems; however, lengthy pedicel provides more feasibility for this kind of procedure by proper gripping, and detachment of fruit from the pedicel (Song et al, 2016 ).…”

Comparative Transcriptome Analysis Identified Key Pathways and Genes Regulating Differentiated Stigma Color in Melon (Cucumis melo L.)

“…First strand complementary DNA (cDNA) was synthesized from 100 ng of total isolated RNA using the TRUEscript 1st Stand cDNA Synthesis Kit (Aidlab, Beijing, China) [ 65 ]. The gene primers were designed using Primer Premier 6.0 software, and relative expression levels of 5 key genes of the chlorophyll synthesis pathway were analyzed, and transcriptome data between MR-1 and M4-7 was validated using qRT-PCR.…”