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Comparative Transcriptome Analysis of Cultivated and Wild Watermelon during Fruit Development.

Guo S, Sun H, Zhang H, Liu J, Ren Y, Gong G, Jiao C, Zheng Y, Yang W, Fei Z, Xu Y - PLoS ONE (2015)

Bottom Line: To systematically understand the molecular basis of these differences, we compared transcriptome profiles of fruit tissues of cultivated watermelon 97103 and wild watermelon PI296341-FR.In addition, we found that genes in the ethylene biosynthesis and signaling pathway including ACC oxidase, ethylene receptor and ethylene responsive factor showed highly ripening-associated expression patterns, indicating a possible role of ethylene in fruit development and ripening of watermelon, a non-climacteric fruit.Furthermore, the comparative expression profile data we developed provides a valuable resource to accelerate functional studies in watermelon and facilitate watermelon crop improvement.

View Article: PubMed Central - PubMed

Affiliation: Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), National Engineering Research Center for Vegetables, Beijing, China.

ABSTRACT
Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an important vegetable crop world-wide. Watermelon fruit quality is a complex trait determined by various factors such as sugar content, flesh color and flesh texture. Fruit quality and developmental process of cultivated and wild watermelon are highly different. To systematically understand the molecular basis of these differences, we compared transcriptome profiles of fruit tissues of cultivated watermelon 97103 and wild watermelon PI296341-FR. We identified 2,452, 826 and 322 differentially expressed genes in cultivated flesh, cultivated mesocarp and wild flesh, respectively, during fruit development. Gene ontology enrichment analysis of these genes indicated that biological processes and metabolic pathways related to fruit quality such as sweetness and flavor were significantly changed only in the flesh of 97103 during fruit development, while those related to abiotic stress response were changed mainly in the flesh of PI296341-FR. Our comparative transcriptome profiling analysis identified critical genes potentially involved in controlling fruit quality traits including α-galactosidase, invertase, UDP-galactose/glucose pyrophosphorylase and sugar transporter genes involved in the determination of fruit sugar content, phytoene synthase, β-carotene hydroxylase, 9-cis-epoxycarotenoid dioxygenase and carotenoid cleavage dioxygenase genes involved in carotenoid metabolism, and 4-coumarate:coenzyme A ligase, cellulose synthase, pectinesterase, pectinesterase inhibitor, polygalacturonase inhibitor and α-mannosidase genes involved in the regulation of flesh texture. In addition, we found that genes in the ethylene biosynthesis and signaling pathway including ACC oxidase, ethylene receptor and ethylene responsive factor showed highly ripening-associated expression patterns, indicating a possible role of ethylene in fruit development and ripening of watermelon, a non-climacteric fruit. Our analysis provides novel insights into watermelon fruit quality and ripening biology. Furthermore, the comparative expression profile data we developed provides a valuable resource to accelerate functional studies in watermelon and facilitate watermelon crop improvement.

No MeSH data available.


Venn diagram of differentially expressed genes in three tissues during watermelon fruit development.
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pone.0130267.g002: Venn diagram of differentially expressed genes in three tissues during watermelon fruit development.

Mentions: RNA-Seq is powerful and efficient for large-scale gene expression analysis. In this study, we found that 18,198 (77.6%), 18,392 (78.5%) and 17,954 (76.6%) genes were expressed in the flesh and mesocarp of 97103 fruit and the flesh of PI296341-FR fruit, respectively. The number of genes covered by our RNA-Seq data was comparable to that in other RNA-Seq studies [19]. Gene expression analysis identified 2,452, 826 and 322 genes that were differentially expressed in the flesh and mesocarp of 97103 and flesh of PI296341-FR, respectively, during fruit development and ripening (S3 Table). Further analysis indicated that 2,064, 530 and 139 genes were specifically differentially expressed in the flesh and mesocarp of 97103 fruit and the flesh of PI296341-FR fruit, respectively (Fig 2 and S3 Table). As expected, many more genes were differentially expressed in the flesh of 97103, in concordance with the fact that a series of physiological and biochemical changes, such as those in color, texture and sugar content, were only observed in the flesh of 97103 during fruit development. These results reflected more complicated regulatory networks of gene expression in the 97103 fruit flesh.


Comparative Transcriptome Analysis of Cultivated and Wild Watermelon during Fruit Development.

Guo S, Sun H, Zhang H, Liu J, Ren Y, Gong G, Jiao C, Zheng Y, Yang W, Fei Z, Xu Y - PLoS ONE (2015)

Venn diagram of differentially expressed genes in three tissues during watermelon fruit development.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4469606&req=5

pone.0130267.g002: Venn diagram of differentially expressed genes in three tissues during watermelon fruit development.
Mentions: RNA-Seq is powerful and efficient for large-scale gene expression analysis. In this study, we found that 18,198 (77.6%), 18,392 (78.5%) and 17,954 (76.6%) genes were expressed in the flesh and mesocarp of 97103 fruit and the flesh of PI296341-FR fruit, respectively. The number of genes covered by our RNA-Seq data was comparable to that in other RNA-Seq studies [19]. Gene expression analysis identified 2,452, 826 and 322 genes that were differentially expressed in the flesh and mesocarp of 97103 and flesh of PI296341-FR, respectively, during fruit development and ripening (S3 Table). Further analysis indicated that 2,064, 530 and 139 genes were specifically differentially expressed in the flesh and mesocarp of 97103 fruit and the flesh of PI296341-FR fruit, respectively (Fig 2 and S3 Table). As expected, many more genes were differentially expressed in the flesh of 97103, in concordance with the fact that a series of physiological and biochemical changes, such as those in color, texture and sugar content, were only observed in the flesh of 97103 during fruit development. These results reflected more complicated regulatory networks of gene expression in the 97103 fruit flesh.

Bottom Line: To systematically understand the molecular basis of these differences, we compared transcriptome profiles of fruit tissues of cultivated watermelon 97103 and wild watermelon PI296341-FR.In addition, we found that genes in the ethylene biosynthesis and signaling pathway including ACC oxidase, ethylene receptor and ethylene responsive factor showed highly ripening-associated expression patterns, indicating a possible role of ethylene in fruit development and ripening of watermelon, a non-climacteric fruit.Furthermore, the comparative expression profile data we developed provides a valuable resource to accelerate functional studies in watermelon and facilitate watermelon crop improvement.

View Article: PubMed Central - PubMed

Affiliation: Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), National Engineering Research Center for Vegetables, Beijing, China.

ABSTRACT
Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an important vegetable crop world-wide. Watermelon fruit quality is a complex trait determined by various factors such as sugar content, flesh color and flesh texture. Fruit quality and developmental process of cultivated and wild watermelon are highly different. To systematically understand the molecular basis of these differences, we compared transcriptome profiles of fruit tissues of cultivated watermelon 97103 and wild watermelon PI296341-FR. We identified 2,452, 826 and 322 differentially expressed genes in cultivated flesh, cultivated mesocarp and wild flesh, respectively, during fruit development. Gene ontology enrichment analysis of these genes indicated that biological processes and metabolic pathways related to fruit quality such as sweetness and flavor were significantly changed only in the flesh of 97103 during fruit development, while those related to abiotic stress response were changed mainly in the flesh of PI296341-FR. Our comparative transcriptome profiling analysis identified critical genes potentially involved in controlling fruit quality traits including α-galactosidase, invertase, UDP-galactose/glucose pyrophosphorylase and sugar transporter genes involved in the determination of fruit sugar content, phytoene synthase, β-carotene hydroxylase, 9-cis-epoxycarotenoid dioxygenase and carotenoid cleavage dioxygenase genes involved in carotenoid metabolism, and 4-coumarate:coenzyme A ligase, cellulose synthase, pectinesterase, pectinesterase inhibitor, polygalacturonase inhibitor and α-mannosidase genes involved in the regulation of flesh texture. In addition, we found that genes in the ethylene biosynthesis and signaling pathway including ACC oxidase, ethylene receptor and ethylene responsive factor showed highly ripening-associated expression patterns, indicating a possible role of ethylene in fruit development and ripening of watermelon, a non-climacteric fruit. Our analysis provides novel insights into watermelon fruit quality and ripening biology. Furthermore, the comparative expression profile data we developed provides a valuable resource to accelerate functional studies in watermelon and facilitate watermelon crop improvement.

No MeSH data available.