scholarly journals Genome-wide identification and expression profiling of durian CYPome related to fruit ripening

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260665
Author(s):  
Nithiwat Suntichaikamolkul ◽  
Lalida Sangpong ◽  
Hubert Schaller ◽  
Supaart Sirikantaramas
Keyword(s):  
Fruit Ripening ◽  
Expression Patterns ◽  
Biological Traits ◽  
Asian Countries ◽  
Plant Metabolites ◽  
Abscisic Acid Biosynthesis ◽  
Deep Mining ◽  
Durio Zibethinus ◽  
Climacteric Fruit ◽  
Genome Wide

Durian (Durio zibethinus L.) is a major economic crop native to Southeast Asian countries, including Thailand. Accordingly, understanding durian fruit ripening is an important factor in its market worldwide, owing to the fact that it is a climacteric fruit with a strikingly limited shelf life. However, knowledge regarding the molecular regulation of durian fruit ripening is still limited. Herein, we focused on cytochrome P450, a large enzyme family that regulates many biosynthetic pathways of plant metabolites and phytohormones. Deep mining of the durian genome and transcriptome libraries led to the identification of all P450s that are potentially involved in durian fruit ripening. Gene expression validation by RT-qPCR showed a high correlation with the transcriptome libraries at five fruit ripening stages. In addition to aril-specific and ripening-associated expression patterns, putative P450s that are potentially involved in phytohormone metabolism were selected for further study. Accordingly, the expression of CYP72, CYP83, CYP88, CYP94, CYP707, and CYP714 was significantly modulated by external treatment with ripening regulators, suggesting possible crosstalk between phytohormones during the regulation of fruit ripening. Interestingly, the expression levels of CYP88, CYP94, and CYP707, which are possibly involved in gibberellin, jasmonic acid, and abscisic acid biosynthesis, respectively, were significantly different between fast- and slow-post-harvest ripening cultivars, strongly implying important roles of these hormones in fruit ripening. Taken together, these phytohormone-associated P450s are potentially considered additional molecular regulators controlling ripening processes, besides ethylene and auxin, and are economically important biological traits.

Genome-wide identification and analysis of the MADS-box gene family and its potential role in fruit ripening in black raspberry (Rubus occidentalis L.)

2021 ◽  
pp. 1-15
Author(s):  
Yaqiong Wu ◽  
Chunhong Zhang ◽  
Wenlong Wu ◽  
Weilin Li ◽  
Lianfei Lyu
Keyword(s):  
Gene Family ◽  
Fruit Ripening ◽  
Fruit Development ◽  
Expression Patterns ◽  
Type I ◽  
Black Raspberry ◽  
Mads Box ◽  
Mads Box Genes ◽  
Genome Wide ◽  
Mads Box Gene

BACKGROUND: Black raspberry is a vital fruit crop with a high antioxidant function. MADS-box genes play an important role in the regulation of fruit development in angiosperms. OBJECTIVE: To understand the regulatory role of the MADS-box family, a total of 80 MADS-box genes were identified and analyzed. METHODS: The MADS-box genes in the black raspberry genome were analyzed using bioinformatics methods. Through an analysis of the promoter elements, the possible functions of different members of the family were predicted. The spatiotemporal expression patterns of members of the MADS-box family during black raspberry fruit development and ripening were systematically analyzed. RESULTS: The genes were classified into type I (Mα: 33; Mβ: 6; Mγ: 10) and type II (MIKC *: 2; MIKCC: 29) genes. We also obtained a complete overview of the RoMADS-box gene family through phylogenetic, gene structure, conserved motif, and cis element analyses. The relative expression analysis showed different expression patterns, and most RoMADS-box genes were more highly expressed in fruit than in other tissues of black raspberry. CONCLUSIONS: This finding indicates that the MADS-box gene family is involved in the regulation of fruit ripening processes in black raspberry.

scholarly journals Comprehensive genome-wide analysis of calmodulin-binding transcription activator (CAMTA) in Durio zibethinus and identification of fruit ripening-associated DzCAMTAs

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zahra Iqbal ◽  
Mohammed Shariq Iqbal ◽  
Lalida Sangpong ◽  
Gholamreza Khaksar ◽  
Supaart Sirikantaramas ◽  
...  
Keyword(s):  
Fruit Ripening ◽  
Developmental Process ◽  
Dependent Manner ◽  
Transcription Activator ◽  
Ripening Process ◽  
Post Harvest ◽  
Calmodulin Binding ◽  
Durio Zibethinus ◽  
Genome Wide ◽  
Recognition Motifs

Abstract Background Fruit ripening is an intricate developmental process driven by a highly coordinated action of complex hormonal networks. Ethylene is considered as the main phytohormone that regulates the ripening of climacteric fruits. Concomitantly, several ethylene-responsive transcription factors (TFs) are pivotal components of the regulatory network underlying fruit ripening. Calmodulin-binding transcription activator (CAMTA) is one such ethylene-induced TF implicated in various stress and plant developmental processes. Results Our comprehensive analysis of the CAMTA gene family in Durio zibethinus (durian, Dz) identified 10 CAMTAs with conserved domains. Phylogenetic analysis of DzCAMTAs, positioned DzCAMTA3 with its tomato ortholog that has already been validated for its role in the fruit ripening process through ethylene-mediated signaling. Furthermore, the transcriptome-wide analysis revealed DzCAMTA3 and DzCAMTA8 as the highest expressing durian CAMTA genes. These two DzCAMTAs possessed a distinct ripening-associated expression pattern during post-harvest ripening in Monthong, a durian cultivar native to Thailand. The expression profiling of DzCAMTA3 and DzCAMTA8 under natural ripening conditions and ethylene-induced/delayed ripening conditions substantiated their roles as ethylene-induced transcriptional activators of ripening. Similarly, auxin-suppressed expression of DzCAMTA3 and DzCAMTA8 confirmed their responsiveness to exogenous auxin treatment in a time-dependent manner. Accordingly, we propose that DzCAMTA3 and DzCAMTA8 synergistically crosstalk with ethylene during durian fruit ripening. In contrast, DzCAMTA3 and DzCAMTA8 antagonistically with auxin could affect the post-harvest ripening process in durian. Furthermore, DzCAMTA3 and DzCAMTA8 interacting genes contain significant CAMTA recognition motifs and regulated several pivotal fruit-ripening-associated pathways. Conclusion Taken together, the present study contributes to an in-depth understanding of the structure and probable function of CAMTA genes in the post-harvest ripening of durian.

scholarly journals Fruit ripening-associated leucylaminopeptidase with cysteinylglycine dipeptidase activity from durian suggests its involvement in glutathione recycling

2020 ◽  
Author(s):  
Pawinee Panpetch ◽  
Supaart Sirikantaramas
Keyword(s):  
Fruit Ripening ◽  
Kinetic Studies ◽  
Peptidase Activity ◽  
Fruit Pulp ◽  
Asian Countries ◽  
Ripe Fruit ◽  
Durio Zibethinus ◽  
Biochemical Characterisation ◽  
Genes Encoding ◽  
Dipeptidase Activity

Abstract BackgroundDurian (Durio zibethinus M.) is a highly popular fruit in Thailand and several other Southeast Asian countries. It is abundant in essential nutrients and several sulphur-containing compounds such as glutathione (GSH) and γ-glutamylcysteine (γ-EC). Cysteinylglycine (Cys-Gly) generated by GSH catabolism is also found in durian fruit pulp. Cysteine (Cys) is a precursor of the sulphur-containing volatiles produced during durian fruit ripening and accounting for the strong odour and flavour of the ripe fruit. However, the genes encoding plant Cys-Gly dipeptidases have seldom been identified. Our aim was to analyse the Cys-Gly peptidase activity of leucylaminopeptidase (LAP) in durian fruit pulp. ResultsDzLAP1 and DzLAP2 were identified, which the former was highly expressed in the fruit pulp. DzLAP1 expression at various ripening stages and in response to ethephon/1-MCP treatments suggested that DzLAP1 is active and important at the early stages of fruit ripening. Biochemical characterisation showed that DzLAP1 is a metalloenzyme activated by Mg2+ or Mn2+, is approximately 63 kDa in size, and has an optimal alkaline pH of 9.5 which is typical of LAPs. Kinetic studies revealed that DzLAP1 had a Km of 1.62 mM for its preferred substrate Cys-Gly. DzLAP1-GFP was localised to the cytosol and targeted to the plastids. ConclusionsDzLAP1 has Cys-Gly dipeptidase activity in the γ-glutamyl cycle. The present study discloses that the LAPs identified in durian fruit pulp are implicated in the high sulphur-containing compound levels observed at full ripening.

scholarly journals Fruit ripening-associated leucylaminopeptidase with cysteinylglycine dipeptidase activity from durian suggests its involvement in glutathione recycling

2020 ◽  
Author(s):  
Pawinee Panpetch ◽  
Supaart Sirikantaramas
Keyword(s):  
Fruit Ripening ◽  
Kinetic Studies ◽  
Fruit Pulp ◽  
Asian Countries ◽  
In Planta ◽  
Ripe Fruit ◽  
Durio Zibethinus ◽  
Ripening Stages ◽  
Genes Encoding ◽  
Dipeptidase Activity

Abstract Background: Durian ( Durio zibethinus L.) is a highly popular fruit in Thailand and several other Southeast Asian countries. It is abundant in essential nutrients and sulphur-containing compounds such as glutathione (GSH) and γ-glutamylcysteine (γ-EC). Cysteinylglycine (Cys-Gly) is produced by GSH catabolism and occurs in durian fruit pulp. Cysteine (Cys) is a precursor of sulphur-containing volatiles generated during fruit ripening. The aforementioned substances contribute to the strong odour and flavour of the ripe fruit. However, the genes encoding plant Cys-Gly dipeptidases are unknown. The aim of this study was to measure leucylaminopeptidase (LAP) activity in durian fruit pulp. Results: We identified DzLAP1 and DzLAP2, which the former was highly expressed in the fruit pulp. DzLAP1 was expressed at various ripening stages and in response to ethephon/1-MCP treatment. Hence, DzLAP1 is active at the early stages of fruit ripening. DzLAP1 is a metalloenzyme ~ 63 kDa in size. It is activated by Mg 2+ or Mn 2+ and, like other LAPs, its optimal alkaline pH is 9.5. Kinetic studies revealed that DzLAP1 has K m = 1.62 mM for its preferred substrate Cys-Gly. DzLAP1-GFP was localised to the cytosol and targeted the plastids. In planta Cys-Gly hydrolysis was confirmed for Nicotiana benthamiana leaves co-infiltrated with Cys-Gly and expressing DzLAP1 . Conclusions: DzLAP1 has Cys-Gly dipeptidase activity in the γ-glutamyl cycle. The present study revealed that the LAPs account for the high sulphur-containing compound levels identified in fully ripened durian fruit pulp.

scholarly journals Comparative and Expression Analysis of Ubiquitin Conjugating Domain-Containing Genes in Two Pyrus Species

Cells ◽  
2018 ◽  
Vol 7 (7) ◽  
pp. 77 ◽  
Author(s):  
Yunpeng Cao ◽  
Dandan Meng ◽  
Yu Chen ◽  
Muhammad Abdullah ◽  
Qing Jin ◽  
...  
Keyword(s):  
Fruit Ripening ◽  
Fruit Development ◽  
Expression Patterns ◽  
Orthologous Gene ◽  
Gene Families ◽  
Pyrus Communis ◽  
Functional Verification ◽  
Systematic Analysis ◽  
Gene Pairs ◽  
Genome Wide

Ripening affects the nutritional contents and quality of fleshy fruits, and it plays an important role during the process of fruit development. Studies have demonstrated that ubiquitin-conjugating (UBC or E2) genes can regulate fruit ripening, but the characterization of UBCs in pear is not well documented. The recently published genome-wide sequences of Pyrus bretschneideri and Pyrus communis have allowed a comprehensive analysis of this important gene family in pear. Using bioinformatics approaches, we identified 83 (PbrUBCs) and 84 (PcpUBCs) genes from P. bretschneideri and P. communis, respectively, which were divided into 13 subfamilies. In total, 198 PbrUBC paralogous, 215 PcpUBC paralogous, and 129 orthologous gene pairs were detected. Some paralogous gene pairs were found to be distributed on the same chromosome, suggesting that these paralogs may be caused by tandem duplications. The expression patterns of most UBC genes were divergent between Pyrus bretschneideri and Pyrus communis during pear fruit development. Remarkably, the transcriptome data showed that UBC genes might play a more important role in fruit ripening for further study. This is the first report on the systematic analysis of two Pyrus UBC gene families, and these data will help further study the role of UBC genes in fruit development and ripening, as well as contribute to the functional verification of UBC genes in pear.

scholarly journals Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Ryoichi Yano ◽  
Tohru Ariizumi ◽  
Satoko Nonaka ◽  
Yoichi Kawazu ◽  
Silin Zhong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruit Ripening ◽  
Expression Patterns ◽  
Rna Seq ◽  
Protein Coding ◽  
Genome Wide ◽  
Oxford Nanopore ◽  
Melon Genome ◽  
Number Variation ◽  
Genome Assemblies

AbstractMelon exhibits substantial natural variation especially in fruit ripening physiology, including both climacteric (ethylene-producing) and non-climacteric types. However, genomic mechanisms underlying such variation are not yet fully understood. Here, we report an Oxford Nanopore-based high-grade genome reference in the semi-climacteric cultivar Harukei-3 (378 Mb + 33,829 protein-coding genes), with an update of tissue-wide RNA-seq atlas in the Melonet-DB database. Comparison between Harukei-3 and DHL92, the first published melon genome, enabled identification of 24,758 one-to-one orthologue gene pairs, whereas others were candidates of copy number variation or presence/absence polymorphisms (PAPs). Further comparison based on 10 melon genome assemblies identified genome-wide PAPs of 415 retrotransposon Gag-like sequences. Of these, 160 showed fruit ripening-inducible expression, with 59.4% of the neighboring genes showing similar expression patterns (r > 0.8). Our results suggest that retrotransposons contributed to the modification of gene expression during diversification of melon genomes, and may affect fruit ripening-inducible gene expression.

scholarly journals Genome-wide identification and transcriptome profiling reveal that E3 ubiquitin ligase genes relevant to ethylene, auxin and abscisic acid are differentially expressed in the fruit of melting flesh and stony hard peach varieties

2019 ◽  
Author(s):  
Bin Tan ◽  
Xiaodong Lian ◽  
Jun Cheng ◽  
Wenfang Zeng ◽  
Xianbo Zheng ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Ubiquitin Ligase ◽  
Fruit Ripening ◽  
Expression Patterns ◽  
E3 Ligase ◽  
26S Proteasome ◽  
Differentially Expressed ◽  
Genome Wide ◽  
Stony Hard

Abstract Background Ubiquitin ligases (E3) are the enzymes in the ubiquitin/26S proteasome pathway responsible for targeting proteins to the degradation pathway and play major roles in multiple biological activities. However, the E3s family is still yet to be identified, and the functions of E3 ligase genes on fruit flesh are unknown in peach. Results In this study, genome-wide identification, classification and characterization of the E3 ligase genes within the genome of peach was carried out. In total, 765 E3 (PpE3) ligase genes were identified in the peach genome. The PpE3 ligase genes were divided into eight subfamilies according to the presence of known functional domains. The RBX subfamily was not detected in peach. The PpE3 ligase genes were not randomly distributed among the 8 chromosomes, with a greater concentration on the longer chromosomes. The primary mode of gene duplication of the PpE3 ligase genes was dispersed gene duplication (DSD). Four new types of proteins in the BTB subfamily were first identified in peach, namely BTBAND, BTBBL, BTBP and BTBAN. The expression patterns of the identified E3 ligase genes in two peach varieties that display different types of fruit softening (melting flesh, MF, and stony hard, SH) were analyzed at 4 different stages of ripening using Illumina technology. Among the 765 PpE3 ligase genes, 515 (67.3%) were expressed (FPKM >1) in either MF or SH during fruit ripening. In same-stage comparisons, 231 differentially expressed genes (DEGs) were identified between the two peach cultivars. The number of DEGs in each subfamily varied. Most DEGs were members of the BTB, F-box, U-box and RING subfamilies. PpE3 ligase genes predicted to be involved in ethylene, auxin, or ABA synthesis or signaling and DNA methylation were differentially regulated. Eight PpE3 ligase genes with possible roles in peach flesh texture and fruit ripening were discussed. Conclusions The results of this study provide useful information for further understanding the functional characterization of the ubiquitin ligase genes in peach. In addition, the findings also provide the first clues of E3 ligase gene function in the regulation of peach ripening.

scholarly journals Genome-Wide Identification and Characterization of the NAC Transcription Factor Family in Musa Acuminata and Expression Analysis during Fruit Ripening

2020 ◽  
Vol 21 (2) ◽  
pp. 634
Author(s):  
Bin Li ◽  
Ruiyi Fan ◽  
Qiaosong Yang ◽  
Chunhua Hu ◽  
Ou Sheng ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Fruit Ripening ◽  
Expression Patterns ◽  
Musa Acuminata ◽  
Nac Transcription Factor ◽  
Banana Fruit ◽  
Transcription Factor Family ◽  
Climacteric Fruit ◽  
Identification And Characterization

Banana (Musa acuminata, AAA group) is a representative climacteric fruit with essential nutrients and pleasant flavors. Control of its ripening determines both the fruit quality and the shelf life. NAC (NAM, ATAF, CUC2) proteins, as one of the largest superfamilies of transcription factors, play crucial roles in various functions, especially developmental processes. Thus, it is important to conduct a comprehensive identification and characterization of the NAC transcription factor family at the genomic level in M. acuminata. In this article, a total of 181 banana NAC genes were identified. Phylogenetic analysis indicated that NAC genes in M. acuminata, Arabidopsis, and rice were clustered into 18 groups (S1–S18), and MCScanX analysis disclosed that the evolution of MaNAC genes was promoted by segmental duplication events. Expression patterns of NAC genes during banana fruit ripening induced by ethylene were investigated using RNA-Seq data, and 10 MaNAC genes were identified as related to fruit ripening. A subcellular localization assay of selected MaNACs revealed that they were all localized to the nucleus. These results lay a good foundation for the investigation of NAC genes in banana toward the biological functions and evolution.

scholarly journals Genome-wide identification and transcriptome profiling reveal that E3 ubiquitin ligase genes relevant to ethylene, auxin and abscisic acid are differentially expressed in the fruits of melting flesh and stony hard peach varieties

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Bin Tan ◽  
Xiaodong Lian ◽  
Jun Cheng ◽  
Wenfang Zeng ◽  
Xianbo Zheng ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Ubiquitin Ligase ◽  
Fruit Ripening ◽  
Prunus Persica ◽  
Expression Patterns ◽  
E3 Ligase ◽  
26S Proteasome ◽  
Differentially Expressed ◽  
Genome Wide ◽  
Stony Hard

Abstract Background Ubiquitin ligases (E3) are the enzymes in the ubiquitin/26S proteasome pathway responsible for targeting proteins to the degradation pathway and play major roles in multiple biological activities. However, the E3 family and their functions are yet to be identified in the fruit of peach. Results In this study, genome-wide identification, classification and characterization of the E3 ligase genes within the genome of peach (Prunus persica) was carried out. In total, 765 E3 (PpE3) ligase genes were identified in the peach genome. The PpE3 ligase genes were divided into eight subfamilies according to the presence of known functional domains. The RBX subfamily was not detected in peach. The PpE3 ligase genes were not randomly distributed among the 8 chromosomes, with a greater concentration on the longer chromosomes. The primary mode of gene duplication of the PpE3 ligase genes was dispersed gene duplication (DSD). Four subgroups of the BTB subfamily never characterized before were newly identified in peach, namely BTBAND, BTBBL, BTBP and BTBAN. The expression patterns of the identified E3 ligase genes in two peach varieties that display different types of fruit softening (melting flesh, MF, and stony hard, SH) were analyzed at 4 different stages of ripening using Illumina technology. Among the 765 PpE3 ligase genes, 515 (67.3%) were expressed (FPKM > 1) in the fruit of either MF or SH during fruit ripening. In same-stage comparisons, 231 differentially expressed genes (DEGs) were identified between the two peach cultivars. The number of DEGs in each subfamily varied. Most DEGs were members of the BTB, F-box, U-box and RING subfamilies. PpE3 ligase genes predicted to be involved in ethylene, auxin, or ABA synthesis or signaling and DNA methylation were differentially regulated. Eight PpE3 ligase genes with possible roles in peach flesh texture and fruit ripening were discussed. Conclusions The results of this study provide useful information for further understanding the functional roles of the ubiquitin ligase genes in peach. The findings also provide the first clues that E3 ligase genes may function in the regulation of peach ripening.

scholarly journals Genome-wide identification and transcriptome profiling reveal that E3 ubiquitin ligase genes relevant to ethylene, auxin and abscisic acid are differentially expressed in the fruits of melting flesh and stony hard peach varieties

2019 ◽  
Author(s):  
Bin Tan ◽  
Xiaodong Lian ◽  
Jun Cheng ◽  
Wenfang Zeng ◽  
Xianbo Zheng ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Ubiquitin Ligase ◽  
Fruit Ripening ◽  
Prunus Persica ◽  
Expression Patterns ◽  
E3 Ligase ◽  
26S Proteasome ◽  
Differentially Expressed ◽  
Genome Wide ◽  
Stony Hard

Abstract Background: Ubiquitin ligases (E3) are the enzymes in the ubiquitin/26S proteasome pathway responsible for targeting proteins to the degradation pathway and play major roles in multiple biological activities. However, the E3 family is still yet to be identified, and the functions of E3 ligase genes on fruit flesh are unknown in peach. Results: In this study, genome-wide identification, classification and characterization of the E3 ligase genes within the genome of peach (Prunus persica) was carried out. In total, 765 E3 (PpE3) ligase genes were identified in the peach genome. The PpE3 ligase genes were divided into eight subfamilies according to the presence of known functional domains. The RBX subfamily was not detected in peach. The PpE3 ligase genes were not randomly distributed among the 8 chromosomes, with a greater concentration on the longer chromosomes. The primary mode of gene duplication of the PpE3 ligase genes was dispersed gene duplication (DSD). Four subgroups of the BTB subfamily never characterized before were newly identified in peach, namely BTBAND, BTBBL, BTBP and BTBAN. The expression patterns of the identified E3 ligase genes in two peach varieties that display different types of fruit softening (melting flesh, MF, and stony hard, SH) were analyzed at 4 different stages of ripening using Illumina technology. Among the 765 PpE3 ligase genes, 515 (67.3%) were expressed (FPKM >1) in the fruit of either MF or SH during fruit ripening. In same-stage comparisons, 231 differentially expressed genes (DEGs) were identified between the two peach cultivars. The number of DEGs in each subfamily varied. Most DEGs were members of the BTB, F-box, U-box and RING subfamilies. PpE3 ligase genes predicted to be involved in ethylene, auxin, or ABA synthesis or signaling and DNA methylation were differentially regulated. Eight PpE3 ligase genes with possible roles in peach flesh texture and fruit ripening were discussed. Conclusions: The results of this study provide useful information for further understanding the functional roles of the ubiquitin ligase genes in peach. The findings also provide the first clues that E3 ligase genes may function in the regulation of peach ripening.

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