Yuanting Shen, Lidan Tao, Rengang Zhang, Gang Yao, Minjie Zhou, Weibang Sun, Yongpeng Ma
{"title":"基因组学对蒜果树(Malania oleifera)--一种种群数量极少的植物物种--的濒危和保护的启示。","authors":"Yuanting Shen, Lidan Tao, Rengang Zhang, Gang Yao, Minjie Zhou, Weibang Sun, Yongpeng Ma","doi":"10.1093/gigascience/giae070","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Advanced whole-genome sequencing techniques enable covering nearly all genome nucleotide variations and thus can provide deep insights into protecting endangered species. However, the use of genomic data to make conservation strategies is still rare, particularly for endangered plants. Here we performed comprehensive conservation genomic analysis for Malania oleifera, an endangered tree species with a high amount of nervonic acid. We used whole-genome resequencing data of 165 samples, covering 16 populations across the entire distribution range, to investigate the formation reasons of its extremely small population sizes and to evaluate the possible genomic offsets and changes of ecology niche suitability under future climate change.</p><p><strong>Results: </strong>Although M. oleifera maintains relatively high genetic diversity among endangered woody plants (θπ = 3.87 × 10-3), high levels of inbreeding have been observed, which have reduced genetic diversity in 3 populations (JM, NP, and BM2) and caused the accumulation of deleterious mutations. Repeated bottleneck events, recent inbreeding (∼490 years ago), and anthropogenic disturbance to wild habitats have aggravated the fragmentation of M. oleifera and made it endangered. Due to the significant effect of higher average annual temperature, populations distributed in low altitude exhibit a greater genomic offset. Furthermore, ecological niche modeling shows the suitable habitats for M. oleifera will decrease by 71.15% and 98.79% in 2100 under scenarios SSP126 and SSP585, respectively.</p><p><strong>Conclusions: </strong>The basic realizations concerning the threats to M. oleifera provide scientific foundation for defining management and adaptive units, as well as prioritizing populations for genetic rescue. Meanwhile, we highlight the importance of integrating genomic offset and ecological niche modeling to make targeted conservation actions under future climate change. Overall, our study provides a paradigm for genomics-directed conservation.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"13 ","pages":""},"PeriodicalIF":11.8000,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11417964/pdf/","citationCount":"0","resultStr":"{\"title\":\"Genomic insights into endangerment and conservation of the garlic-fruit tree (Malania oleifera), a plant species with extremely small populations.\",\"authors\":\"Yuanting Shen, Lidan Tao, Rengang Zhang, Gang Yao, Minjie Zhou, Weibang Sun, Yongpeng Ma\",\"doi\":\"10.1093/gigascience/giae070\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Advanced whole-genome sequencing techniques enable covering nearly all genome nucleotide variations and thus can provide deep insights into protecting endangered species. However, the use of genomic data to make conservation strategies is still rare, particularly for endangered plants. Here we performed comprehensive conservation genomic analysis for Malania oleifera, an endangered tree species with a high amount of nervonic acid. We used whole-genome resequencing data of 165 samples, covering 16 populations across the entire distribution range, to investigate the formation reasons of its extremely small population sizes and to evaluate the possible genomic offsets and changes of ecology niche suitability under future climate change.</p><p><strong>Results: </strong>Although M. oleifera maintains relatively high genetic diversity among endangered woody plants (θπ = 3.87 × 10-3), high levels of inbreeding have been observed, which have reduced genetic diversity in 3 populations (JM, NP, and BM2) and caused the accumulation of deleterious mutations. Repeated bottleneck events, recent inbreeding (∼490 years ago), and anthropogenic disturbance to wild habitats have aggravated the fragmentation of M. oleifera and made it endangered. Due to the significant effect of higher average annual temperature, populations distributed in low altitude exhibit a greater genomic offset. Furthermore, ecological niche modeling shows the suitable habitats for M. oleifera will decrease by 71.15% and 98.79% in 2100 under scenarios SSP126 and SSP585, respectively.</p><p><strong>Conclusions: </strong>The basic realizations concerning the threats to M. oleifera provide scientific foundation for defining management and adaptive units, as well as prioritizing populations for genetic rescue. Meanwhile, we highlight the importance of integrating genomic offset and ecological niche modeling to make targeted conservation actions under future climate change. Overall, our study provides a paradigm for genomics-directed conservation.</p>\",\"PeriodicalId\":12581,\"journal\":{\"name\":\"GigaScience\",\"volume\":\"13 \",\"pages\":\"\"},\"PeriodicalIF\":11.8000,\"publicationDate\":\"2024-01-02\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11417964/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"GigaScience\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/gigascience/giae070\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"MULTIDISCIPLINARY SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"GigaScience","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/gigascience/giae070","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}
Genomic insights into endangerment and conservation of the garlic-fruit tree (Malania oleifera), a plant species with extremely small populations.
Background: Advanced whole-genome sequencing techniques enable covering nearly all genome nucleotide variations and thus can provide deep insights into protecting endangered species. However, the use of genomic data to make conservation strategies is still rare, particularly for endangered plants. Here we performed comprehensive conservation genomic analysis for Malania oleifera, an endangered tree species with a high amount of nervonic acid. We used whole-genome resequencing data of 165 samples, covering 16 populations across the entire distribution range, to investigate the formation reasons of its extremely small population sizes and to evaluate the possible genomic offsets and changes of ecology niche suitability under future climate change.
Results: Although M. oleifera maintains relatively high genetic diversity among endangered woody plants (θπ = 3.87 × 10-3), high levels of inbreeding have been observed, which have reduced genetic diversity in 3 populations (JM, NP, and BM2) and caused the accumulation of deleterious mutations. Repeated bottleneck events, recent inbreeding (∼490 years ago), and anthropogenic disturbance to wild habitats have aggravated the fragmentation of M. oleifera and made it endangered. Due to the significant effect of higher average annual temperature, populations distributed in low altitude exhibit a greater genomic offset. Furthermore, ecological niche modeling shows the suitable habitats for M. oleifera will decrease by 71.15% and 98.79% in 2100 under scenarios SSP126 and SSP585, respectively.
Conclusions: The basic realizations concerning the threats to M. oleifera provide scientific foundation for defining management and adaptive units, as well as prioritizing populations for genetic rescue. Meanwhile, we highlight the importance of integrating genomic offset and ecological niche modeling to make targeted conservation actions under future climate change. Overall, our study provides a paradigm for genomics-directed conservation.
期刊介绍:
GigaScience seeks to transform data dissemination and utilization in the life and biomedical sciences. As an online open-access open-data journal, it specializes in publishing "big-data" studies encompassing various fields. Its scope includes not only "omic" type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale shareable data.