Genome-wide identification and expression analysis of genes associated with peach (Prunus persica) fruit ripening

2019 ◽  
Vol 246 ◽  
pp. 317-327 ◽  
Author(s):  
Maosong Pei ◽  
Chao Gu ◽  
Shaoling Zhang
Keyword(s):  
Expression Analysis ◽  
Fruit Ripening ◽  
Prunus Persica ◽  
Genome Wide

scholarly journals Genome-Wide Identification of Mango (Mangifera indica L.) Polygalacturonases: Expression Analysis of Family Members and Total Enzyme Activity During Fruit Ripening

2019 ◽  
Vol 10 ◽  
Author(s):  
Mitzuko Dautt-Castro ◽  
Andrés G. López-Virgen ◽  
Adrian Ochoa-Leyva ◽  
Carmen A. Contreras-Vergara ◽  
Ana P. Sortillón-Sortillón ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Expression Analysis ◽  
Fruit Ripening ◽  
Mangifera Indica ◽  
Family Members ◽  
Total Enzyme Activity ◽  
Genome Wide ◽  
Total Enzyme

Genome-wide expression analysis at three fruit ripening stages for tomato genotypes differing in fruit shelf life

2018 ◽  
Vol 229 ◽  
pp. 125-131 ◽  
Author(s):  
J.H. Pereira da Costa ◽  
G.R. Rodríguez ◽  
L.A. Picardi ◽  
R. Zorzoli ◽  
G.R. Pratta
Keyword(s):  
Shelf Life ◽  
Expression Analysis ◽  
Fruit Ripening ◽  
Ripening Stages ◽  
Genome Wide ◽  
Fruit Shelf Life ◽  
Genome Wide Expression ◽  
Tomato Genotypes

Genome-wide identification, characterization and expression analysis of NF-Y gene family in relation to fruit ripening in banana

2019 ◽  
Vol 151 ◽  
pp. 98-110 ◽  
Author(s):  
Huiling Yan ◽  
Fuwang Wu ◽  
Guoxiang Jiang ◽  
Lu Xiao ◽  
Zhiwei Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Fruit Ripening ◽  
Genome Wide

scholarly journals Genome-Wide Identification of the Vacuolar H+-ATPase Gene Family in Five Rosaceae Species and Expression Analysis in Pear (Pyrus bretschneideri)

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1661
Author(s):  
Hongsheng Zhou ◽  
Wen Huang ◽  
Shufen Luo ◽  
Huali Hu ◽  
Yingtong Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Prunus Persica ◽  
Proton Pumps ◽  
Event Analysis ◽  
Specific Expression ◽  
Rosaceae Species ◽  
Genome Wide ◽  
A Genome ◽  
Atpase Gene

Vacuolar H+-ATPases (V-ATPase) are multi-subunit complexes that function as ATP hydrolysis-driven proton pumps. They play pivotal roles in physiological processes, such as development, metabolism, stress, and growth. However, there have been very few studies on the characterisation of V-ATPase (VHA) genes in Rosaceae species. Therefore, in the present study, we performed a genome-wide analysis and identified VHA gene family members in five Rosaceae species (Pyrus bretschneideri, Malus domestica, Prunus persica, Fragaria vesca, and Prunus mume). A total of 159 VHA genes were identified, and were classified into 13 subfamilies according to the phylogenetic analysis. The structure of VHA proteins revealed high similarity among different VHA genes within the same subgroup. Gene duplication event analysis revealed that whole-genome duplications represented the major pathway for expansion of the Pyrus bretschneideri VHA genes (PbrVHA genes). The tissue-specific expression analysis of the pear showed that 36 PbrVHA genes were expressed in major tissues. Seven PbrVHA genes were significantly downregulated when the pollen tube growth stopped. Moreover, many PbrVHA genes were differentially expressed during fruit development and storage, suggesting that VHA genes play specific roles in development and senescence. The present study provides fundamental information for further elucidating the potential roles of VHA genes during development and senescence.

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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