The chromosome-level genome provides insights into the adaptive evolution of the visual system in Oratosquilla oratoria
Abstract Background The marine crustacean Oratosquilla oratoria is economically significant in seafood and aquaculture industries. However, the lack of high-quality genome assembly has hindered our understanding of O. oratoria, particularly the mechanisms underlying its developed visual system. Resu...
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2025-02-01
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| Online Access: | https://doi.org/10.1186/s12915-025-02146-6 |
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| author | Daizhen Zhang Xiaoli Sun Lianfu Chen Lianyu Lin Chijie Yin Wenqi Yang Jun Liu Qiuning Liu Huabin Zhang Senhao Jiang Yongxin Li Boping Tang Gang Wang |
| author_facet | Daizhen Zhang Xiaoli Sun Lianfu Chen Lianyu Lin Chijie Yin Wenqi Yang Jun Liu Qiuning Liu Huabin Zhang Senhao Jiang Yongxin Li Boping Tang Gang Wang |
| author_sort | Daizhen Zhang |
| collection | DOAJ |
| description | Abstract Background The marine crustacean Oratosquilla oratoria is economically significant in seafood and aquaculture industries. However, the lack of high-quality genome assembly has hindered our understanding of O. oratoria, particularly the mechanisms underlying its developed visual system. Results We generated a chromosome-level genome assembly for O. oratoria (2.97 Gb, 44 pseudo-chromosomes) using combination sequencing strategies. Our analysis revealed that more than half of the genome was covered by repeat sequences, and LINE elements showed significant expansion. Furthermore, phylogenetic analysis revealed a close relationship of O. oratoria with Dendrobranchiata and Pleocyemata. In addition, the evolutionary rate of O. oratoria was slightly faster than that of Dendrobranchiata and slower than that of Pleocyemata. Interestingly, we observed the significant expansion of middle-wavelength-sensitive (MWS) opsins in the O. oratoria genome by tandem duplication, partially contributing to their unique visual capabilities. Compared with other crustaceans, O. oratoria has evolved a thicker cornea that was possibly driven by visual adaptations and ecological requirements. Employing comparative transcriptome analysis, we identified a tandemly duplicated cuticle protein (CP) cluster that was specifically expanded and expressed in the ocular tissues of O. oratoria, potentially contributing to the thick cornea of O. oratoria. Conclusions Our study established the first chromosome-level genome for Stomatopoda species, providing a valuable genomic resource for studying the molecular mechanisms underlying the developed visual system of O. oratoria. |
| format | Article |
| id | doaj-art-84519fa9bdd9496db355eed8dd228ea7 |
| institution | Kabale University |
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| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj-art-84519fa9bdd9496db355eed8dd228ea72025-02-09T12:54:25ZengBMCBMC Biology1741-70072025-02-0123111510.1186/s12915-025-02146-6The chromosome-level genome provides insights into the adaptive evolution of the visual system in Oratosquilla oratoriaDaizhen Zhang0Xiaoli Sun1Lianfu Chen2Lianyu Lin3Chijie Yin4Wenqi Yang5Jun Liu6Qiuning Liu7Huabin Zhang8Senhao Jiang9Yongxin Li10Boping Tang11Gang Wang12Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Yancheng Teachers UniversityJiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Yancheng Teachers UniversityInstitute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural UniversityState Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry UniversityJiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Yancheng Teachers UniversityJiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Yancheng Teachers UniversityLianyungang Key Laboratory of Biotechnology, Lianyungang Normal CollegeJiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Yancheng Teachers UniversityJiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Yancheng Teachers UniversityJiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Yancheng Teachers UniversityCenter for Ecological and Environmental Sciences, Northwestern Polytechnical UniversityJiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Yancheng Teachers UniversityJiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Yancheng Teachers UniversityAbstract Background The marine crustacean Oratosquilla oratoria is economically significant in seafood and aquaculture industries. However, the lack of high-quality genome assembly has hindered our understanding of O. oratoria, particularly the mechanisms underlying its developed visual system. Results We generated a chromosome-level genome assembly for O. oratoria (2.97 Gb, 44 pseudo-chromosomes) using combination sequencing strategies. Our analysis revealed that more than half of the genome was covered by repeat sequences, and LINE elements showed significant expansion. Furthermore, phylogenetic analysis revealed a close relationship of O. oratoria with Dendrobranchiata and Pleocyemata. In addition, the evolutionary rate of O. oratoria was slightly faster than that of Dendrobranchiata and slower than that of Pleocyemata. Interestingly, we observed the significant expansion of middle-wavelength-sensitive (MWS) opsins in the O. oratoria genome by tandem duplication, partially contributing to their unique visual capabilities. Compared with other crustaceans, O. oratoria has evolved a thicker cornea that was possibly driven by visual adaptations and ecological requirements. Employing comparative transcriptome analysis, we identified a tandemly duplicated cuticle protein (CP) cluster that was specifically expanded and expressed in the ocular tissues of O. oratoria, potentially contributing to the thick cornea of O. oratoria. Conclusions Our study established the first chromosome-level genome for Stomatopoda species, providing a valuable genomic resource for studying the molecular mechanisms underlying the developed visual system of O. oratoria.https://doi.org/10.1186/s12915-025-02146-6Oratosquilla oratoriaChromosome-level genome assemblyOpsinsThick cornea |
| spellingShingle | Daizhen Zhang Xiaoli Sun Lianfu Chen Lianyu Lin Chijie Yin Wenqi Yang Jun Liu Qiuning Liu Huabin Zhang Senhao Jiang Yongxin Li Boping Tang Gang Wang The chromosome-level genome provides insights into the adaptive evolution of the visual system in Oratosquilla oratoria BMC Biology Oratosquilla oratoria Chromosome-level genome assembly Opsins Thick cornea |
| title | The chromosome-level genome provides insights into the adaptive evolution of the visual system in Oratosquilla oratoria |
| title_full | The chromosome-level genome provides insights into the adaptive evolution of the visual system in Oratosquilla oratoria |
| title_fullStr | The chromosome-level genome provides insights into the adaptive evolution of the visual system in Oratosquilla oratoria |
| title_full_unstemmed | The chromosome-level genome provides insights into the adaptive evolution of the visual system in Oratosquilla oratoria |
| title_short | The chromosome-level genome provides insights into the adaptive evolution of the visual system in Oratosquilla oratoria |
| title_sort | chromosome level genome provides insights into the adaptive evolution of the visual system in oratosquilla oratoria |
| topic | Oratosquilla oratoria Chromosome-level genome assembly Opsins Thick cornea |
| url | https://doi.org/10.1186/s12915-025-02146-6 |
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