Genome-Wide Identification and Expression Analysis of Eggplant <i>DIR</i> Gene Family in Response to Biotic and Abiotic Stresses
Dirigent proteins (<i>DIR</i>) play important roles in the biosynthesis of lignins and lignans, defensive responses, secondary metabolism, and disease resistance in plants. The <i>DIR</i> gene family has been identified and studied in many plants. However, the identification...
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MDPI AG
2022-08-01
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| Series: | Horticulturae |
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| Online Access: | https://www.mdpi.com/2311-7524/8/8/732 |
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| author | Kaijing Zhang Wujun Xing Suao Sheng Dekun Yang Fengxian Zhen Haikun Jiang Congsheng Yan Li Jia |
| author_facet | Kaijing Zhang Wujun Xing Suao Sheng Dekun Yang Fengxian Zhen Haikun Jiang Congsheng Yan Li Jia |
| author_sort | Kaijing Zhang |
| collection | DOAJ |
| description | Dirigent proteins (<i>DIR</i>) play important roles in the biosynthesis of lignins and lignans, defensive responses, secondary metabolism, and disease resistance in plants. The <i>DIR</i> gene family has been identified and studied in many plants. However, the identification of <i>DIR</i> gene family in eggplant has not been conducted yet. Therefore, in this study, based on the available genome information of eggplant, the <i>DIR</i> family genes in eggplant were identified with bioinformatics methods. The expression pattern analyses of eggplant <i>DIR</i> family genes in different organs and stresses were also conducted to understand their biological functions. The results showed that a total of 24 <i>DIR</i> genes were identified in the eggplant, which were divided into three subfamilies (<i>DIR</i>-<i>a</i>, <i>DIR</i>-<i>b/d</i>, and <i>DIR</i>-<i>e</i>). Synteny analysis of <i>DIR</i> genes among eggplant, <i>Arabidopsis</i>, and rice showed that 15 eggplant <i>DIR</i> genes were colinear with 18 <i>Arabidopsis DIR</i> genes, and 16 eggplant <i>DIR</i> genes were colinear with 15 rice <i>DIR</i> genes. Phylogenetic tree analysis showed that 19 pairs of orthologous genes were identified between eggplant and pepper. The <i>cis</i>-acting elements analysis implied that the eggplant <i>DIR</i> genes contained a lot of <i>cis</i>-elements associated with stress and hormone response. The organ-specific expression analysis of eggplant <i>DIR</i> family genes revealed that only the <i>SmDIR3</i> gene was highly expressed in all the 19 organs of eggplant. Some <i>SmDIR</i> genes, including <i>SmDIR7</i>, <i>SmDIR8</i>, <i>SmDIR11</i>, <i>SmDIR14</i>, <i>SmDIR18</i>, <i>SmDIR19</i>, <i>SmDIR20</i>, and <i>SmDIR23</i>, were not or were lowly expressed in the eggplant organs, while the other eggplant <i>DIR</i> family genes showed an organ-specific expression pattern. Furthermore, 19 of 24 <i>SmDIR</i> genes were differentially expressed in response to abiotic and biotic stresses. 5 <i>SmDIR</i> genes, including <i>SmDIR3</i>, <i>SmDIR5</i>, <i>SmDIR6</i>, <i>SmDIR12</i>, and <i>SmDIR22</i>, were differentially expressed under multiple types of abiotic and biotic stresses. Especially notable, the <i>SmDIR22</i> gene was differentially expressed under three types of abiotic stresses and two types of biotic stresses, which indicated that the <i>SmDIR22</i> gene plays an important role in the response to abiotic and biotic stresses. These results provide valuable evidence for a better understanding of the biological role of <i>DIR</i> genes in eggplant. |
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| spelling | doaj.art-6af5697666eb49e0b4b1f30c21a8421e2023-11-30T21:31:21ZengMDPI AGHorticulturae2311-75242022-08-018873210.3390/horticulturae8080732Genome-Wide Identification and Expression Analysis of Eggplant <i>DIR</i> Gene Family in Response to Biotic and Abiotic StressesKaijing Zhang0Wujun Xing1Suao Sheng2Dekun Yang3Fengxian Zhen4Haikun Jiang5Congsheng Yan6Li Jia7College of Agriculture, Anhui Science and Technology University, Chuzhou 233100, ChinaCollege of Agriculture, Anhui Science and Technology University, Chuzhou 233100, ChinaCollege of Agriculture, Anhui Science and Technology University, Chuzhou 233100, ChinaCollege of Agriculture, Anhui Science and Technology University, Chuzhou 233100, ChinaCollege of Agriculture, Anhui Science and Technology University, Chuzhou 233100, ChinaInstitute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, ChinaInstitute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, ChinaInstitute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230001, ChinaDirigent proteins (<i>DIR</i>) play important roles in the biosynthesis of lignins and lignans, defensive responses, secondary metabolism, and disease resistance in plants. The <i>DIR</i> gene family has been identified and studied in many plants. However, the identification of <i>DIR</i> gene family in eggplant has not been conducted yet. Therefore, in this study, based on the available genome information of eggplant, the <i>DIR</i> family genes in eggplant were identified with bioinformatics methods. The expression pattern analyses of eggplant <i>DIR</i> family genes in different organs and stresses were also conducted to understand their biological functions. The results showed that a total of 24 <i>DIR</i> genes were identified in the eggplant, which were divided into three subfamilies (<i>DIR</i>-<i>a</i>, <i>DIR</i>-<i>b/d</i>, and <i>DIR</i>-<i>e</i>). Synteny analysis of <i>DIR</i> genes among eggplant, <i>Arabidopsis</i>, and rice showed that 15 eggplant <i>DIR</i> genes were colinear with 18 <i>Arabidopsis DIR</i> genes, and 16 eggplant <i>DIR</i> genes were colinear with 15 rice <i>DIR</i> genes. Phylogenetic tree analysis showed that 19 pairs of orthologous genes were identified between eggplant and pepper. The <i>cis</i>-acting elements analysis implied that the eggplant <i>DIR</i> genes contained a lot of <i>cis</i>-elements associated with stress and hormone response. The organ-specific expression analysis of eggplant <i>DIR</i> family genes revealed that only the <i>SmDIR3</i> gene was highly expressed in all the 19 organs of eggplant. Some <i>SmDIR</i> genes, including <i>SmDIR7</i>, <i>SmDIR8</i>, <i>SmDIR11</i>, <i>SmDIR14</i>, <i>SmDIR18</i>, <i>SmDIR19</i>, <i>SmDIR20</i>, and <i>SmDIR23</i>, were not or were lowly expressed in the eggplant organs, while the other eggplant <i>DIR</i> family genes showed an organ-specific expression pattern. Furthermore, 19 of 24 <i>SmDIR</i> genes were differentially expressed in response to abiotic and biotic stresses. 5 <i>SmDIR</i> genes, including <i>SmDIR3</i>, <i>SmDIR5</i>, <i>SmDIR6</i>, <i>SmDIR12</i>, and <i>SmDIR22</i>, were differentially expressed under multiple types of abiotic and biotic stresses. Especially notable, the <i>SmDIR22</i> gene was differentially expressed under three types of abiotic stresses and two types of biotic stresses, which indicated that the <i>SmDIR22</i> gene plays an important role in the response to abiotic and biotic stresses. These results provide valuable evidence for a better understanding of the biological role of <i>DIR</i> genes in eggplant.https://www.mdpi.com/2311-7524/8/8/732eggplant<i>DIR</i>gene familybioinformaticsexpression analysis |
| spellingShingle | Kaijing Zhang Wujun Xing Suao Sheng Dekun Yang Fengxian Zhen Haikun Jiang Congsheng Yan Li Jia Genome-Wide Identification and Expression Analysis of Eggplant <i>DIR</i> Gene Family in Response to Biotic and Abiotic Stresses Horticulturae eggplant <i>DIR</i> gene family bioinformatics expression analysis |
| title | Genome-Wide Identification and Expression Analysis of Eggplant <i>DIR</i> Gene Family in Response to Biotic and Abiotic Stresses |
| title_full | Genome-Wide Identification and Expression Analysis of Eggplant <i>DIR</i> Gene Family in Response to Biotic and Abiotic Stresses |
| title_fullStr | Genome-Wide Identification and Expression Analysis of Eggplant <i>DIR</i> Gene Family in Response to Biotic and Abiotic Stresses |
| title_full_unstemmed | Genome-Wide Identification and Expression Analysis of Eggplant <i>DIR</i> Gene Family in Response to Biotic and Abiotic Stresses |
| title_short | Genome-Wide Identification and Expression Analysis of Eggplant <i>DIR</i> Gene Family in Response to Biotic and Abiotic Stresses |
| title_sort | genome wide identification and expression analysis of eggplant i dir i gene family in response to biotic and abiotic stresses |
| topic | eggplant <i>DIR</i> gene family bioinformatics expression analysis |
| url | https://www.mdpi.com/2311-7524/8/8/732 |
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