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

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.

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Genome-wide identification of the class III aminotransferase gene family in rice and expression analysis under abiotic stress

Genes & Genomics ◽

10.1007/s13258-013-0108-2 ◽

2013 ◽

Vol 35 (5) ◽

pp. 597-608 ◽

Cited By ~ 4

Author(s):

Jian Sun ◽

Dong-Wei Xie ◽

Hong-Wei Zhao ◽

De-Tang Zou

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Expression Analysis ◽

Class Iii ◽

Genome Wide

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Genome-Wide Identification and Expression Profiling of the PDI Gene Family Reveals Their Probable Involvement in Abiotic Stress Tolerance in Tomato (Solanum lycopersicum L.)

Genes ◽

10.3390/genes12010023 ◽

2020 ◽

Vol 12 (1) ◽

pp. 23

Author(s):

Antt Htet Wai ◽

Muhammad Waseem ◽

A B M Mahbub Morshed Khan ◽

Ujjal Kumar Nath ◽

Do Jin Lee ◽

...

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Stress Tolerance ◽

Solanum Lycopersicum ◽

Expression Profiling ◽

Abiotic Stress Tolerance ◽

Dependent Manner ◽

Solanum Lycopersicum L ◽

Genome Wide ◽

Protein Disulfide

Protein disulfide isomerases (PDI) and PDI-like proteins catalyze the formation and isomerization of protein disulfide bonds in the endoplasmic reticulum and prevent the buildup of misfolded proteins under abiotic stress conditions. In the present study, we conducted the first comprehensive genome-wide exploration of the PDI gene family in tomato (Solanum lycopersicum L.). We identified 19 tomato PDI genes that were unevenly distributed on 8 of the 12 tomato chromosomes, with segmental duplications detected for 3 paralogous gene pairs. Expression profiling of the PDI genes revealed that most of them were differentially expressed across different organs and developmental stages of the fruit. Furthermore, most of the PDI genes were highly induced by heat, salt, and abscisic acid (ABA) treatments, while relatively few of the genes were induced by cold and nutrient and water deficit (NWD) stresses. The predominant expression of SlPDI1-1, SlPDI1-3, SlPDI1-4, SlPDI2-1, SlPDI4-1, and SlPDI5-1 in response to abiotic stress and ABA treatment suggested they play regulatory roles in abiotic stress tolerance in tomato in an ABA-dependent manner. Our results provide new insight into the structure and function of PDI genes and will be helpful for the selection of candidate genes involved in fruit development and abiotic stress tolerance in tomato.

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Characterisation of the class III peroxidase gene family in carrot taproots and its role in anthocyanin and lignin accumulation

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2021.08.004 ◽

2021 ◽

Author(s):

Geng Meng ◽

Weiyao Fan ◽

Søren K. Rasmussen

Keyword(s):

Gene Family ◽

Class Iii ◽

Peroxidase Gene ◽

Lignin Accumulation ◽

Class Iii Peroxidase

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Genome-wide identification and expression analysis of the GA2ox gene family in maize (Zea mays L.) under various abiotic stress conditions

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2021.06.043 ◽

2021 ◽

Author(s):

Yidan Li ◽

Xiaohui Shan ◽

Zhilei Jiang ◽

Lei Zhao ◽

Fengxue Jin

Keyword(s):

Zea Mays ◽

Abiotic Stress ◽

Gene Family ◽

Expression Analysis ◽

Zea Mays L ◽

Stress Conditions ◽

Genome Wide

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Genome-wide analysis of the UNIVERSAL STRESS PROTEIN A gene family in Vitis and expression in response to abiotic stress

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2021.04.033 ◽

2021 ◽

Author(s):

Xiaoyue Cui ◽

Pingying Zhang ◽

Yafan Hu ◽

Chengcheng Chen ◽

Qiying Liu ◽

...

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Protein A ◽

Stress Protein ◽

Universal Stress Protein ◽

Genome Wide Analysis ◽

Genome Wide

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The PIN gene family in relic plant L. chinense: genome-wide identification and gene expression profiling in different organizations and abiotic stress responses

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2021.03.030 ◽

2021 ◽

Author(s):

Lingfeng Hu ◽

Pengkai Wang ◽

Xiaofei Long ◽

Weihuang Wu ◽

Jiaji Zhang ◽

...

Keyword(s):

Gene Expression ◽

Abiotic Stress ◽

Gene Family ◽

Gene Expression Profiling ◽

Stress Responses ◽

Expression Profiling ◽

Genome Wide

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Genome-Wide Identification, Evolutionary And Expression Analyses of LEA Gene Family In Peanut (Arachis Hypogaea L.)

10.21203/rs.3.rs-775523/v1 ◽

2021 ◽

Author(s):

RuoLan Huang ◽

Dong Xiao ◽

Xin Wang ◽

Yi Shen ◽

Jie Zhan ◽

...

Keyword(s):

Salicylic Acid ◽

Abiotic Stress ◽

Stress Response ◽

Gene Family ◽

Segmental Duplication ◽

Abiotic Stresses ◽

Tandem Duplication ◽

Critical Role ◽

Recognition Sites ◽

Genome Wide

Abstract Background: Late embryogenesis abundant (LEA) proteins are a group of highly hydrophilic glycine-rich proteins, which accumulate in the late stage of seed maturation and are associated with many abiotic stresses. However, few peanut LEA genes had been reported, and the research on the number, location, structure, molecular phylogeny and expression of AhLEAs was very limited. Results: In this study, 126 LEA genes were identified in the peanut genome through genome-wide analysis and were further divided into eight groups. Sequence analysis showed that most of the AhLEAs (85.7 %) had no or only one intron. LEA genes were randomly distributed on 20 chromosomes. Compared with tandem duplication, segmental duplication played a more critical role in AhLEAs amplication, and 93 segmental duplication AhLEAs and 5 pairs of tandem duplication genes were identified. Synteny analysis showed that some AhLEAs genes come from a common ancestor, and genome rearrangement and translocation occurred among these genomes. Almost all promoters of LEAs contain ABRE, MYB recognition sites, MYC recognition sites, and ERE cis-acting elements, suggesting that the LEA genes were involved in stress response. Gene expression analyses revealed that most of the LEAs were expressed in the late stages of peanut embryonic development. LEA3 (AH16G06810.1, AH06G03960.1), and Dehydrin (AH07G18700.1, AH17G19710.1) were highly expressed in roots, stems, leaves and flowers. Moreover, 100 AhLEAs were involved in response to drought, low-temperature, or Al stresses. Some LEAs that were regulated by different abiotic stresses were also regulated by hormones including ABA, brassinolide, ethylene and salicylic acid. Interestingly, AhLEAs that were up-regulated by ethylene and salicylic acid showed obvious subfamily preferences.Conclusions: AhLEAs are involved in abiotic stress response, and segmental duplication plays an important role in the evolution and amplification of AhLEAs. The genome-wide identification, classification, evolutionary and expression analyses of the AhLEA gene family provide a foundation for further exploring the LEA genes’ function in response to abiotic stress in peanuts.

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