Genome-Wide Identification and Expression of the PIN Auxin Efflux Carrier Gene Family in Watermelon (<i>Citrullus lanatus</i>)
As one of the world’s most popular fruits, watermelon (<i>Citrus lanatus</i>) is cultivated in more than 3 million hectares across the globe, with a yearly yield of more than 100 million tons. According to ‘97103’ genome version 1, a previous study has shown that the watermelon genome co...
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| Format: | Article |
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MDPI AG
2021-05-01
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| Series: | Agriculture |
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| Online Access: | https://www.mdpi.com/2077-0472/11/5/447 |
| _version_ | 1827692411404419072 |
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| author | Huaiguo Shang Na Zhang Zhouli Xie Siyu Deng Licong Yi Xing Huang |
| author_facet | Huaiguo Shang Na Zhang Zhouli Xie Siyu Deng Licong Yi Xing Huang |
| author_sort | Huaiguo Shang |
| collection | DOAJ |
| description | As one of the world’s most popular fruits, watermelon (<i>Citrus lanatus</i>) is cultivated in more than 3 million hectares across the globe, with a yearly yield of more than 100 million tons. According to ‘97103’ genome version 1, a previous study has shown that the watermelon genome consists of 11 PIN genes. However, the higher quality ‘97103’ genome version 2 was recently assembled by using PacBio long reads with the benefit of fast development sequencing technology. Using this new assembly, we conducted a new genome-wide search for PIN genes in watermelon and compared it with cucumber and melon genomes. We identified nine, nine, and eight PINs in watermelon, cucumber, and melon, respectively. Phylogenetic analysis revealed a distinct evolutionary history of PIN proteins in watermelon, which is shown by the orphan <i>PIN6</i> in watermelon. We further conducted an expression analysis of the watermelon PIN genes in silico and by qRT-PCR. <i>ClaPIN6</i> might not play an essential role during shoot regeneration, which is closely related to species-specific evolution. However, the up-regulated expression patterns of <i>ClaPIN1-1</i> and <i>ClaPIN1-3</i> indicated their important roles during shoot regeneration. The result of this research will benefit future studies to understand the regulating mechanisms of auxin in watermelon shoot regeneration. |
| first_indexed | 2024-03-10T11:22:39Z |
| format | Article |
| id | doaj.art-228c49d9fb9743aea9e88a23fc2477f9 |
| institution | Directory Open Access Journal |
| issn | 2077-0472 |
| language | English |
| last_indexed | 2024-03-10T11:22:39Z |
| publishDate | 2021-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agriculture |
| spelling | doaj.art-228c49d9fb9743aea9e88a23fc2477f92023-11-21T19:53:37ZengMDPI AGAgriculture2077-04722021-05-0111544710.3390/agriculture11050447Genome-Wide Identification and Expression of the PIN Auxin Efflux Carrier Gene Family in Watermelon (<i>Citrullus lanatus</i>)Huaiguo Shang0Na Zhang1Zhouli Xie2Siyu Deng3Licong Yi4Xing Huang5National Agro-Tech Extension and Service Center, Beijing 100125, ChinaInstitute of Crop Science, Wuhan Academy of Agricultural Sciences, Wuhan 430345, ChinaSchool of Life Sciences, Peking University, Beijing 100871, ChinaSchool of Biological Sciences, The University of Hong Kong, Hong Kong 999077, ChinaHubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Institute of Cash Crops, Hubei Academy of Agricultural Science, Wuhan 430064, ChinaEnvironment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, ChinaAs one of the world’s most popular fruits, watermelon (<i>Citrus lanatus</i>) is cultivated in more than 3 million hectares across the globe, with a yearly yield of more than 100 million tons. According to ‘97103’ genome version 1, a previous study has shown that the watermelon genome consists of 11 PIN genes. However, the higher quality ‘97103’ genome version 2 was recently assembled by using PacBio long reads with the benefit of fast development sequencing technology. Using this new assembly, we conducted a new genome-wide search for PIN genes in watermelon and compared it with cucumber and melon genomes. We identified nine, nine, and eight PINs in watermelon, cucumber, and melon, respectively. Phylogenetic analysis revealed a distinct evolutionary history of PIN proteins in watermelon, which is shown by the orphan <i>PIN6</i> in watermelon. We further conducted an expression analysis of the watermelon PIN genes in silico and by qRT-PCR. <i>ClaPIN6</i> might not play an essential role during shoot regeneration, which is closely related to species-specific evolution. However, the up-regulated expression patterns of <i>ClaPIN1-1</i> and <i>ClaPIN1-3</i> indicated their important roles during shoot regeneration. The result of this research will benefit future studies to understand the regulating mechanisms of auxin in watermelon shoot regeneration.https://www.mdpi.com/2077-0472/11/5/447PIN familyauxin efflux carrierphylogenetic analysisexpressionshoot regeneration watermeloncucumber |
| spellingShingle | Huaiguo Shang Na Zhang Zhouli Xie Siyu Deng Licong Yi Xing Huang Genome-Wide Identification and Expression of the PIN Auxin Efflux Carrier Gene Family in Watermelon (<i>Citrullus lanatus</i>) Agriculture PIN family auxin efflux carrier phylogenetic analysis expression shoot regeneration watermelon cucumber |
| title | Genome-Wide Identification and Expression of the PIN Auxin Efflux Carrier Gene Family in Watermelon (<i>Citrullus lanatus</i>) |
| title_full | Genome-Wide Identification and Expression of the PIN Auxin Efflux Carrier Gene Family in Watermelon (<i>Citrullus lanatus</i>) |
| title_fullStr | Genome-Wide Identification and Expression of the PIN Auxin Efflux Carrier Gene Family in Watermelon (<i>Citrullus lanatus</i>) |
| title_full_unstemmed | Genome-Wide Identification and Expression of the PIN Auxin Efflux Carrier Gene Family in Watermelon (<i>Citrullus lanatus</i>) |
| title_short | Genome-Wide Identification and Expression of the PIN Auxin Efflux Carrier Gene Family in Watermelon (<i>Citrullus lanatus</i>) |
| title_sort | genome wide identification and expression of the pin auxin efflux carrier gene family in watermelon i citrullus lanatus i |
| topic | PIN family auxin efflux carrier phylogenetic analysis expression shoot regeneration watermelon cucumber |
| url | https://www.mdpi.com/2077-0472/11/5/447 |
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