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Chen J, Wang Y. Understanding the salinity resilience and productivity of halophytes in saline environments. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112171. [PMID: 38969140 DOI: 10.1016/j.plantsci.2024.112171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 06/15/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024]
Abstract
The escalating salinity levels in cultivable soil pose a significant threat to agricultural productivity and, consequently, human sustenance. This problem is being exacerbated by natural processes and human activities, coinciding with a period of rapid population growth. Developing halophytic crops is needed to ensure food security is not impaired and land resources can be used sustainably. Evolution has created many close halophyte relatives of our major glycophytic crops, such as Puccinellia tenuiflora (relative of barley and wheat), Oryza coarctata (relative of rice) and Glycine soja (relative of soybean). There are also some halophytes have been subjected to semi-domestication and are considered as minor crops, such as Chenopodium quinoa. In this paper, we examine the prevailing comprehension of robust salinity resilience in halophytes. We summarize the existing strategies and technologies that equip researchers with the means to enhance the salt tolerance capabilities of primary crops and investigate the genetic makeup of halophytes.
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Affiliation(s)
- Jiahong Chen
- State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Wang
- State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China; Dalian Practical Biotechnology Co. LTD., Dalian, Liaoning 116200, China.
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2
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Fu R, Zhu Y, Liu Y, Yang Z, Lu R, Qiu Y, Lascoux M, Li P, Chen J. Shared xerophytic genes and their re-use in local adaptation to aridity in the desert plant Gymnocarpos przewalskii. Mol Ecol 2024; 33:e17380. [PMID: 38745400 DOI: 10.1111/mec.17380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 04/13/2024] [Accepted: 04/26/2024] [Indexed: 05/16/2024]
Abstract
In order to thrive and survive, plant species need to combine stability in the long term and rapid response to environmental challenges in the short term. The former would be reflected by parallel or convergent adaptation across species, and the latter by pronounced local adaptation among populations of the same species. In the present study, we generated a high-quality genome and re-sequenced 177 individuals for Gymnocarpos przewalskii, an important desert plant species from North-West China, to detect local adaptation. We first focus on ancient adaptation to aridity at the molecular level by comparing the genomic data of 15 species that vary in their ability to withstand aridity. We found that a total of 118 genes were shared across xerophytic species but absent from non-xerophytic species. Of the 65 found in G. przewalskii, 63 were under purifying selection and two under positive selection. We then focused on local adaptation. Up to 20% of the G. przewalskii genome showed signatures of local adaptation to aridity during population divergence. Thirteen of the selected shared xerophytic genes were reused in local adaptation after population differentiation. Hence, only about 20% of the genes shared and specific to xerophytic species and associated with adaptation to aridity were later recruited for local adaptation in G. przewalskii.
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Affiliation(s)
- Ruirui Fu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuxiang Zhu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ying Liu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhaoping Yang
- College of Life Sciences and Technologies, Tarim University, Aral, China
| | - Ruisen Lu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yingxiong Qiu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Pan Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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3
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Yang X, Su Y, Huang S, Hou Q, Wei P, Hao Y, Huang J, Xiao H, Ma Z, Xu X, Wang X, Cao S, Cao X, Zhang M, Wen X, Ma Y, Peng Y, Zhou Y, Cao K, Qiao G. Comparative population genomics reveals convergent and divergent selection in the apricot-peach-plum-mei complex. HORTICULTURE RESEARCH 2024; 11:uhae109. [PMID: 38883333 PMCID: PMC11179850 DOI: 10.1093/hr/uhae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/06/2024] [Indexed: 06/18/2024]
Abstract
The economically significant genus Prunus includes fruit and nut crops that have been domesticated for shared and specific agronomic traits; however, the genomic signals of convergent and divergent selection have not been elucidated. In this study, we aimed to detect genomic signatures of convergent and divergent selection by conducting comparative population genomic analyses of the apricot-peach-plum-mei (APPM) complex, utilizing a haplotype-resolved telomere-to-telomere (T2T) genome assembly and population resequencing data. The haplotype-resolved T2T reference genome for the plum cultivar was assembled through HiFi and Hi-C reads, resulting in two haplotypes 251.25 and 251.29 Mb in size, respectively. Comparative genomics reveals a chromosomal translocation of ~1.17 Mb in the apricot genomes compared with peach, plum, and mei. Notably, the translocation involves the D locus, significantly impacting titratable acidity (TA), pH, and sugar content. Population genetic analysis detected substantial gene flow between plum and apricot, with introgression regions enriched in post-embryonic development and pollen germination processes. Comparative population genetic analyses revealed convergent selection for stress tolerance, flower development, and fruit ripening, along with divergent selection shaping specific crop, such as somatic embryogenesis in plum, pollen germination in mei, and hormone regulation in peach. Notably, selective sweeps on chromosome 7 coincide with a chromosomal collinearity from the comparative genomics, impacting key fruit-softening genes such as PG, regulated by ERF and RMA1H1. Overall, this study provides insights into the genetic diversity, evolutionary history, and domestication of the APPM complex, offering valuable implications for genetic studies and breeding programs of Prunus crops.
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Affiliation(s)
- Xuanwen Yang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou 450009, China
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Su
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Xinjiang, Urumqi 830046, China
| | - Siyang Huang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Pengcheng Wei
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou 450009, China
| | - Yani Hao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China
| | - Jiaqi Huang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhiyao Ma
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiaodong Xu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuejing Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Mengyan Zhang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Yuhua Ma
- Institute of Pomology Science, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 570100, China
| | - Ke Cao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou 450009, China
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China
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De-Kayne R, Perry BW, McGowan KL, Landers J, Arias-Rodriguez L, Greenway R, Rodríguez Peña CM, Tobler M, Kelley JL. Evolutionary Rate Shifts in Coding and Regulatory Regions Underpin Repeated Adaptation to Sulfidic Streams in Poeciliid Fishes. Genome Biol Evol 2024; 16:evae087. [PMID: 38788745 PMCID: PMC11126329 DOI: 10.1093/gbe/evae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2024] [Indexed: 05/26/2024] Open
Abstract
Adaptation to extreme environments often involves the evolution of dramatic physiological changes. To better understand how organisms evolve these complex phenotypic changes, the repeatability and predictability of evolution, and possible constraints on adapting to an extreme environment, it is important to understand how adaptive variation has evolved. Poeciliid fishes represent a particularly fruitful study system for investigations of adaptation to extreme environments due to their repeated colonization of toxic hydrogen sulfide-rich springs across multiple species within the clade. Previous investigations have highlighted changes in the physiology and gene expression in specific species that are thought to facilitate adaptation to hydrogen sulfide-rich springs. However, the presence of adaptive nucleotide variation in coding and regulatory regions and the degree to which convergent evolution has shaped the genomic regions underpinning sulfide tolerance across taxa are unknown. By sampling across seven independent lineages in which nonsulfidic lineages have colonized and adapted to sulfide springs, we reveal signatures of shared evolutionary rate shifts across the genome. We found evidence of genes, promoters, and putative enhancer regions associated with both increased and decreased convergent evolutionary rate shifts in hydrogen sulfide-adapted lineages. Our analysis highlights convergent evolutionary rate shifts in sulfidic lineages associated with the modulation of endogenous hydrogen sulfide production and hydrogen sulfide detoxification. We also found that regions with shifted evolutionary rates in sulfide spring fishes more often exhibited convergent shifts in either the coding region or the regulatory sequence of a given gene, rather than both.
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Affiliation(s)
- Rishi De-Kayne
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Kerry L McGowan
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Jake Landers
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, México
| | - Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Carlos M Rodríguez Peña
- Instituto de Investigaciones Botánicas y Zoológicas, Universidad Autónoma de Santo Domingo, Santo Domingo 10105, Dominican Republic
| | - Michael Tobler
- Department of Biology, University of Missouri–St. Louis, St. Louis, MO 63131, USA
- Whitney R. Harris World Ecology Center, University of Missouri–St. Louis, St. Louis, MO 63121, USA
- WildCare Institute, Saint Louis Zoo, St. Louis, MO 63110, USA
| | - Joanna L Kelley
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95060, USA
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5
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Li B, Jia Y, Xu L, Zhang S, Long Z, Wang R, Guo Y, Zhang W, Jiao C, Li C, Xu Y. Transcriptional convergence after repeated duplication of an amino acid transporter gene leads to the independent emergence of the black husk/pericarp trait in barley and rice. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1282-1298. [PMID: 38124464 PMCID: PMC11022822 DOI: 10.1111/pbi.14264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/09/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023]
Abstract
The repeated emergence of the same trait (convergent evolution) in distinct species is an interesting phenomenon and manifests visibly the power of natural selection. The underlying genetic mechanisms have important implications to understand how the genome evolves under environmental challenges. In cereal crops, both rice and barley can develop black-coloured husk/pericarp due to melanin accumulation. However, it is unclear if this trait shares a common origin. Here, we fine-mapped the barley HvBlp gene controlling the black husk/pericarp trait and confirmed its function by gene silencing. The result was further supported by a yellow husk/pericarp mutant with deletion of the HvBlp gene, derived from gamma ray radiation of the wild-type W1. HvBlp encodes a putative tyrosine transporter homologous to the black husk gene OsBh4 in rice. Surprisingly, synteny and phylogenetic analyses showed that HvBlp and OsBh4 belonged to different lineages resulted from dispersed and tandem duplications, respectively, suggesting that the black husk/pericarp trait has emerged independently. The dispersed duplication (dated at 21.23 MYA) yielding HvBlp occurred exclusively in the common ancestor of Triticeae. HvBlp and OsBh4 displayed converged transcription in husk/pericarp tissues, contributing to the black husk/pericarp trait. Further transcriptome and metabolome data identified critical candidate genes and metabolites related to melanin production in barley. Taken together, our study described a compelling case of convergent evolution resulted from transcriptional convergence after repeated gene duplication, providing valuable genetic insights into phenotypic evolution. The identification of the black husk/pericarp genes in barley also has great potential in breeding for stress-resilient varieties with higher nutritional values.
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Affiliation(s)
- Bo Li
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Yong Jia
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Le Xu
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Shuo Zhang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Zhoukai Long
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Rong Wang
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Ying Guo
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Wenying Zhang
- Hubei Collaborative Innovation Centre for the industrialization of Major Grain Crops, College of AgricultureYangtze UniversityJingzhouChina
| | - Chunhai Jiao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
| | - Chengdao Li
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
| | - Yanhao Xu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement & Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina
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Morel M, Zhukova A, Lemoine F, Gascuel O. Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor. Genome Biol Evol 2024; 16:evae040. [PMID: 38451738 PMCID: PMC10986858 DOI: 10.1093/gbe/evae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 01/30/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Evolutionary convergences are observed at all levels, from phenotype to DNA and protein sequences, and changes at these different levels tend to be correlated. Notably, convergent mutations can lead to convergent changes in phenotype, such as changes in metabolism, drug resistance, and other adaptations to changing environments. We propose a two-component approach to detect mutations subject to convergent evolution in protein alignments. The "Emergence" component selects mutations that emerge more often than expected, while the "Correlation" component selects mutations that correlate with the convergent phenotype under study. With regard to Emergence, a phylogeny deduced from the alignment is provided by the user and is used to simulate the evolution of each alignment position. These simulations allow us to estimate the expected number of mutations in a neutral model, which is compared to the observed number of mutations in the data studied. In Correlation, a comparative phylogenetic approach, is used to measure whether the presence of each of the observed mutations is correlated with the convergent phenotype. Each component can be used on its own, for example Emergence when no phenotype is available. Our method is implemented in a standalone workflow and a webserver, called ConDor. We evaluate the properties of ConDor using simulated data, and we apply it to three real datasets: sedge PEPC proteins, HIV reverse transcriptase, and fish rhodopsin. The results show that the two components of ConDor complement each other, with an overall accuracy that compares favorably to other available tools, especially on large datasets.
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Affiliation(s)
- Marie Morel
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Université Claude Bernard Lyon 1, LBBE, UMR 5558, CNRS, VAS, Villeurbanne, 69100, France
| | - Anna Zhukova
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
- Institut Pasteur, Université Paris Cité, CNR Virus Des Infections Respiratoires, Paris, France
| | - Olivier Gascuel
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut de Systématique, Evolution, Biodiversité (UMR 7205—CNRS, Muséum National d’Histoire Naturelle, SU, EPHE, UA), Paris, France
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Xu S, Shao S, Feng X, Li S, Zhang L, Wu W, Liu M, Tracy ME, Zhong C, Guo Z, Wu CI, Shi S, He Z. Adaptation in Unstable Environments and Global Gene Losses: Small but Stable Gene Networks by the May-Wigner Theory. Mol Biol Evol 2024; 41:msae059. [PMID: 38507653 PMCID: PMC10991078 DOI: 10.1093/molbev/msae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/07/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024] Open
Abstract
Although gene loss is common in evolution, it remains unclear whether it is an adaptive process. In a survey of seven major mangrove clades that are woody plants in the intertidal zones of daily environmental perturbations, we noticed that they generally evolved reduced gene numbers. We then focused on the largest clade of Rhizophoreae and observed the continual gene set reduction in each of the eight species. A great majority of gene losses are concentrated on environmental interaction processes, presumably to cope with the constant fluctuations in the tidal environments. Genes of the general processes for woody plants are largely retained. In particular, fewer gene losses are found in physiological traits such as viviparous seeds, high salinity, and high tannin content. Given the broad and continual genome reductions, we propose the May-Wigner theory (MWT) of system stability as a possible mechanism. In MWT, the most effective solution for buffering continual perturbations is to reduce the size of the system (or to weaken the total genic interactions). Mangroves are unique as immovable inhabitants of the compound environments in the land-sea interface, where environmental gradients (such as salinity) fluctuate constantly, often drastically. Extending MWT to gene regulatory network (GRN), computer simulations and transcriptome analyses support the stabilizing effects of smaller gene sets in mangroves vis-à-vis inland plants. In summary, we show the adaptive significance of gene losses in mangrove plants, including the specific role of promoting phenotype innovation and a general role in stabilizing GRN in unstable environments as predicted by MWT.
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Affiliation(s)
- Shaohua Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Shao Shao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiao Feng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Sen Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Lingjie Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Weihong Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Min Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Miles E Tracy
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cairong Zhong
- Institute of Wetland Research, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, China
| | - Zixiao Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
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8
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Hou Q, Yu R, Shang C, Deng H, Wen Z, Qiu Z, Qiao G. Molecular characterization and evolutionary relationships of DOFs in four cherry species and functional analysis in sweet cherry. Int J Biol Macromol 2024; 263:130346. [PMID: 38403208 DOI: 10.1016/j.ijbiomac.2024.130346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
The DOF (DNA binding with one finger) has multiple functions in plants. However, it has received little attention in the research field of cherries. In this study, the evolutionary relationship and molecular characterization of DOF in four cherry species were analyzed, revealing its expression pattern in sweet cherry. There are 23 members in Prunus avium cv. 'Tieton', 88 in Prunus cerasus, 53 in Cerasus × yedoensis, and 27 in Cerasus serrulata. Most of these genes are intron-less or non-intron, with a conserved C2-C2 domain. Due to heterozygosity and chromosomal ploidy, whole-genome duplication (WGD) events occur to varying degrees, and DOF genes are contracted during evolution. Furthermore, these genes are affected by purifying selection pressure. Under low-temperature treatment, the expression of PavDOF2 and PavDOF18 were significantly up-regulated, while that of PavDOF16 is significantly down-regulated. The expression of PavDOF9, PavDOF12, PavDOF14, PavDOF16, PavDOF17, PavDOF18, and PavDOF19 exhibits an increasing trend during flower development and varies during sweet cherry fruit development. PavDOF1, PavDOF8, PavDOF9, and PavDOF15 are localized in the nucleus but is not transcriptionally active. The findings systemically demonstrate the molecular characteristics of DOF in different cherry varieties, providing a basis for further research on the functions of these genes.
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Affiliation(s)
- Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Runrun Yu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Chunqiong Shang
- College of Forestry, Guizhou University/ Institute for Forest Resources & Environment of Guizhou, Guiyang 550025, Guizhou Province, China
| | - Hong Deng
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Zhuang Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Zhilang Qiu
- School of Biology & Engineering, School of Health Medicine Modern Industry, Guizhou Medical University, Guiyang 550025, Guizhou Province, China
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China.
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9
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Wang M, Zhang R, Shu JP, Zheng XL, Wu XY, Chen JB, Wang MN, Shen H, Yan YH. Whole Genome Duplication Events Likely Contributed to the Aquatic Adaptive Evolution of Parkerioideae. PLANTS (BASEL, SWITZERLAND) 2024; 13:521. [PMID: 38498522 PMCID: PMC10893450 DOI: 10.3390/plants13040521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 03/20/2024]
Abstract
As the only aquatic lineage of Pteridaceae, Parkerioideae is distinct from many xeric-adapted species of the family and consists of the freshwater Ceratopteris species and the only mangrove ferns from the genus Acrostichum. Previous studies have shown that whole genome duplication (WGD) has occurred in Parkerioideae at least once and may have played a role in their adaptive evolution; however, more in-depth research regarding this is still required. In this study, comparative and evolutionary transcriptomics analyses were carried out to identify WGDs and explore their roles in the environmental adaptation of Parkerioideae. Three putative WGD events were identified within Parkerioideae, two of which were specific to Ceratopteris and Acrostichum, respectively. The functional enrichment analysis indicated that the lineage-specific WGD events have played a role in the adaptation of Parkerioideae to the low oxygen concentrations of aquatic habitats, as well as different aquatic environments of Ceratopteris and Acrostichum, such as the adaptation of Ceratopteris to reduced light levels and the adaptation of Acrostichum to high salinity. Positive selection analysis further provided evidence that the putative WGD events may have facilitated the adaptation of Parkerioideae to changes in habitat. Moreover, the gene family analysis indicated that the plasma membrane H+-ATPase (AHA), vacuolar H+-ATPase (VHA), and suppressor of K+ transport growth defect 1 (SKD1) may have been involved in the high salinity adaptation of Acrostichum. Our study provides new insights into the evolution and adaptations of Parkerioideae in different aquatic environments.
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Affiliation(s)
- Meng Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
| | - Rui Zhang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (R.Z.); (H.S.)
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Jiang-Ping Shu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xi-Long Zheng
- School of Traditional Medicine Materials Resource, Guangdong Pharmaceutical University, Yunfu 527322, China;
| | - Xin-Yi Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
| | - Jian-Bing Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
| | - Mei-Na Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
| | - Hui Shen
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (R.Z.); (H.S.)
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Yue-Hong Yan
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
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10
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Wang Q, Chen X, Meng Y, Niu M, Jia Y, Huang L, Ma W, Liang C, Li Z, Zhao L, Dang Z. The Potential Role of Genic-SSRs in Driving Ecological Adaptation Diversity in Caragana Plants. Int J Mol Sci 2024; 25:2084. [PMID: 38396759 PMCID: PMC10888960 DOI: 10.3390/ijms25042084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Caragana, a xerophytic shrub genus widely distributed in northern China, exhibits distinctive geographical substitution patterns and ecological adaptation diversity. This study employed transcriptome sequencing technology to investigate 12 Caragana species, aiming to explore genic-SSR variations in the Caragana transcriptome and identify their role as a driving force for environmental adaptation within the genus. A total of 3666 polymorphic genic-SSRs were identified across different species. The impact of these variations on the expression of related genes was analyzed, revealing a significant linear correlation (p < 0.05) between the length variation of 264 polymorphic genic-SSRs and the expression of associated genes. Additionally, 2424 polymorphic genic-SSRs were located in differentially expressed genes among Caragana species. Through weighted gene co-expression network analysis, the expressions of these genes were correlated with 19 climatic factors and 16 plant functional traits in various habitats. This approach facilitated the identification of biological processes associated with habitat adaptations in the studied Caragana species. Fifty-five core genes related to functional traits and climatic factors were identified, including various transcription factors such as MYB, TCP, ARF, and structural proteins like HSP90, elongation factor TS, and HECT. The roles of these genes in the ecological adaptation diversity of Caragana were discussed. Our study identified specific genomic components and genes in Caragana plants responsive to heterogeneous habitats. The results contribute to advancements in the molecular understanding of their ecological adaptation, lay a foundation for the conservation and development of Caragana germplasm resources, and provide a scientific basis for plant adaptation to global climate change.
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Affiliation(s)
- Qinglang Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Xing’er Chen
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Yue Meng
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Miaomiao Niu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Yuanyuan Jia
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Lei Huang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Wenhong Ma
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Cunzhu Liang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Zhiyong Li
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Liqing Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Zhenhua Dang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
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11
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Liu M, Song Y, Zhang S, Yu L, Yuan Z, Yang H, Zhang M, Zhou Z, Seim I, Liu S, Fan G, Yang H. A chromosome-level genome of electric catfish ( Malapterurus electricus) provided new insights into order Siluriformes evolution. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:1-14. [PMID: 38433969 PMCID: PMC10901758 DOI: 10.1007/s42995-023-00197-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 09/22/2023] [Indexed: 03/05/2024]
Abstract
The electric catfish (Malapterurus electricus), belonging to the family Malapteruridae, order Siluriformes (Actinopterygii: Ostariophysi), is one of the six branches that has independently evolved electrical organs. We assembled a 796.75 Mb M. electricus genome and anchored 88.72% sequences into 28 chromosomes. Gene family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate receptors. Convergent evolutionary analyses of electric organs among different lineage of electric fishes further revealed that the coding gene of rho guanine nucleotide exchange factor 4-like (arhgef4), which is associated with G-protein coupled receptor (GPCR) signaling pathway, underwent adaptive parallel evolution. Gene identification suggests visual degradation in catfishes, and an important role for taste in environmental adaptation. Our findings fill in the genomic data for a branch of electric fish and provide a relevant genetic basis for the adaptive evolution of Siluriformes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00197-8.
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Affiliation(s)
- Meiru Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Yue Song
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Suyu Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Lili Yu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Zengbao Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Hengjia Yang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Mengqi Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Zhuocheng Zhou
- Professional Committee of Native Aquatic Organisms and Water Ecosystem of China Fisheries Association, Beijing, 100125 China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
| | - Shanshan Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083 China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
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12
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Tong C. Convergent genomics and Arctic adaptation of ruminants. Proc Biol Sci 2024; 291:20232448. [PMID: 38166424 PMCID: PMC10762444 DOI: 10.1098/rspb.2023.2448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/04/2023] [Indexed: 01/04/2024] Open
Affiliation(s)
- Chao Tong
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
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13
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Medina-Chávez NO, Torres-Cerda A, Chacón JM, Harcombe WR, De la Torre-Zavala S, Travisano M. Disentangling a metabolic cross-feeding in a halophilic archaea-bacteria consortium. Front Microbiol 2023; 14:1276438. [PMID: 38179456 PMCID: PMC10764424 DOI: 10.3389/fmicb.2023.1276438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
Microbial syntrophy, a cooperative metabolic interaction among prokaryotes, serves a critical role in shaping communities, due to the auxotrophic nature of many microorganisms. Syntrophy played a key role in the evolution of life, including the hypothesized origin of eukaryotes. In a recent exploration of the microbial mats within the exceptional and uniquely extreme Cuatro Cienegas Basin (CCB), a halophilic isolate, designated as AD140, emerged as a standout due to its distinct growth pattern. Subsequent genome sequencing revealed AD140 to be a co-culture of a halophilic archaeon from the Halorubrum genus and a marine halophilic bacterium, Marinococcus luteus, both occupying the same ecological niche. This intriguing coexistence hints at an early-stage symbiotic relationship that thrives on adaptability. By delving into their metabolic interdependence through genomic analysis, this study aims to uncover shared characteristics that enhance their symbiotic association, offering insights into the evolution of halophilic microorganisms and their remarkable adaptations to high-salinity environments.
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Affiliation(s)
- Nahui Olin Medina-Chávez
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States
- BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Abigail Torres-Cerda
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Instituto de Biotecnología, San Nicolás de los Garza, San Nicolás de los Garza, Mexico
| | - Jeremy M. Chacón
- Minnesota Supercomputing Institute, Minneapolis, MN, United States
| | - William R. Harcombe
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States
- BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Susana De la Torre-Zavala
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Instituto de Biotecnología, San Nicolás de los Garza, San Nicolás de los Garza, Mexico
| | - Michael Travisano
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States
- BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
- Minnesota Center for the Philosophy of Science, University of Minnesota, Minneapolis, MN, United States
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14
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Arias PM, Butler J, Randhawa GS, Soltysiak MPM, Hill KA, Kari L. Environment and taxonomy shape the genomic signature of prokaryotic extremophiles. Sci Rep 2023; 13:16105. [PMID: 37752120 PMCID: PMC10522608 DOI: 10.1038/s41598-023-42518-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
This study provides comprehensive quantitative evidence suggesting that adaptations to extreme temperatures and pH imprint a discernible environmental component in the genomic signature of microbial extremophiles. Both supervised and unsupervised machine learning algorithms were used to analyze genomic signatures, each computed as the k-mer frequency vector of a 500 kbp DNA fragment arbitrarily selected to represent a genome. Computational experiments classified/clustered genomic signatures extracted from a curated dataset of [Formula: see text] extremophile (temperature, pH) bacteria and archaea genomes, at multiple scales of analysis, [Formula: see text]. The supervised learning resulted in high accuracies for taxonomic classifications at [Formula: see text], and medium to medium-high accuracies for environment category classifications of the same datasets at [Formula: see text]. For [Formula: see text], our findings were largely consistent with amino acid compositional biases and codon usage patterns in coding regions, previously attributed to extreme environment adaptations. The unsupervised learning of unlabelled sequences identified several exemplars of hyperthermophilic organisms with large similarities in their genomic signatures, in spite of belonging to different domains in the Tree of Life.
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Affiliation(s)
- Pablo Millán Arias
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada.
| | - Joseph Butler
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Gurjit S Randhawa
- School of Mathematical and Computational Sciences, University of Prince Edward Island, Charlottetown, PE, Canada
| | | | - Kathleen A Hill
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Lila Kari
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada
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15
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Gonçalves C, Harrison MC, Steenwyk JL, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Rokas A. Diverse signatures of convergent evolution in cacti-associated yeasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557833. [PMID: 37745407 PMCID: PMC10515907 DOI: 10.1101/2023.09.14.557833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently ~17 times. Using machine-learning, we further found that cactophily can be predicted with 76% accuracy from functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which is likely associated with duplication and altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall-degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved through disparate molecular mechanisms. Remarkably, multiple cactophilic lineages and their close relatives are emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle-and perhaps more generally lifestyles favoring thermotolerance-may preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.
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Affiliation(s)
- Carla Gonçalves
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Present address: Associate Laboratory i4HB—Institute for Health and Bioeconomy and UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Present address: UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Marie-Claire Harrison
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Jacob L. Steenwyk
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Dana A. Opulente
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institu te, University of Wisconsin-Madison, Madison, WI 53726, USA
- Biology Department, Villanova University, Villanova, PA 19085, USA
| | - Abigail L. LaBella
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte NC 28223
| | - John F. Wolters
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institu te, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Xiaofan Zhou
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | | | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institu te, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Antonis Rokas
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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16
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Wang Z, Pu J, Richards C, Giannetti E, Cong H, Lin Z, Chung H. Evolution of a fatty acyl-CoA elongase underlies desert adaptation in Drosophila. SCIENCE ADVANCES 2023; 9:eadg0328. [PMID: 37647401 PMCID: PMC10468142 DOI: 10.1126/sciadv.adg0328] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
Traits that allow species to survive in extreme environments such as hot-arid deserts have independently evolved in multiple taxa. However, the genetic and evolutionary mechanisms underlying these traits have thus far not been elucidated. Here, we show that Drosophila mojavensis, a desert-adapted fruit fly species, has evolved high desiccation resistance by producing long-chain methyl-branched cuticular hydrocarbons (mbCHCs) that contribute to a cuticular lipid layer reducing water loss. We show that the ability to synthesize these longer mbCHCs is due to evolutionary changes in a fatty acyl-CoA elongase (mElo). mElo knockout in D. mojavensis led to loss of longer mbCHCs and reduction of desiccation resistance at high temperatures but did not affect mortality at either high temperatures or desiccating conditions individually. Phylogenetic analysis showed that mElo is a Drosophila-specific gene, suggesting that while the physiological mechanisms underlying desert adaptation may be similar between species, the genes involved in these mechanisms may be species or lineage specific.
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Affiliation(s)
- Zinan Wang
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - Jian Pu
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
- College of Agriculture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Cole Richards
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Elaina Giannetti
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Haosu Cong
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO 63104, USA
| | - Henry Chung
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
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17
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Ryan K, Greenway R, Landers J, Arias-Rodriguez L, Tobler M, Kelley JL. Selection on standing genetic variation mediates convergent evolution in extremophile fish. Mol Ecol 2023; 32:5042-5054. [PMID: 37548336 DOI: 10.1111/mec.17081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/23/2023] [Accepted: 07/11/2023] [Indexed: 08/08/2023]
Abstract
Hydrogen sulfide is a toxic gas that disrupts numerous biological processes, including energy production in the mitochondria, yet fish in the Poecilia mexicana species complex have independently evolved sulfide tolerance several times. Despite clear evidence for convergence at the phenotypic level in these fishes, it is unclear if the repeated evolution of hydrogen sulfide tolerance is the result of similar genomic changes. To address this gap, we used a targeted capture approach to sequence genes associated with sulfide processes and toxicity from five sulfidic and five nonsulfidic populations in the species complex. By comparing sequence variation in candidate genes to a reference set, we identified similar population structure and differentiation, suggesting that patterns of variation in most genes associated with sulfide processes and toxicity are due to demographic history and not selection. But the presence of tree discordance for a subset of genes suggests that several loci are evolving divergently between ecotypes. We identified two differentiation outlier genes that are associated with sulfide detoxification in the mitochondria that have signatures of selection in all five sulfidic populations. Further investigation into these regions identified long, shared haplotypes among sulfidic populations. Together, these results reveal that selection on standing genetic variation in putatively adaptive genes may be driving phenotypic convergence in this species complex.
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Affiliation(s)
- Kara Ryan
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Ryan Greenway
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Constance, Germany
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Jake Landers
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, Mexico
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, USA
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18
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Belcour A, Got J, Aite M, Delage L, Collén J, Frioux C, Leblanc C, Dittami SM, Blanquart S, Markov GV, Siegel A. Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe. Genome Res 2023; 33:gr.277056.122. [PMID: 37468308 PMCID: PMC10629481 DOI: 10.1101/gr.277056.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 05/23/2023] [Indexed: 07/21/2023]
Abstract
Comparative analysis of genome-scale metabolic networks (GSMNs) may yield important information on the biology, evolution, and adaptation of species. However, it is impeded by the high heterogeneity of the quality and completeness of structural and functional genome annotations, which may bias the results of such comparisons. To address this issue, we developed AuCoMe, a pipeline to automatically reconstruct homogeneous GSMNs from a heterogeneous set of annotated genomes without discarding available manual annotations. We tested AuCoMe with three data sets, one bacterial, one fungal, and one algal, and showed that it successfully reduces technical biases while capturing the metabolic specificities of each organism. Our results also point out shared and divergent metabolic traits among evolutionarily distant algae, underlining the potential of AuCoMe to accelerate the broad exploration of metabolic evolution across the tree of life.
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Affiliation(s)
| | - Jeanne Got
- Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France
| | - Méziane Aite
- Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France
| | - Ludovic Delage
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Jonas Collén
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | | | - Catherine Leblanc
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Simon M Dittami
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | | | - Gabriel V Markov
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Anne Siegel
- Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France;
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19
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Cao Y, Almeida-Silva F, Zhang WP, Ding YM, Bai D, Bai WN, Zhang BW, Van de Peer Y, Zhang DY. Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae). Mol Biol Evol 2023; 40:msad121. [PMID: 37216901 PMCID: PMC10257982 DOI: 10.1093/molbev/msad121] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/06/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023] Open
Abstract
When challenged by similar environmental conditions, phylogenetically distant taxa often independently evolve similar traits (convergent evolution). Meanwhile, adaptation to extreme habitats might lead to divergence between taxa that are otherwise closely related. These processes have long existed in the conceptual sphere, yet molecular evidence, especially for woody perennials, is scarce. The karst endemic Platycarya longipes and its only congeneric species, Platycarya strobilacea, which is widely distributed in the mountains in East Asia, provide an ideal model for examining the molecular basis of both convergent evolution and speciation. Using chromosome-level genome assemblies of both species, and whole-genome resequencing data from 207 individuals spanning their entire distribution range, we demonstrate that P. longipes and P. strobilacea form two species-specific clades, which diverged around 2.09 million years ago. We find an excess of genomic regions exhibiting extreme interspecific differentiation, potentially due to long-term selection in P. longipes, likely contributing to the incipient speciation of the genus Platycarya. Interestingly, our results unveil underlying karst adaptation in both copies of the calcium influx channel gene TPC1 in P. longipes. TPC1 has previously been identified as a selective target in certain karst-endemic herbs, indicating a convergent adaptation to high calcium stress among karst-endemic species. Our study reveals the genic convergence of TPC1 among karst endemics and the driving forces underneath the incipient speciation of the two Platycarya lineages.
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Affiliation(s)
- Yu Cao
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Fabricio Almeida-Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Wei-Ping Zhang
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ya-Mei Ding
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Dan Bai
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Bo-Wen Zhang
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
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20
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Li J, Xiao X, Zhou M, Zhang Y. Strategy for the Adaptation to Stressful Conditions of the Novel Isolated Conditional Piezophilic Strain Halomonas titanicae ANRCS81. Appl Environ Microbiol 2023; 89:e0130422. [PMID: 36912687 PMCID: PMC10057041 DOI: 10.1128/aem.01304-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 02/10/2023] [Indexed: 03/14/2023] Open
Abstract
Microorganisms have successfully predominated deep-sea ecosystems, while we know little about their adaptation strategy to multiple environmental stresses therein, including high hydrostatic pressure (HHP). Here, we focused on the genus Halomonas, one of the most widely distributed halophilic bacterial genera in marine ecosystems and isolated a piezophilic strain Halomonas titanicae ANRCS81 from Antarctic deep-sea sediment. The strain grew under a broad range of temperatures (2 to 45°C), pressures (0.1 to 55 MPa), salinities (NaCl, 0.5 to 17.5%, wt/vol), and chaotropic agent (Mg2+, 0 to 0.9 M) with either oxygen or nitrate as an electron acceptor. Genome annotation revealed that strain ANRCS81 expressed potential antioxidant genes/proteins and possessed versatile energy generation pathways. Based on the transcriptomic analysis, when the strain was incubated at 40 MPa, genes related to antioxidant defenses, anaerobic respiration, and fermentation were upregulated, indicating that HHP induced intracellular oxidative stress. Under HHP, superoxide dismutase (SOD) activity increased, glucose consumption increased with less CO2 generation, and nitrate/nitrite consumption increased with more ammonium generation. The cellular response to HHP represents the common adaptation developed by Halomonas to inhabit and drive geochemical cycling in deep-sea environments. IMPORTANCE Microbial growth and metabolic responses to environmental changes are core aspects of adaptation strategies developed during evolution. In particular, high hydrostatic pressure (HHP) is the most common but least examined environmental factor driving microbial adaptation in the deep sea. According to recent studies, microorganisms developed a common adaptation strategy to multiple stresses, including HHP, with antioxidant defenses and energy regulation as key components, but experimental data are lacking. Meanwhile, cellular SOD activity is elevated under HHP. The significance of this research lies in identifying the HHP adaptation strategy of a Halomonas strain at the genomic, transcriptomic, and metabolic activity levels, which will allow researchers to bridge environmental factors with the ecological function of marine microorganisms.
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Affiliation(s)
- Jiakang Li
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Meng Zhou
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zhang
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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21
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Zhang X, Kuang T, Dong W, Qian Z, Zhang H, Landis JB, Feng T, Li L, Sun Y, Huang J, Deng T, Wang H, Sun H. Genomic convergence underlying high-altitude adaptation in alpine plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36960823 DOI: 10.1111/jipb.13485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/21/2023] [Indexed: 06/18/2023]
Abstract
Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection. However, genomic evidence for convergent adaptation to extreme environments remains scarce. Here, we assembled reference genomes of two alpine plants, Saussurea obvallata (Asteraceae) and Rheum alexandrae (Polygonaceae), with 37,938 and 61,463 annotated protein-coding genes. By integrating an additional five alpine genomes, we elucidated genomic convergence underlying high-altitude adaptation in alpine plants. Our results detected convergent contractions of disease-resistance genes in alpine genomes, which might be an energy-saving strategy for surviving in hostile environments with only a few pathogens present. We identified signatures of positive selection on a set of genes involved in reproduction and respiration (e.g., MMD1, NBS1, and HPR), and revealed signatures of molecular convergence on genes involved in self-incompatibility, cell wall modification, DNA repair and stress resistance, which may underlie adaptation to extreme cold, high ultraviolet radiation and hypoxia environments. Incorporating transcriptomic data, we further demonstrated that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding light on the genetic mechanisms of the adaptive "greenhouse" morphology. Our integrative data provide novel insights into convergent evolution at a high-taxonomic level, aiding in a deep understanding of genetic adaptation to complex environments.
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Affiliation(s)
- Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
| | - Tianhui Kuang
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
| | - Wenlin Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhihao Qian
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey Hortorium, Cornell University, Ithaca, New York, 14850, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Tao Feng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
| | - Lijuan Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
| | - Jinling Huang
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Department of Biology, East Carolina University, Greenville, North Carolina, 27858, USA
| | - Tao Deng
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
| | - Hang Sun
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
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22
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Hu Y, Wang X, Xu Y, Yang H, Tong Z, Tian R, Xu S, Yu L, Guo Y, Shi P, Huang S, Yang G, Shi S, Wei F. Molecular mechanisms of adaptive evolution in wild animals and plants. SCIENCE CHINA. LIFE SCIENCES 2023; 66:453-495. [PMID: 36648611 PMCID: PMC9843154 DOI: 10.1007/s11427-022-2233-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/30/2022] [Indexed: 01/18/2023]
Abstract
Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.
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Affiliation(s)
- Yibo Hu
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiaoping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yongchao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zeyu Tong
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ran Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Shuangquan Huang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Fuwen Wei
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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23
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Hotaling S, Desvignes T, Sproul JS, Lins LSF, Kelley JL. Pathways to polar adaptation in fishes revealed by long-read sequencing. Mol Ecol 2023; 32:1381-1397. [PMID: 35561000 DOI: 10.1111/mec.16501] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/31/2022] [Accepted: 05/05/2022] [Indexed: 11/28/2022]
Abstract
Long-read sequencing is driving a new reality for genome science in which highly contiguous assemblies can be produced efficiently with modest resources. Genome assemblies from long-read sequences are particularly exciting for understanding the evolution of complex genomic regions that are often difficult to assemble. In this study, we utilized long-read sequencing data to generate a high-quality genome assembly for an Antarctic eelpout, Ophthalmolycus amberensis, the first for the globally distributed family Zoarcidae. We used this assembly to understand how O. amberensis has adapted to the harsh Southern Ocean and compared it to another group of Antarctic fishes: the notothenioids. We showed that selection has largely acted on different targets in eelpouts relative to notothenioids. However, we did find some overlap; in both groups, genes involved in membrane structure, thermal tolerance and vision have evidence of positive selection. We found evidence for historical shifts of transposable element activity in O. amberensis and other polar fishes, perhaps reflecting a response to environmental change. We were specifically interested in the evolution of two complex genomic loci known to underlie key adaptations to polar seas: haemoglobin and antifreeze proteins (AFPs). We observed unique evolution of the haemoglobin MN cluster in eelpouts and related fishes in the suborder Zoarcoidei relative to other Perciformes. For AFPs, we identified the first species in the suborder with no evidence of afpIII sequences (Cebidichthys violaceus) in the genomic region where they are found in all other Zoarcoidei, potentially reflecting a lineage-specific loss of this cluster. Beyond polar fishes, our results highlight the power of long-read sequencing to understand genome evolution.
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Affiliation(s)
- Scott Hotaling
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - John S Sproul
- Department of Biology, University of Nebraska Omaha, Omaha, Nebraska, USA
| | - Luana S F Lins
- Australian National Insect Collection, CSIRO, Canberra, Australia
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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24
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Wee GN, Lyou ES, Hong JK, No JH, Kim SB, Lee TK. Phenotypic convergence of bacterial adaption to sub-lethal antibiotic treatment. Front Cell Infect Microbiol 2022; 12:913415. [PMID: 36467735 PMCID: PMC9714565 DOI: 10.3389/fcimb.2022.913415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 10/05/2022] [Indexed: 01/01/2024] Open
Abstract
Microorganisms can adapt quickly to changes in their environment, leading to various phenotypes. The dynamic for phenotypic plasticity caused by environmental variations has not yet been fully investigated. In this study, we analyzed the time-series of phenotypic changes in Staphylococcus cells during adaptive process to antibiotics stresses using flow cytometry and Raman spectroscopy. The nine antibiotics with four different mode of actions were treated in bacterial cells at a sub-lethal concentration to give adaptable stress. Although the growth rate initially varied depending on the type of antibiotic, most samples reached the maximum growth comparable to the control through the short-term adaptation after 24 h. The phenotypic diversity, which showed remarkable changes depending on antibiotic treatment, converged identical to the control over time. In addition, the phenotype with cellular biomolecules converted into a bacterial cell that enhance tolerance to antibiotic stress with increases in cytochrome and lipid. Our findings demonstrated that the convergence into the phenotypes that enhance antibiotic tolerance in a short period when treated with sub-lethal concentrations, and highlight the feasibility of phenotypic approaches in the advanced antibiotic treatment.
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Affiliation(s)
| | | | | | | | | | - Tae Kwon Lee
- Department of Environmental and Energy Engineering, Yonsei University, Wonju, South Korea
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Yang X, Yu H, Duncan S, Zhang Y, Cheema J, Liu H, Benjamin Miller J, Zhang J, Kwok CK, Zhang H, Ding Y. RNA G-quadruplex structure contributes to cold adaptation in plants. Nat Commun 2022; 13:6224. [PMID: 36266343 PMCID: PMC9585020 DOI: 10.1038/s41467-022-34040-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/11/2022] [Indexed: 12/24/2022] Open
Abstract
Nucleotide composition is suggested to infer gene functionality and ecological adaptation of species to distinct environments. However, the underlying biological function of nucleotide composition dictating environmental adaptations is largely unknown. Here, we systematically analyze the nucleotide composition of transcriptomes across 1000 plants (1KP) and their corresponding habitats. Intriguingly, we find that plants growing in cold climates have guanine (G)-enriched transcriptomes, which are prone to forming RNA G-quadruplex structures. Both immunofluorescence detection and in vivo structure profiling reveal that RNA G-quadruplex formation in plants is globally enhanced in response to cold. Cold-responsive RNA G-quadruplexes strongly enhanced mRNA stability, rather than affecting translation. Disruption of individual RNA G-quadruplex promotes mRNA decay in the cold, leading to impaired plant cold response. Therefore, we propose that plants adopted RNA G-quadruplex structure as a molecular signature to facilitate their adaptation to the cold during evolution.
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Affiliation(s)
- Xiaofei Yang
- grid.27446.330000 0004 1789 9163Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024 China ,grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,grid.9227.e0000000119573309CAS-JIC Center of Excellence for Plant and Microbial Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Haopeng Yu
- grid.27446.330000 0004 1789 9163Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024 China ,grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Susan Duncan
- grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Yueying Zhang
- grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Jitender Cheema
- grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Haifeng Liu
- grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom ,grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018 China
| | - J. Benjamin Miller
- grid.8273.e0000 0001 1092 7967School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ United Kingdom
| | - Jie Zhang
- grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Chun Kit Kwok
- grid.35030.350000 0004 1792 6846Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China ,grid.35030.350000 0004 1792 6846Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057 China
| | - Huakun Zhang
- grid.27446.330000 0004 1789 9163Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024 China
| | - Yiliang Ding
- grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
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Guo Z, Xu S, Xie W, Shao S, Feng X, He Z, Zhong C, Huang K, Wu CI, Shi S. Adaptation to a new environment with pre-adaptive genomic features - Evidence from woody plants colonizing the land-sea interface. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1411-1424. [PMID: 35796621 DOI: 10.1111/tpj.15899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 06/12/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Adaptation to new environments is a key evolutionary process which presumably involves complex genomic changes. Mangroves, a collection of approximately 80 woody plants that have independently invaded intertidal zones >20 times, are ideal for studying this process. We assembled near-chromosome-scale genomes of three Xylocarpus species as well as an outgroup species using single-molecule real-time sequencing. Phylogenomic analysis reveals two separate lineages, one with the mangrove Xylocarpus granatum and the other comprising a mangrove Xylocarpus moluccensis and a terrestrial Xylocarpus rumphii. In conjunction with previous studies, we identified several genomic features associated with mangroves: (i) signals of positive selection in genes related to salt tolerance and root development; (ii) genome-wide elevated ratios of non-synonymous to synonymous substitution relative to terrestrial relatives; and (iii) active elimination of long terminal repeats. These features are found in the terrestrial X. rumphii in addition to the two mangroves. These genomic features, not being strictly mangrove-specific, are hence considered pre-adaptive. We infer that the coastal but non-intertidal habitat of X. rumphii may have predisposed the common ancestor to invasion of true mangrove habitats. Other features including the preferential retention of duplicated genes and intolerance to pseudogenization are not found in X. rumphii and are likely true adaptive features in mangroves. In conclusion, by studying adaptive shift and partial shifts among closely related species, we set up a framework to study genomic features that are acquired at different stages of the pre-adaptation and adaptation to new environments.
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Affiliation(s)
- Zixiao Guo
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, Guangdong, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, Guangdong, China
| | - Wei Xie
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, Guangdong, China
| | - Shao Shao
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, Guangdong, China
| | - Xiao Feng
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, Guangdong, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, Guangdong, China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), 571199, Haikou, Hainan, China
| | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, Guangdong, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, Guangdong, China
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Exploitation of Plant Growth Promoting Bacteria for Sustainable Agriculture: Hierarchical Approach to Link Laboratory and Field Experiments. Microorganisms 2022; 10:microorganisms10050865. [PMID: 35630310 PMCID: PMC9144938 DOI: 10.3390/microorganisms10050865] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 11/24/2022] Open
Abstract
To feed a world population, which will reach 9.7 billion in 2050, agricultural production will have to increase by 35–56%. Therefore, more food is urgently needed. Yield improvements for any given crop would require adequate fertilizer, water, and plant protection from pests and disease, but their further abuse will be economically disadvantageous and will have a negative impact on the environment. Using even more agricultural inputs is simply not possible, and the availability of arable land will be increasingly reduced due to climate changes. To improve agricultural production without further consumption of natural resources, farmers have a powerful ally: the beneficial microorganisms inhabiting the rhizosphere. However, to fully exploit the benefits of these microorganisms and therefore to widely market microbial-based products, there are still gaps that need to be filled, and here we will describe some critical issues that should be better addressed.
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Nizam A, Meera SP, Kumar A. Genetic and molecular mechanisms underlying mangrove adaptations to intertidal environments. iScience 2022; 25:103547. [PMID: 34988398 PMCID: PMC8693430 DOI: 10.1016/j.isci.2021.103547] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mangroves are halophytic plants belonging to diverse angiosperm families that are adapted to highly stressful intertidal zones between land and sea. They are special, unique, and one of the most productive ecosystems that play enormous ecological roles and provide a large number of benefits to the coastal communities. To thrive under highly stressful conditions, mangroves have innovated several key morphological, anatomical, and physio-biochemical adaptations. The evolution of the unique adaptive modifications might have resulted from a host of genetic and molecular changes and to date we know little about the nature of these genetic and molecular changes. Although slow, new information has accumulated over the last few decades on the genetic and molecular regulation of the mangrove adaptations, a comprehensive review on it is not yet available. This review provides up-to-date consolidated information on the genetic, epigenetic, and molecular regulation of mangrove adaptive traits.
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Affiliation(s)
- Ashifa Nizam
- Department of Plant Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala 671316, India
| | - Suraj Prasannakumari Meera
- Department of Biotechnology and Microbiology, Dr. Janaki Ammal Campus, Kannur University, Palayad, Kerala 670661, India
| | - Ajay Kumar
- Department of Plant Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala 671316, India
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Wang W, Gao L, Cui X. A New Year's spotlight on two years of publication. PLANT COMMUNICATIONS 2022; 3:100274. [PMID: 35059635 PMCID: PMC8760135 DOI: 10.1016/j.xplc.2021.100274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
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Raman G, Nam GH, Park S. Extensive reorganization of the chloroplast genome of Corydalis platycarpa: A comparative analysis of their organization and evolution with other Corydalis plastomes. FRONTIERS IN PLANT SCIENCE 2022; 13:1043740. [PMID: 37090468 PMCID: PMC10115153 DOI: 10.3389/fpls.2022.1043740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/07/2022] [Indexed: 05/03/2023]
Abstract
Introduction The chloroplast (cp) is an autonomous plant organelle with an individual genome that encodes essential cellular functions. The genome architecture and gene content of the cp is highly conserved in angiosperms. The plastome of Corydalis belongs to the Papaveraceae family, and the genome is comprised of unusual rearrangements and gene content. Thus far, no extensive comparative studies have been carried out to understand the evolution of Corydalis chloroplast genomes. Methods Therefore, the Corydalis platycarpa cp genome was sequenced, and wide-scale comparative studies were conducted using publicly available twenty Corydalis plastomes. Results Comparative analyses showed that an extensive genome rearrangement and IR expansion occurred, and these events evolved independently in the Corydalis species. By contrast, the plastomes of its closely related subfamily Papaveroideae and other Ranunculales taxa are highly conserved. On the other hand, the synapomorphy characteristics of both accD and the ndh gene loss events happened in the common ancestor of the Corydalis and sub-clade of the Corydalis lineage, respectively. The Corydalis-sub clade species (ndh lost) are distributed predominantly in the Qinghai-Tibetan plateau (QTP) region. The phylogenetic analysis and divergence time estimation were also employed for the Corydalis species. Discussion The divergence time of the ndh gene in the Corydalis sub-clade species (44.31 - 15.71 mya) coincides very well with the uplift of the Qinghai-Tibet Plateau in Oligocene and Miocene periods, and maybe during this period, it has probably triggered the radiation of the Corydalis species. Conclusion To the best of the authors' knowledge, this is the first large-scale comparative study of Corydalis plastomes and their evolution. The present study may provide insights into the plastome architecture and the molecular evolution of Corydalis species.
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Affiliation(s)
- Gurusamy Raman
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Gi-Heum Nam
- Plants Resource Division, Biological Resources Research Department, National Institute of Biological Resources, Seo-gu, Incheon, Republic of Korea
- *Correspondence: SeonJoo Park, ; Gi-Heum Nam,
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
- *Correspondence: SeonJoo Park, ; Gi-Heum Nam,
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Tanigaki S, Uchino A, Okawa S, Miura C, Hamamura K, Matsuo M, Yoshino N, Ueno N, Toyama Y, Fukumi N, Kijima E, Masuda T, Shimono Y, Tominaga T, Iwakami S. Gene expression shapes the patterns of parallel evolution of herbicide resistance in the agricultural weed Monochoria vaginalis. THE NEW PHYTOLOGIST 2021; 232:928-940. [PMID: 34270808 DOI: 10.1111/nph.17624] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
The evolution of herbicide resistance in weeds is an example of parallel evolution, through which genes encoding herbicide target proteins are repeatedly represented as evolutionary targets. The number of herbicide target-site genes differs among species, and little is known regarding the effects of duplicate gene copies on the evolution of herbicide resistance. We investigated the evolution of herbicide resistance in Monochoria vaginalis, which carries five copies of sulfonylurea target-site acetolactate synthase (ALS) genes. Suspected resistant populations collected across Japan were investigated for herbicide sensitivity and ALS gene sequences, followed by functional characterization and ALS gene expression analysis. We identified over 60 resistant populations, all of which carried resistance-conferring amino acid substitutions exclusively in MvALS1 or MvALS3. All MvALS4 alleles carried a loss-of-function mutation. Although the enzymatic properties of ALS encoded by these genes were not markedly different, the expression of MvALS1 and MvALS3 was prominently higher among all ALS genes. The higher expression of MvALS1 and MvALS3 is the driving force of the biased representation of genes during the evolution of herbicide resistance in M. vaginalis. Our findings highlight that gene expression is a key factor in creating evolutionary hotspots.
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Affiliation(s)
- Shinji Tanigaki
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Akira Uchino
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Tsu, 514-2392, Japan
| | - Shigenori Okawa
- Miyagi Prefectural Furukawa Agricultural Experiment Station, Fukoku 88, Furukawa-Osaki, 989-6227, Japan
| | - Chikako Miura
- Akita Prefectural Agricultural Experiment Station, 34-1 Yuwaaikawa-azagenpachizawa, Akita, 010-1231, Japan
| | - Kenshiro Hamamura
- Japan Association for Advancement of Phyto-Regulators (JAPR), 860 Kashiwada-cho, Ushiku, 300-1211, Japan
| | - Mitsuhiro Matsuo
- Field Science Center, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-kibanadai-nishi, Miyazaki, 889-2192, Japan
| | - Namiko Yoshino
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, 50 Harajukuminami, Arai, 960-2156, Japan
| | - Naoya Ueno
- Yamanashi Prefectural Agritechnology Center, 1100 Shimoimai, Kai, 400-0105, Japan
| | - Yusuke Toyama
- Shizuoka Prefectural Research Institute of Agriculture and Forestry, 678-1 Tomigaoka, Iwata, 438-0803, Japan
| | - Naoya Fukumi
- Tottori Agricultural Experiment Station, 260 Hashimoto, Tottori, 680-1142, Japan
| | - Eiji Kijima
- Yamaguchi Prefectural Agriculture and Forestry General Technology Center, 1-1-1 Ouchihikami, Yamaguchi, 753-0231, Japan
| | - Taro Masuda
- Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, 573-0101, Japan
| | - Yoshiko Shimono
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tohru Tominaga
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Satoshi Iwakami
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
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Rieseberg LH, Gao L. Plant Evolutionary Adaptation. PLANT COMMUNICATIONS 2020; 1:100118. [PMID: 33367271 PMCID: PMC7747965 DOI: 10.1016/j.xplc.2020.100118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver BC V6T1Z4, Canada
| | - Lexuan Gao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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