Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes
Orphan genes (OGs) that are missing identifiable homologs in other lineages may potentially make contributions to a variety of biological functions. The Cucurbitaceae family consists of a wide range of fruit crops of worldwide or local economic significance. To date, very few functional mechanisms o...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-05-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.872137/full |
| _version_ | 1818205899322294272 |
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| author | Dongna Ma Dongna Ma Zhengfeng Lai Qiansu Ding Kun Zhang Kaizhen Chang Shuhao Li Zhizhu Zhao Fenglin Zhong |
| author_facet | Dongna Ma Dongna Ma Zhengfeng Lai Qiansu Ding Kun Zhang Kaizhen Chang Shuhao Li Zhizhu Zhao Fenglin Zhong |
| author_sort | Dongna Ma |
| collection | DOAJ |
| description | Orphan genes (OGs) that are missing identifiable homologs in other lineages may potentially make contributions to a variety of biological functions. The Cucurbitaceae family consists of a wide range of fruit crops of worldwide or local economic significance. To date, very few functional mechanisms of OGs in Cucurbitaceae are known. In this study, we systematically identified the OGs of eight Cucurbitaceae species using a comparative genomics approach. The content of OGs varied widely among the eight Cucurbitaceae species, ranging from 1.63% in chayote to 16.55% in wax gourd. Genetic structure analysis showed that OGs have significantly shorter protein lengths and fewer exons in Cucurbitaceae. The subcellular localizations of OGs were basically the same, with only subtle differences. Except for aggregation in some chromosomal regions, the distribution density of OGs was higher near the telomeres and relatively evenly distributed on the chromosomes. Gene expression analysis revealed that OGs had less abundantly and highly tissue-specific expression. Interestingly, the largest proportion of these OGs was significantly more tissue-specific expressed in the flower than in other tissues, and more detectable expression was found in the male flower. Functional prediction of OGs showed that (1) 18 OGs associated with male sterility in watermelon; (2) 182 OGs associated with flower development in cucumber; (3) 51 OGs associated with environmental adaptation in watermelon; (4) 520 OGs may help with the large fruit size in wax gourd. Our results provide the molecular basis and research direction for some important mechanisms in Cucurbitaceae species and domesticated crops. |
| first_indexed | 2024-12-12T04:04:28Z |
| format | Article |
| id | doaj.art-fc5bd5ac94ec4c55a42d85de22112e8e |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-12T04:04:28Z |
| publishDate | 2022-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-fc5bd5ac94ec4c55a42d85de22112e8e2022-12-22T00:38:48ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-05-011310.3389/fpls.2022.872137872137Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae GenomesDongna Ma0Dongna Ma1Zhengfeng Lai2Qiansu Ding3Kun Zhang4Kaizhen Chang5Shuhao Li6Zhizhu Zhao7Fenglin Zhong8College of Horticulture, Fujian Agriculture and Forestry University, Fujian, ChinaCollege of the Environment and Ecology, Xiamen University, Fujian, ChinaSubtropical Agricultural Research Institute, Fujian Academy of Agriculture Sciences, Fujian, ChinaCollege of the Environment and Ecology, Xiamen University, Fujian, ChinaCollege of Horticulture, Fujian Agriculture and Forestry University, Fujian, ChinaCollege of Horticulture, Fujian Agriculture and Forestry University, Fujian, ChinaCollege of Horticulture, Fujian Agriculture and Forestry University, Fujian, ChinaCollege of the Environment and Ecology, Xiamen University, Fujian, ChinaCollege of Horticulture, Fujian Agriculture and Forestry University, Fujian, ChinaOrphan genes (OGs) that are missing identifiable homologs in other lineages may potentially make contributions to a variety of biological functions. The Cucurbitaceae family consists of a wide range of fruit crops of worldwide or local economic significance. To date, very few functional mechanisms of OGs in Cucurbitaceae are known. In this study, we systematically identified the OGs of eight Cucurbitaceae species using a comparative genomics approach. The content of OGs varied widely among the eight Cucurbitaceae species, ranging from 1.63% in chayote to 16.55% in wax gourd. Genetic structure analysis showed that OGs have significantly shorter protein lengths and fewer exons in Cucurbitaceae. The subcellular localizations of OGs were basically the same, with only subtle differences. Except for aggregation in some chromosomal regions, the distribution density of OGs was higher near the telomeres and relatively evenly distributed on the chromosomes. Gene expression analysis revealed that OGs had less abundantly and highly tissue-specific expression. Interestingly, the largest proportion of these OGs was significantly more tissue-specific expressed in the flower than in other tissues, and more detectable expression was found in the male flower. Functional prediction of OGs showed that (1) 18 OGs associated with male sterility in watermelon; (2) 182 OGs associated with flower development in cucumber; (3) 51 OGs associated with environmental adaptation in watermelon; (4) 520 OGs may help with the large fruit size in wax gourd. Our results provide the molecular basis and research direction for some important mechanisms in Cucurbitaceae species and domesticated crops.https://www.frontiersin.org/articles/10.3389/fpls.2022.872137/fullCucurbitaceaeorphan genestranscriptomemale sterilityenvironmental adaptation |
| spellingShingle | Dongna Ma Dongna Ma Zhengfeng Lai Qiansu Ding Kun Zhang Kaizhen Chang Shuhao Li Zhizhu Zhao Fenglin Zhong Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes Frontiers in Plant Science Cucurbitaceae orphan genes transcriptome male sterility environmental adaptation |
| title | Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes |
| title_full | Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes |
| title_fullStr | Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes |
| title_full_unstemmed | Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes |
| title_short | Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes |
| title_sort | identification characterization and function of orphan genes among the current cucurbitaceae genomes |
| topic | Cucurbitaceae orphan genes transcriptome male sterility environmental adaptation |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.872137/full |
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