Identification of Candidate Genes Associated with Pulp Color by Transcriptomic Analysis of ‘Huaxiu’ Plum (<i>Prunus salicina</i> Lindl.) during Fruit-Ripening
The plum (<i>Prunus salicina</i> Lindl.) is one of the traditional and economically important stone fruit trees in China. Anthocyanins are important pigments in plums. However, little is known about the molecular mechanisms underlying anthocyanin accumulation in plum fruits, which has hi...
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MDPI AG
2022-12-01
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| Series: | Current Issues in Molecular Biology |
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| Online Access: | https://www.mdpi.com/1467-3045/44/12/434 |
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| author | Gang Wang Wenxin Weng Zhanhui Jia Jiyu Zhang Tao Wang Jiping Xuan |
| author_facet | Gang Wang Wenxin Weng Zhanhui Jia Jiyu Zhang Tao Wang Jiping Xuan |
| author_sort | Gang Wang |
| collection | DOAJ |
| description | The plum (<i>Prunus salicina</i> Lindl.) is one of the traditional and economically important stone fruit trees in China. Anthocyanins are important pigments in plums. However, little is known about the molecular mechanisms underlying anthocyanin accumulation in plum fruits, which has hindered research on the molecular mechanism of its utilization. Our research shows that the chlorophyll content was gradually decreased and the contents of anthocyanin and flavonoid increased during the coloring process of the pulp in ‘Huaxiu’ plums (<i>P. salicina</i>). Then, the RNA-Seq technique was used to analyze the transcriptome of pulp color changes with three different stages (yellow, orange, and red) in the ‘Huaxiu’ plum (<i>P. salicina</i>). A total of 57,119 unigenes with a mean length of 953 bp were generated, and 61.6% of them were annotated to public databases. The Gene Ontology (GO) database assigned 21,438 unigenes with biological process, cellular components, and molecular function. In addition, 32,146 unigenes were clustered into 25 categories for functional classification by the COG database, and 7595 unigenes were mapped to 128 KEGG pathways by the KEGG pathway database. Of these, 1095 (YS-versus-OS), 4947 (YS-versus-RS), and 3414 (OS-versus-RS) genes were significantly expressed differentially between two coloration stages. The GO and KEGG pathway enrichment analysis revealed that 20 and 1 differentially expressed genes (DEG) are involved in flavonoid biosynthesis and anthocyanin biosynthesis, respectively. Finally, we mainly identified three structural genes as candidate genes. The transcriptome information in this study provide a basis for further studies of pulp colors in plum and contribute to our understanding of the molecular mechanisms underlying anthocyanin biosynthesis in pulp. |
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| spelling | doaj.art-043256df3f084345a7f626e49b1b41ea2023-11-24T14:03:59ZengMDPI AGCurrent Issues in Molecular Biology1467-30371467-30452022-12-0144126368638410.3390/cimb44120434Identification of Candidate Genes Associated with Pulp Color by Transcriptomic Analysis of ‘Huaxiu’ Plum (<i>Prunus salicina</i> Lindl.) during Fruit-RipeningGang Wang0Wenxin Weng1Zhanhui Jia2Jiyu Zhang3Tao Wang4Jiping Xuan5Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaJiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaJiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaJiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaJiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaJiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaThe plum (<i>Prunus salicina</i> Lindl.) is one of the traditional and economically important stone fruit trees in China. Anthocyanins are important pigments in plums. However, little is known about the molecular mechanisms underlying anthocyanin accumulation in plum fruits, which has hindered research on the molecular mechanism of its utilization. Our research shows that the chlorophyll content was gradually decreased and the contents of anthocyanin and flavonoid increased during the coloring process of the pulp in ‘Huaxiu’ plums (<i>P. salicina</i>). Then, the RNA-Seq technique was used to analyze the transcriptome of pulp color changes with three different stages (yellow, orange, and red) in the ‘Huaxiu’ plum (<i>P. salicina</i>). A total of 57,119 unigenes with a mean length of 953 bp were generated, and 61.6% of them were annotated to public databases. The Gene Ontology (GO) database assigned 21,438 unigenes with biological process, cellular components, and molecular function. In addition, 32,146 unigenes were clustered into 25 categories for functional classification by the COG database, and 7595 unigenes were mapped to 128 KEGG pathways by the KEGG pathway database. Of these, 1095 (YS-versus-OS), 4947 (YS-versus-RS), and 3414 (OS-versus-RS) genes were significantly expressed differentially between two coloration stages. The GO and KEGG pathway enrichment analysis revealed that 20 and 1 differentially expressed genes (DEG) are involved in flavonoid biosynthesis and anthocyanin biosynthesis, respectively. Finally, we mainly identified three structural genes as candidate genes. The transcriptome information in this study provide a basis for further studies of pulp colors in plum and contribute to our understanding of the molecular mechanisms underlying anthocyanin biosynthesis in pulp.https://www.mdpi.com/1467-3045/44/12/434<i>Prunus salicina</i>pulp colortranscriptomeRNA-SeqDGEanthocyanin and flavonoid biosynthesis |
| spellingShingle | Gang Wang Wenxin Weng Zhanhui Jia Jiyu Zhang Tao Wang Jiping Xuan Identification of Candidate Genes Associated with Pulp Color by Transcriptomic Analysis of ‘Huaxiu’ Plum (<i>Prunus salicina</i> Lindl.) during Fruit-Ripening Current Issues in Molecular Biology <i>Prunus salicina</i> pulp color transcriptome RNA-Seq DGE anthocyanin and flavonoid biosynthesis |
| title | Identification of Candidate Genes Associated with Pulp Color by Transcriptomic Analysis of ‘Huaxiu’ Plum (<i>Prunus salicina</i> Lindl.) during Fruit-Ripening |
| title_full | Identification of Candidate Genes Associated with Pulp Color by Transcriptomic Analysis of ‘Huaxiu’ Plum (<i>Prunus salicina</i> Lindl.) during Fruit-Ripening |
| title_fullStr | Identification of Candidate Genes Associated with Pulp Color by Transcriptomic Analysis of ‘Huaxiu’ Plum (<i>Prunus salicina</i> Lindl.) during Fruit-Ripening |
| title_full_unstemmed | Identification of Candidate Genes Associated with Pulp Color by Transcriptomic Analysis of ‘Huaxiu’ Plum (<i>Prunus salicina</i> Lindl.) during Fruit-Ripening |
| title_short | Identification of Candidate Genes Associated with Pulp Color by Transcriptomic Analysis of ‘Huaxiu’ Plum (<i>Prunus salicina</i> Lindl.) during Fruit-Ripening |
| title_sort | identification of candidate genes associated with pulp color by transcriptomic analysis of huaxiu plum i prunus salicina i lindl during fruit ripening |
| topic | <i>Prunus salicina</i> pulp color transcriptome RNA-Seq DGE anthocyanin and flavonoid biosynthesis |
| url | https://www.mdpi.com/1467-3045/44/12/434 |
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