Genome-Wide Identification of the Sweet Orange <i>bZIP</i> Gene Family and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i>
(1) Background: The sweet orange (<i>Citrus sinensis</i>) is the most widely cultivated and productive citrus fruit in the world, with considerable economic value and good prospects for development. However, post-harvest storage and transport of the fruit are often affected by infestatio...
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| Format: | Article |
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MDPI AG
2023-03-01
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| Series: | Horticulturae |
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| Online Access: | https://www.mdpi.com/2311-7524/9/3/393 |
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| author | Peichen Han Tuo Yin Dengxian Xi Xiuyao Yang Mengjie Zhang Ling Zhu Hanyao Zhang Xiaozhen Liu |
| author_facet | Peichen Han Tuo Yin Dengxian Xi Xiuyao Yang Mengjie Zhang Ling Zhu Hanyao Zhang Xiaozhen Liu |
| author_sort | Peichen Han |
| collection | DOAJ |
| description | (1) Background: The sweet orange (<i>Citrus sinensis</i>) is the most widely cultivated and productive citrus fruit in the world, with considerable economic value and good prospects for development. However, post-harvest storage and transport of the fruit are often affected by infestation by <i>Penicillium</i> species, leading to many losses. (2) Methods: In this study, the family of <i>bZIP</i> genes from the whole genome of sweet orange was identified and analyzed in detail in terms of gene structure, physicochemical properties, protein structure, conserved structural domains, chromosomal positioning, and promoter analysis using bioinformatic analysis, in addition to an analysis of the expression patterns of the fruit following <i>Penicillium</i> infection. (3) Results: In this study, 50 <i>CsbZIP</i> genes were identified from the sweet orange genome. In silico analysis showed that <i>Cs_ont_3g005140</i> was presumably localized in the chloroplasts, while the rest of the family members were located in the nucleus. Phylogenetic trees of grape, apple, <i>Arabidopsis</i>, and sweet orange were constructed on the basis of evolutionary relationships and divided into 16 subfamilies. Conserved motif analysis showed that all <i>CsbZIP</i> family genes encode proteins containing the highly conserved Motif 1. Promoter prediction analysis showed the chromosomal positioning, and the covariance analysis showed that the 50 <i>CsbZIPs</i> were unevenly distributed on nine chromosomes, with 10 pairs of duplicated genes. In the analysis of expression patterns, 11 of the 50 <i>CsbZIP</i> genes were not expressed, 12 were upregulated, 27 were downregulated, and five of the upregulated genes were highly expressed. (4) Conclusions: In this study, two <i>CsbZIP</i> members were each closely related to two <i>Arabidopsis thaliana</i> genes associated with salt stress. The functions of the replicated and re-differentiated <i>CsbZIP</i> homologs (<i>Cs_ont_1g027160</i> and <i>Cs_ont_8g020880</i>) divergee further, with one responding to inoculation by <i>Penicillium</i> and the other not doing so. Five genes associated with sweet orange in response to <i>Penicillium</i> infestation were initially screened (<i>Cs_ont_3g000400</i>, <i>Cs_ont_3g003210</i>, <i>Cs_ont_5g007090</i>, <i>Cs_ont_5g011180</i>, <i>Cs_ont_8g020880</i>). This study provides some theoretical basis for subsequent research into the response mechanism of sweet orange <i>bZIP</i> transcription factors under biotic stresses. |
| first_indexed | 2024-03-11T06:27:47Z |
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| last_indexed | 2024-03-11T06:27:47Z |
| publishDate | 2023-03-01 |
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| spelling | doaj.art-229064ad0d364ab1ba9cb68adc6ad1c02023-11-17T11:25:01ZengMDPI AGHorticulturae2311-75242023-03-019339310.3390/horticulturae9030393Genome-Wide Identification of the Sweet Orange <i>bZIP</i> Gene Family and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i>Peichen Han0Tuo Yin1Dengxian Xi2Xiuyao Yang3Mengjie Zhang4Ling Zhu5Hanyao Zhang6Xiaozhen Liu7Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory of Biodiversity Conservation in Southwest China, National Forest and Glassland Administration, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory of Biodiversity Conservation in Southwest China, National Forest and Glassland Administration, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory of Biodiversity Conservation in Southwest China, National Forest and Glassland Administration, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory of Biodiversity Conservation in Southwest China, National Forest and Glassland Administration, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China(1) Background: The sweet orange (<i>Citrus sinensis</i>) is the most widely cultivated and productive citrus fruit in the world, with considerable economic value and good prospects for development. However, post-harvest storage and transport of the fruit are often affected by infestation by <i>Penicillium</i> species, leading to many losses. (2) Methods: In this study, the family of <i>bZIP</i> genes from the whole genome of sweet orange was identified and analyzed in detail in terms of gene structure, physicochemical properties, protein structure, conserved structural domains, chromosomal positioning, and promoter analysis using bioinformatic analysis, in addition to an analysis of the expression patterns of the fruit following <i>Penicillium</i> infection. (3) Results: In this study, 50 <i>CsbZIP</i> genes were identified from the sweet orange genome. In silico analysis showed that <i>Cs_ont_3g005140</i> was presumably localized in the chloroplasts, while the rest of the family members were located in the nucleus. Phylogenetic trees of grape, apple, <i>Arabidopsis</i>, and sweet orange were constructed on the basis of evolutionary relationships and divided into 16 subfamilies. Conserved motif analysis showed that all <i>CsbZIP</i> family genes encode proteins containing the highly conserved Motif 1. Promoter prediction analysis showed the chromosomal positioning, and the covariance analysis showed that the 50 <i>CsbZIPs</i> were unevenly distributed on nine chromosomes, with 10 pairs of duplicated genes. In the analysis of expression patterns, 11 of the 50 <i>CsbZIP</i> genes were not expressed, 12 were upregulated, 27 were downregulated, and five of the upregulated genes were highly expressed. (4) Conclusions: In this study, two <i>CsbZIP</i> members were each closely related to two <i>Arabidopsis thaliana</i> genes associated with salt stress. The functions of the replicated and re-differentiated <i>CsbZIP</i> homologs (<i>Cs_ont_1g027160</i> and <i>Cs_ont_8g020880</i>) divergee further, with one responding to inoculation by <i>Penicillium</i> and the other not doing so. Five genes associated with sweet orange in response to <i>Penicillium</i> infestation were initially screened (<i>Cs_ont_3g000400</i>, <i>Cs_ont_3g003210</i>, <i>Cs_ont_5g007090</i>, <i>Cs_ont_5g011180</i>, <i>Cs_ont_8g020880</i>). This study provides some theoretical basis for subsequent research into the response mechanism of sweet orange <i>bZIP</i> transcription factors under biotic stresses.https://www.mdpi.com/2311-7524/9/3/393sweet orange<i>bZIP</i> transcription factor<i>Penicillium</i>biological stressstress resistanceresponse mechanisms |
| spellingShingle | Peichen Han Tuo Yin Dengxian Xi Xiuyao Yang Mengjie Zhang Ling Zhu Hanyao Zhang Xiaozhen Liu Genome-Wide Identification of the Sweet Orange <i>bZIP</i> Gene Family and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i> Horticulturae sweet orange <i>bZIP</i> transcription factor <i>Penicillium</i> biological stress stress resistance response mechanisms |
| title | Genome-Wide Identification of the Sweet Orange <i>bZIP</i> Gene Family and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i> |
| title_full | Genome-Wide Identification of the Sweet Orange <i>bZIP</i> Gene Family and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i> |
| title_fullStr | Genome-Wide Identification of the Sweet Orange <i>bZIP</i> Gene Family and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i> |
| title_full_unstemmed | Genome-Wide Identification of the Sweet Orange <i>bZIP</i> Gene Family and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i> |
| title_short | Genome-Wide Identification of the Sweet Orange <i>bZIP</i> Gene Family and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i> |
| title_sort | genome wide identification of the sweet orange i bzip i gene family and analysis of their expression in response to infection by i penicillium digitatum i |
| topic | sweet orange <i>bZIP</i> transcription factor <i>Penicillium</i> biological stress stress resistance response mechanisms |
| url | https://www.mdpi.com/2311-7524/9/3/393 |
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