Genome assembly of an endemic butterfly (Minois aurata) shed light on the genetic mechanisms underlying ecological adaptation to arid valley habitat
Abstract Background The Hengduan Mountains, one of the global biodiversity hotspots with exceptional species richness and high endemism, contains numerous arid valleys that create a distinctive geographical and ecological landscape. However, the adaptive evolutionary mechanisms of organism in the ar...
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BMC
2024-11-01
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| Online Access: | https://doi.org/10.1186/s12864-024-11058-8 |
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| author | Wenqian Hu Yi Wang Xiaoxiao Chen Jialong Huang Jingge Kuang Lei Wang Kangshan Mao Liang Dou |
| author_facet | Wenqian Hu Yi Wang Xiaoxiao Chen Jialong Huang Jingge Kuang Lei Wang Kangshan Mao Liang Dou |
| author_sort | Wenqian Hu |
| collection | DOAJ |
| description | Abstract Background The Hengduan Mountains, one of the global biodiversity hotspots with exceptional species richness and high endemism, contains numerous arid valleys that create a distinctive geographical and ecological landscape. However, the adaptive evolutionary mechanisms of organism in the arid valley remain poorly understood. Minois aurata, an endemic butterfly species found exclusively in the arid valley of the upper Minjiang River, represents an attractive model system for studying adaptive evolutionary mechanisms to arid valley environments. Results Here, we present the first chromosome-level genome assembly for Minois aurata, with a total size of approximately 609.17 Mb, and a scaffold N50 size of 23.88 Mb. These scaffolds were further clustered and anchored onto 29 chromosomes based on Hi-C data. A total of 16,163 protein-coding genes were predicted, of which 91.83% were functionally annotated. The expansion of transposable elements (TEs) accounts for the relatively large genome size of M. aurata, potentially aiding its adaptation to environmental conditions. Phylogenomic analyses based on 3,785 single-copy genes revealed that M. aurata is most closely related to Hipparchia semele. Further mitochondrial genome analysis of four Minois species placed M. aurata in a basal position within the genus, supporting it as an independent species. A total of 185 rapidly evolving and 232 specific gene families were identified in M. aurata. Functional enrichment analysis indicated that these gene families were mainly associated with ultraviolet radiation, heat and hypoxia responses. We also identified 234 positive selected genes in M. aurata, some of which are related to compound eye photoreceptor development, osmotic stress, and light stimulus response. Demographic analysis indicated that the effective population size of M. aurata decreased around 0.4 and 0.04 million years ago, respectively, coinciding with the localized sub-glaciation. Conclusion The chromosome-level genome offers a comprehensive genomic basis for understanding the evolutionary and adaptive strategies of Minois aurata in the unique arid valley environment of the Hengduan Mountains, while also providing valuable insights into the broader mechanisms of organism adaptation to such habitats. |
| format | Article |
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| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2024-11-01 |
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| series | BMC Genomics |
| spelling | doaj-art-9e55e6a8427c434ea25ccd23c19fa3462025-02-02T12:10:02ZengBMCBMC Genomics1471-21642024-11-0125111410.1186/s12864-024-11058-8Genome assembly of an endemic butterfly (Minois aurata) shed light on the genetic mechanisms underlying ecological adaptation to arid valley habitatWenqian Hu0Yi Wang1Xiaoxiao Chen2Jialong Huang3Jingge Kuang4Lei Wang5Kangshan Mao6Liang Dou7Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan UniversitySichuan Key Laboratory of Ecological Restoration and Conservation for Forest and Wetland, Sichuan Academy of ForestryKey Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan UniversityFujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang UniversityMinistry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan UniversityInstitute of Plant Protection, Sichuan Academy of Agricultural SciencesKey Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan UniversityKey Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan UniversityAbstract Background The Hengduan Mountains, one of the global biodiversity hotspots with exceptional species richness and high endemism, contains numerous arid valleys that create a distinctive geographical and ecological landscape. However, the adaptive evolutionary mechanisms of organism in the arid valley remain poorly understood. Minois aurata, an endemic butterfly species found exclusively in the arid valley of the upper Minjiang River, represents an attractive model system for studying adaptive evolutionary mechanisms to arid valley environments. Results Here, we present the first chromosome-level genome assembly for Minois aurata, with a total size of approximately 609.17 Mb, and a scaffold N50 size of 23.88 Mb. These scaffolds were further clustered and anchored onto 29 chromosomes based on Hi-C data. A total of 16,163 protein-coding genes were predicted, of which 91.83% were functionally annotated. The expansion of transposable elements (TEs) accounts for the relatively large genome size of M. aurata, potentially aiding its adaptation to environmental conditions. Phylogenomic analyses based on 3,785 single-copy genes revealed that M. aurata is most closely related to Hipparchia semele. Further mitochondrial genome analysis of four Minois species placed M. aurata in a basal position within the genus, supporting it as an independent species. A total of 185 rapidly evolving and 232 specific gene families were identified in M. aurata. Functional enrichment analysis indicated that these gene families were mainly associated with ultraviolet radiation, heat and hypoxia responses. We also identified 234 positive selected genes in M. aurata, some of which are related to compound eye photoreceptor development, osmotic stress, and light stimulus response. Demographic analysis indicated that the effective population size of M. aurata decreased around 0.4 and 0.04 million years ago, respectively, coinciding with the localized sub-glaciation. Conclusion The chromosome-level genome offers a comprehensive genomic basis for understanding the evolutionary and adaptive strategies of Minois aurata in the unique arid valley environment of the Hengduan Mountains, while also providing valuable insights into the broader mechanisms of organism adaptation to such habitats.https://doi.org/10.1186/s12864-024-11058-8Arid valleyChromosome-level genomeMinois aurataAdaptive evolution |
| spellingShingle | Wenqian Hu Yi Wang Xiaoxiao Chen Jialong Huang Jingge Kuang Lei Wang Kangshan Mao Liang Dou Genome assembly of an endemic butterfly (Minois aurata) shed light on the genetic mechanisms underlying ecological adaptation to arid valley habitat BMC Genomics Arid valley Chromosome-level genome Minois aurata Adaptive evolution |
| title | Genome assembly of an endemic butterfly (Minois aurata) shed light on the genetic mechanisms underlying ecological adaptation to arid valley habitat |
| title_full | Genome assembly of an endemic butterfly (Minois aurata) shed light on the genetic mechanisms underlying ecological adaptation to arid valley habitat |
| title_fullStr | Genome assembly of an endemic butterfly (Minois aurata) shed light on the genetic mechanisms underlying ecological adaptation to arid valley habitat |
| title_full_unstemmed | Genome assembly of an endemic butterfly (Minois aurata) shed light on the genetic mechanisms underlying ecological adaptation to arid valley habitat |
| title_short | Genome assembly of an endemic butterfly (Minois aurata) shed light on the genetic mechanisms underlying ecological adaptation to arid valley habitat |
| title_sort | genome assembly of an endemic butterfly minois aurata shed light on the genetic mechanisms underlying ecological adaptation to arid valley habitat |
| topic | Arid valley Chromosome-level genome Minois aurata Adaptive evolution |
| url | https://doi.org/10.1186/s12864-024-11058-8 |
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