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Xu W, Wu YH, Zhou WW, Chen HM, Zhang BL, Chen JM, Xu W, Rao DQ, Zhao H, Yan F, Yuan Z, Jiang K, Jin JQ, Hou M, Zou D, Wang LJ, Zheng Y, Li JT, Jiang J, Zeng XM, Chen Y, Liao ZY, Li C, Li XY, Gao W, Wang K, Zhang DR, Lu C, Yin T, Ding Z, Zhao GG, Chai J, Zhao WG, Zhang YP, Wiens JJ, Che J. Hidden hotspots of amphibian biodiversity in China. Proc Natl Acad Sci U S A 2024; 121:e2320674121. [PMID: 38684007 PMCID: PMC11098104 DOI: 10.1073/pnas.2320674121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/21/2024] [Indexed: 05/02/2024] Open
Abstract
Identifying and protecting hotspots of endemism and species richness is crucial for mitigating the global biodiversity crisis. However, our understanding of spatial diversity patterns is far from complete, which severely limits our ability to conserve biodiversity hotspots. Here, we report a comprehensive analysis of amphibian species diversity in China, one of the most species-rich countries on Earth. Our study combines 20 y of field surveys with new molecular analyses of 521 described species and also identifies 100 potential cryptic species. We identify 10 hotspots of amphibian diversity in China, each with exceptional species richness and endemism and with exceptional phylogenetic diversity and phylogenetic endemism (based on a new time-calibrated, species-level phylogeny for Chinese amphibians). These 10 hotspots encompass 59.6% of China's described amphibian species, 49.0% of cryptic species, and 55.6% of species endemic to China. Only four of these 10 hotspots correspond to previously recognized biodiversity hotspots. The six new hotspots include the Nanling Mountains and other mountain ranges in South China. Among the 186 species in the six new hotspots, only 9.7% are well covered by protected areas and most (88.2%) are exposed to high human impacts. Five of the six new hotspots are under very high human pressure and are in urgent need of protection. We also find that patterns of richness in cryptic species are significantly related to those in described species but are not identical.
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Affiliation(s)
- Wei Xu
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Yun-He Wu
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
| | - Wei-Wei Zhou
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Hong-Man Chen
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Bao-Lin Zhang
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Jin-Min Chen
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Weihua Xu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
| | - Ding-Qi Rao
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Haipeng Zhao
- School of Life Sciences, Henan University, Kaifeng475004, China
| | - Fang Yan
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Zhiyong Yuan
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Ke Jiang
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Jie-Qiong Jin
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Mian Hou
- Institute of Continuing Education, Sichuan Normal University, Chengdu610068, China
| | - Dahu Zou
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- College of Science, Tibet University, Lhasa850000, China
| | - Li-Jun Wang
- School of Life Sciences, Hainan Normal University, Haikou571158, China
| | - Yuchi Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu610041, China
| | - Jia-Tang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu610041, China
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu610041, China
| | - Xiao-Mao Zeng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu610041, China
| | - Youhua Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu610041, China
| | - Zi-Yan Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu610041, China
| | - Cheng Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu610041, China
| | - Xue-You Li
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Wei Gao
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Kai Wang
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
| | - Dong-Ru Zhang
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Chenqi Lu
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming650204, China
| | - Tingting Yin
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Zhaoli Ding
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Gui-Gang Zhao
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Jing Chai
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Wen-Ge Zhao
- Department of Biology, College of Life and Environment Science, Harbin Normal University, Harbin150080, China
| | - Ya-Ping Zhang
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - John J. Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ85721-0088
| | - Jing Che
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
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Chen LQ, Li X, Yao X, Li DZ, Barrett C, dePamphilis CW, Yu WB. Variations and reduction of plastome are associated with the evolution of parasitism in Convolvulaceae. Plant Mol Biol 2024; 114:40. [PMID: 38622367 DOI: 10.1007/s11103-024-01440-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/09/2024] [Indexed: 04/17/2024]
Abstract
Parasitic lifestyle can often relax the constraint on the plastome, leading to gene pseudogenization and loss, and resulting in diverse genomic structures and rampant genome degradation. Although several plastomes of parasitic Cuscuta have been reported, the evolution of parasitism in the family Convolvulaceae which is linked to structural variations and reduction of plastome has not been well investigated. In this study, we assembled and collected 40 plastid genomes belonging to 23 species representing four subgenera of Cuscuta and ten species of autotrophic Convolvulaceae. Our findings revealed nine types of structural variations and six types of inverted repeat (IR) boundary variations in the plastome of Convolvulaceae spp. These structural variations were associated with the shift of parasitic lifestyle, and IR boundary shift, as well as the abundance of long repeats. Overall, the degradation of Cuscuta plastome proceeded gradually, with one clade exhibiting an accelerated degradation rate. We observed five stages of gene loss in Cuscuta, including NAD(P)H complex → PEP complex → Photosynthesis-related → Ribosomal protein subunits → ATP synthase complex. Based on our results, we speculated that the shift of parasitic lifestyle in early divergent time promoted relaxed selection on plastomes, leading to the accumulation of microvariations, which ultimately resulted in the plastome reduction. This study provides new evidence towards a better understanding of plastomic evolution, variation, and reduction in the genus Cuscuta.
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Affiliation(s)
- Li-Qiong Chen
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Xin Li
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Division of BiologicalScience, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Xin Yao
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Craig Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Claude W dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, State College, Pennsylvania, 16802, USA
| | - Wen-Bin Yu
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
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Liu Y, Cai L, Sun W. Transcriptome data analysis provides insights into the conservation of Michelia lacei, a plant species with extremely small populations distributed in Yunnan province, China. BMC Plant Biol 2024; 24:200. [PMID: 38500068 PMCID: PMC10949798 DOI: 10.1186/s12870-024-04892-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/08/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND Michelia lacei W.W.Smith (Magnoliaceae), was classified as a Plant Species with Extremely Small Populations (PSESP) by the Yunnan Provincial Government in both action plans of 2012 and 2021. This evergreen tree is known for its high ornamental and scientific value, but it faces significant threats due to its extremely small population size and narrow geographical distribution. The study aims to understand the genetic structure, diversity, and demographic history of this species to inform its conservation strategies. RESULTS The analysis of transcriptome data from 64 individuals across seven populations of M. lacei identified three distinct genetic clusters and generated 104,616 single-nucleotide polymorphisms (SNPs). The KM ex-situ population, originating from Longling County, exhibited unique genetic features, suggesting limited gene flow. The genetic diversity was substantial, with significant differences between populations, particularly between the KM lineage and the OTHER lineage. Demographic history inferred from the data indicated population experienced three significant population declines during glaciations, followed by periods of recovery. We estimated the effective population size (Ne) of the KM and OTHER lineages 1,000 years ago were 85,851 and 416,622, respectively. Gene flow analysis suggested past gene flow between populations, but the KM ex-situ population showed no recent gene flow. A total of 805 outlier SNPs, associated with four environmental factors, suggest potential local adaptation and showcase the species' adaptive potential. Particularly, the BZ displayed 515 adaptive loci, highlighting its strong potential for adaptation within this group. CONCLUSIONS The comprehensive genomic analysis of M. lacei provides valuable insights into its genetic background and highlights the urgent need for conservation efforts. The study underscores the importance of ex-situ conservation methods, such as seed collection and vegetative propagation, to safeguard genetic diversity and promote population restoration. The preservation of populations like MC and BZ is crucial for maintaining the species' genetic diversity. In-situ conservation measures, including the establishment of in-situ conservation sites and community engagement, are essential to enhance protection awareness and ensure the long-term survival of this threatened plant species.
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Affiliation(s)
- Yang Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations/ Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Cai
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations/ Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations/ Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
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Zhao L, Zhou W, He J, Li DZ, Li HT. Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant. eLife 2024; 12:RP89941. [PMID: 38353667 PMCID: PMC10942601 DOI: 10.7554/elife.89941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Sex-biased genes offer insights into the evolution of sexual dimorphism. Sex-biased genes, especially those with male bias, show elevated evolutionary rates of protein sequences driven by positive selection and relaxed purifying selection in animals. Although rapid sequence evolution of sex-biased genes and evolutionary forces have been investigated in animals and brown algae, less is known about evolutionary forces in dioecious angiosperms. In this study, we separately compared the expression of sex-biased genes between female and male floral buds and between female and male flowers at anthesis in dioecious Trichosanthes pilosa (Cucurbitaceae). In floral buds, sex-biased gene expression was pervasive, and had significantly different roles in sexual dimorphism such as physiology. We observed higher rates of sequence evolution for male-biased genes in floral buds compared to female-biased and unbiased genes. Male-biased genes under positive selection were mainly associated with functions to abiotic stress and immune responses, suggesting that high evolutionary rates are driven by adaptive evolution. Additionally, relaxed purifying selection may contribute to accelerated evolution in male-biased genes generated by gene duplication. Our findings, for the first time in angiosperms, suggest evident rapid evolution of male-biased genes, advance our understanding of the patterns and forces driving the evolution of sexual dimorphism in dioecious plants.
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Affiliation(s)
- Lei Zhao
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
| | - Wei Zhou
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
| | - Jun He
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
| | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
- Kunming College of Life Science, University of Chinese Academy of SciencesKunmingChina
| | - Hong-Tao Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
- Kunming College of Life Science, University of Chinese Academy of SciencesKunmingChina
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Tian Q, Stull GW, Kellermann J, Medan D, Nge FJ, Liu SY, Kates HR, Soltis DE, Soltis PS, Guralnick RP, Folk RA, Onstein RE, Yi TS. Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales. New Phytol 2024; 241:1851-1865. [PMID: 38229185 DOI: 10.1111/nph.19504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 11/20/2023] [Indexed: 01/18/2024]
Abstract
The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than the other regions. The relatively common lineage dispersals out of temperate hotspots highlight strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.
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Affiliation(s)
- Qin Tian
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, the Netherlands
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jürgen Kellermann
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Hackney Road, Adelaide, SA, 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Diego Medan
- Cátedra de Botánica General, Facultad de Agronomía, Universidad de Buenos Aires, Ave San Martín 4453, C1417DSE, Buenos Aires, Argentina
| | - Francis J Nge
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Hackney Road, Adelaide, SA, 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
- IRD - Institut de Recherche pour le Développement, Ave Agropolis BP 64501, Montpellier, 34394, France
| | - Shui-Yin Liu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
| | - Heather R Kates
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi, MS, 39762, USA
| | - Renske E Onstein
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, the Netherlands
- Evolution and Adaptation, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
- Leipzig University, Leipzig, 04013, Germany
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
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Cao J, Yang B, Zhang M, Yu F. Regulation of T16H subcellular localization for promoting its catalytic efficiency in yeast cells. Biotechnol Lett 2024; 46:29-35. [PMID: 37971563 DOI: 10.1007/s10529-023-03442-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/03/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
To investigate the effect of subcellular localization on the transformation efficiency of heterologous expressed functional P450s in yeast. Microbial biotransformation offers a promising substitute for the direct extraction of natural products, but its viability in industrial applications depends on achieving high transformation efficiencies. To investigate the influence of subcellular microenvironments on the activity of heterologously expressed P450s, Catharanthus roseus tabersonine 16-hydroxylase (T16H) was chosen, and its subcellular localization was regulated by fusing organelle-localization signals. Interestingly, this manipulation had no effect on the gene expression levels of T16H, but resulted in varying conversion rates from tabersonine to 16-hydroxy tabersonine. Notably, the highest transformation efficiency was observed in yeast cells expressing peroxisome-localized T16H. Given the alkaline pH optimum for P450s, the alkaline peroxisomal lumen could be a suitable compartment for P450s reactions to achieve high transformation efficiency using yeast cells. Different organelle-localization of T16H in yeast cells resulted in varying conversion rates, suggesting that compartmentalizing the expression of target enzymes could be a viable approach to increase transformation efficiency in yeast.
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Affiliation(s)
- Jiancong Cao
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Bingrun Yang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Mengxia Zhang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Fang Yu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
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7
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Liu X, Bai Y, Wang Y, Chen Y, Dong W, Zhang Z. Complete Chloroplast Genome of Hypericum perforatum and Dynamic Evolution in Hypericum (Hypericaceae). Int J Mol Sci 2023; 24:16130. [PMID: 38003320 PMCID: PMC10671389 DOI: 10.3390/ijms242216130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Hypericum perforatum (St. John's Wort) is a medicinal plant from the Hypericaceae family. Here, we sequenced the whole chloroplast genome of H. perforatum and compared the genome variation among five Hypericum species to discover dynamic changes and elucidate the mechanisms that lead to genome rearrangements in the Hypericum chloroplast genomes. The H. perforatum chloroplast genome is 139,725 bp, exhibiting a circular quadripartite structure with two copies of inverted repeats (IRs) separating a large single-copy region and a small single-copy region. The H. perforatum chloroplast genome encodes 106 unique genes, including 73 protein-coding genes, 29 tRNAs, and 4 rRNAs. Hypericum chloroplast genomes exhibit genome rearrangement and significant variations among species. The genome size variation among the five Hypericum species was remarkably associated with the expansion or contraction of IR regions and gene losses. Three genes-trnK-UUU, infA, and rps16-were lost, and three genes-rps7, rpl23, and rpl32-were pseudogenized in Hypericum. All the Hypericum chloroplast genomes lost the two introns in clpP, the intron in rps12, and the second intron in ycf3. Hypericum chloroplast genomes contain many long repeat sequences, suggesting a role in facilitating rearrangements. Most genes, according to molecular evolution assessments, are under purifying selection.
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Affiliation(s)
- Xinyu Liu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.L.); (Y.B.); (Y.C.)
| | - Yuran Bai
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.L.); (Y.B.); (Y.C.)
| | - Yachao Wang
- School of Life Sciences, Fudan University, Shanghai 200437, China;
| | - Yifeng Chen
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.L.); (Y.B.); (Y.C.)
| | - Wenpan Dong
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.L.); (Y.B.); (Y.C.)
| | - Zhixiang Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.L.); (Y.B.); (Y.C.)
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Xamxidin M, Dong H, Wang JY, Qu W, Xu L, Wu M. Parerythrobacter lacustris sp. nov., a novel member of the family Erythrobacteraceae isolated from an inland alpine lake. Arch Microbiol 2023; 205:279. [PMID: 37420141 DOI: 10.1007/s00203-023-03616-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/17/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023]
Abstract
A novel bacterium, designated as strain RS5-5T, was isolated from lake water in northwestern China. Cells of the isolate were observed to be rod shaped and Gram stain negative. Its growth occurred at 4-37 ℃, pH 6.5-9.0 and in the presence of 0-5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RS5-5T was most closely related to Qipengyuania sediminis GDMCC 1.2497T (97.5%), followed by Erythrobacter dokdonensis DSW-74T (97.3%) and Qipengyuania algicida GDMCC 1.2535T (97.0%). Phylogenomic analysis revealed that strain RS5-5T formed a distinct branch with the genus Parerythrobacter. The sole quinone was ubiquinone-10, and the major fatty acids (≥ 10%) were unsaturated fatty acids including C17:1 ω6c, summed feature 3 (C16:1 ω7c/C16:1 ω6c) and summed feature 8 (C18:1 ω7c/C18:1 ω6c). The polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, one unidentified sphingoglycolipid, three unidentified glycolipids, one unidentified aminoglycolipid, one unidentified aminolipid, two unidentified phospholipids and four unidentified polar lipids. Chemotaxonomic characteristics of strain RS5-5T were coincident with those of the genus Parerythrobacter members. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain RS5-5T and two Parerythrobacter reference strains were in the ranges of 73.2-77.7%, 69.0-78.0% and 18.9-20.4%, respectively. The genomic DNA G + C content of strain RS5-5T was 64.1%. The results of phenotypic, phylogenetic and genomic analyses suggested that strain RS5-5T represents a novel species in the genus Parerythrobacter, for which the name Parerythrobacter lacustris sp. nov. is proposed. The type strain is RS5-5T (= GDMCC 1.3163T = KCTC 92277T).
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Affiliation(s)
- Maripat Xamxidin
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Han Dong
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Jia-Yan Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316000, People's Republic of China
| | - Lin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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Wang SQ, Dong XY, Ye L, Wang HF, Ma KP. Flora of Northeast Asia. Plants (Basel) 2023; 12:2240. [PMID: 37375866 DOI: 10.3390/plants12122240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/26/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023]
Abstract
As a component of the MAP project, the study of the flora in Northeast Asia (comprising Japan, South Korea, North Korea, Northeast China, and Mongolia) convincingly underscores the indispensability of precise and comprehensive diversity data for flora research. Due to variations in the description of flora across different countries in Northeast Asia, it is essential to update our understanding of the region's overall flora using the latest high-quality diversity data. This study employed the most recently published authoritative data from various countries to conduct a statistical analysis of 225 families, 1782 genera, and 10,514 native vascular species and infraspecific taxa in Northeast Asia. Furthermore, species distribution data were incorporated to delineate three gradients in the overall distribution pattern of plant diversity in Northeast Asia. Specifically, Japan (excluding Hokkaido) emerged as the most prolific hotspot for species, followed by the Korean Peninsula and the coastal areas of Northeast China as the second richest hotspots. Conversely, Hokkaido, inland Northeast China, and Mongolia constituted species barren spots. The formation of the diversity gradients is primarily attributed to the effects of latitude and continental gradients, with altitude and topographic factors within the gradients modulating the distribution of species.
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Affiliation(s)
- Si-Qi Wang
- School of Forestry, Northeast Forestry University, Harbin 150040, China
- Northeast Asia Biodiversity Research Center, Harbin 150040, China
| | - Xue-Yun Dong
- Northeast Asia Biodiversity Research Center, Harbin 150040, China
- School of Geography and Tourism, Harbin University, Harbin 150040, China
| | - Liang Ye
- Northeast Asia Biodiversity Research Center, Harbin 150040, China
- Folia Multidimensional Innovate Lab, Anshan 114000, China
| | - Hong-Feng Wang
- School of Forestry, Northeast Forestry University, Harbin 150040, China
- Northeast Asia Biodiversity Research Center, Harbin 150040, China
| | - Ke-Ping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 150093, China
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Li SQ, Zhang C, Gao XF. Geographic isolation and climatic heterogeneity drive population differentiation of Rosa chinensis var. spontanea complex. Plant Biol (Stuttg) 2023; 25:620-630. [PMID: 36972024 DOI: 10.1111/plb.13521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 03/19/2023] [Indexed: 05/17/2023]
Abstract
Global biodiversity is contracting rapidly due to potent anthropogenic activities and severe climate change. Wild populations of Rosa chinensis var. spontanea and Rosa lucidissima are rare species endemic to China, as well as important germplasm resources for rose breeding. However, these populations are at acute risk of extinction and require urgent action to ensure their preservation. We harnessed 16 microsatellite loci to 44 populations of these species and analysed population structure and differentiation, demographic history, gene flow and barrier effect. In addition, a niche overlap test and potential distribution modelling in different time periods were also carried out. The data indicate that: (1) R. lucidissima cannot be regarded as a separate species from R. chinensis var. spontanea; (2) the Yangtze River and the Wujiang River function as barriers in population structure and differentiation, and precipitation in the coldest quarter may be the key factor for niche divergence of R. chinensis var. spontanea complex; (3) historical gene flow showed a converse tendency to current gene flow, indicating that alternate migration events of R. chinensis var. spontanea complex between south and north were a response to climate oscillations; and (4) extreme climate change will decrease the distribution range of R. chinensis var. spontanea complex, whereas the opposite will occur under a moderate scenario for the future. Our results resolve the relationship between R. chinensis var. spontanea and R. lucidissima, highlight the pivotal roles of geographic isolation and climate heterogeneity in their population differentiation, and provide an important reference for comparable conservation studies on other endangered species.
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Affiliation(s)
- S Q Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - C Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - X F Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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Pan D, Xia M, Luo Q, Li C, Yuan G, Wang J, Dou W. Sublethal and transgenerational effects of pyridaben exposure on the fitness and gene expression of Panonychus citri. Pest Manag Sci 2023. [PMID: 37071486 DOI: 10.1002/ps.7506] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/15/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Panonychus citri is a globally dominant citrus plant pest mite. Pesticide-induced population resurgence is a concern for mite control. Exposure to sublethal concentrations of pesticides has stimulated reproduction and outbreak risks in many pests. Pyridaben, a mitochondrial electron transport inhibitor, has been frequently used worldwide in mite control. In the study, sublethal and transgenerational effects of pyridaben exposure on Pyr_Rs (resistant) and Pyr_Control (susceptible) strains were systematically investigated in both exposed parental generation (F0 ) and unexposed offspring generations (F1 and F2 ) by evaluating life-table and physiological parameters. RESULTS After exposure to pyridaben, the fecundity of both strains was significantly reduced in F0 generation while significantly induced in F1 generation. Interestingly, these effects also stimulated the fecundity of the F2 generation in Pyr_Control strain while no significant effects occurred for Pyr_Rs strain. The intrinsic rate of increase (r) and finite rate of increase (λ) were significantly decreased only in F1 generation of Pyr_Control strain after exposure treatment. Meanwhile, the population projection indicated a smaller population size in F1 generation of Pyr_Control strain while a population increase for Pyr_Rs strain after sublethal treatment. Subsequent detoxification enzyme assays indicated that only P450 activities in F0 generation were significantly activated by LC30 exposure to pyridaben in both strains. Significant downregulation of reproduction-related (Pc_Vg) genes was observed in the F0 generations of both strains. Significant upregulation of P450 (CYP4CL2) and Pc_Vg of the F1 generation in both strains suggested the presence of delayed hormesis effects on the reproduction and developed tolerance to pyridaben, although the effects did not last over a longer period (F2 generation). CONCLUSION These results provide evidence for transgenerational hormesis effects of low concentrations of pyridaben exposure that may lead to population increase and resurgence risks of resistant-mites in natural settings by stimulating reproduction. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Deng Pan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Menghao Xia
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Qiujuan Luo
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Chuanzhen Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Guorui Yuan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jinjun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Wei Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
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Chen H, Visscher AM, Ai Q, Yang L, Pritchard HW, Li W. Intra-Specific Variation in Desiccation Tolerance of Citrus sinensis 'bingtangcheng' (L.) Seeds under Different Environmental Conditions in China. Int J Mol Sci 2023; 24:ijms24087393. [PMID: 37108552 PMCID: PMC10139128 DOI: 10.3390/ijms24087393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Intra-specific variation in seed storage behaviour observed in several species has been related to different maternal environments. However, the particular environmental conditions and molecular processes involved in intra-specific variation of desiccation tolerance remain unclear. We chose Citrus sinensis 'bingtangcheng' for the present study due to its known variability in desiccation tolerance amongst seed lots. Six seed lots of mature fruits were harvested across China and systematically compared for drying sensitivity. Annual sunshine hours and average temperature from December to May showed positive correlations with the level of seed survival of dehydration. Transcriptional analysis indicated significant variation in gene expression between relatively desiccation-tolerant (DT) and -sensitive (DS) seed lots after harvest. The major genes involved in late seed maturation, such as heat shock proteins, showed higher expression in the DT seed lot. Following the imposition of drying, 80% of stress-responsive genes in the DS seed lot changed to the stable levels seen in the DT seed lot prior to and post-desiccation. However, the changes in expression of stress-responsive genes in DS seeds did not improve their tolerance to desiccation. Thus, higher desiccation tolerance of Citrus sinensis 'bingtangcheng' seeds is modulated by the maternal environment (e.g., higher annual sunshine hours and seasonal temperature) during seed development and involves stable expression levels of stress-responsive genes.
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Affiliation(s)
- Hongying Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Anne M Visscher
- Trait Diversity and Function Department, Royal Botanic Gardens, Kew, Wakehurst, Ardingly, West Sussex RH17 6TN, UK
| | - Qin Ai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Lan Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hugh W Pritchard
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Trait Diversity and Function Department, Royal Botanic Gardens, Kew, Wakehurst, Ardingly, West Sussex RH17 6TN, UK
| | - Weiqi Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Zhao L, Yang YY, Qu XJ, Ma H, Hu Y, Li HT, Yi TS, Li DZ. Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae. Ann Bot 2023; 131:199-214. [PMID: 35671385 PMCID: PMC9904356 DOI: 10.1093/aob/mcac062] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/13/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny and to interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in the evolution of eight subfamilies remains unclear. METHODS New transcriptomes or low-depth whole-genome sequences of 65 species were generated through Illumina sequencing. We reconstructed the phylogenetic relationships of Araceae using concatenated and species tree methods, and then estimated the age of major clades using TreePL. We inferred the WGD events by Ks and gene tree methods. We investigated the diversification patterns applying time-dependent and trait-dependent models. The expansions of gene families and functional enrichments were analysed using CAFE and InterProScan. KEY RESULTS Gymnostachydoideae was the earliest diverging lineage followed successively by Orontioideae, Lemnoideae and Lasioideae. In turn, they were followed by the clade of 'bisexual climbers' comprised of Pothoideae and Monsteroideae, which was resolved as the sister to the unisexual flowers clade of Zamioculcadoideae and Aroideae. A special WGD event ψ (psi) shared by the True-Araceae clade occurred in the Early Cretaceous. Net diversification rates first declined and then increased through time in the Araceae. The best diversification rate shift along the stem lineage of the True-Araceae clade was detected, and net diversification rates were enhanced following the ψ-WGD. Functional enrichment analyses revealed that some genes, such as those encoding heat shock proteins, glycosyl hydrolase and cytochrome P450, expanded within the True-Araceae clade. CONCLUSIONS Our results improve our understanding of aroid phylogeny using the large number of single-/low-copy nuclear genes. In contrast to the Proto-Araceae group and the lemnoid clade adaption to aquatic environments, our analyses of WGD, diversification and functional enrichment indicated that WGD may play a more important role in the evolution of adaptations to tropical, terrestrial environments in the True-Araceae clade. These insights provide us with new resources to interpret the evolution of the Araceae.
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Affiliation(s)
- Lei Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong 250014, China
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi Hu
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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Li E, Liu K, Deng R, Gao Y, Liu X, Dong W, Zhang Z. Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae). BMC Plant Biol 2023; 23:32. [PMID: 36639619 PMCID: PMC9840334 DOI: 10.1186/s12870-023-04034-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 01/02/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Eriocaulon is a wetland plant genus with important ecological value, and one of the famous taxonomically challenging groups among angiosperms, mainly due to the high intraspecific diversity and low interspecific variation in the morphological characters of species within this genus. In this study, 22 samples representing 15 Eriocaulon species from China, were sequenced and combined with published samples of Eriocaulon to test the phylogenetic resolution using the complete chloroplast genome. Furthermore, comparative analyses of the chloroplast genomes were performed to investigate the chloroplast genome evolution of Eriocaulon. RESULTS The 22 Eriocaulon chloroplast genomes and the nine published samples were proved highly similar in genome size, gene content, and order. The Eriocaulon chloroplast genomes exhibited typical quadripartite structures with lengths from 150,222 bp to 151,584 bp. Comparative analyses revealed that four mutation hotspot regions (psbK-trnS, trnE-trnT, ndhF-rpl32, and ycf1) could serve as effective molecular markers for further phylogenetic analyses and species identification of Eriocaulon species. Phylogenetic results supported Eriocaulon as a monophyletic group. The identified relationships supported the taxonomic treatment of section Heterochiton and Leucantherae, and the section Heterochiton was the first divergent group. Phylogenetic tree supported Eriocaulon was divided into five clades. The divergence times indicated that all the sections diverged in the later Miocene and most of the extant Eriocaulon species diverged in the Quaternary. The phylogeny and divergence times supported rapid radiation occurred in the evolution history of Eriocaulon. CONCLUSION Our study mostly supported the taxonomic treatment at the section level for Eriocaulon species in China and demonstrated the power of phylogenetic resolution using whole chloroplast genome sequences. Comparative analyses of the Eriocaulon chloroplast genome developed molecular markers that can help us better identify and understand the evolutionary history of Eriocaulon species in the future.
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Affiliation(s)
- Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Kangjia Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Rongyan Deng
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yongwei Gao
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Xinyu Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
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Yang J, Yu S, Shi GF, Yan L, Lv RT, Ma Z, Wang L. Comparative analysis of R2R3-MYB transcription factors in the flower of Iris laevigata identifies a novel gene regulating tobacco cold tolerance. Plant Biol (Stuttg) 2022; 24:1066-1075. [PMID: 35779251 DOI: 10.1111/plb.13452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Breeding for flower cold resistance is a priority for flower breeding research in northern China. The identification of cold resistance genes will not only provide genetic resources for cold resistance breeding, but also form a basis for the study of plant cold resistance mechanisms. Based on the flower transcriptome of Iris laevigata, 20 R2R3-MYBs were identified and comprehensive analysis, including conservative domain, phylogenetic analyses and functional distribution, were performed for R2R3-MYBs. Expression patterns of the abiotic stress genes under cold stress were detected, the upregulated gene was genetically transformed into tobacco, and the related physiological indicators of the transgenic tobacco were measured. A novel cold resistance gene, IlMYB306, was obtained. qRT-PCR indicated that IlMYB306 was dramatically induced by cold stress and was significantly upregulated in roots. The free proline content, MDA, SOD and POD activity of the transgenic tobacco improved after cold stress, and the chlorophyll content decreased slowly. In addition, overexpression of IlMYB306 improved cold resistance of the seeds. SEM results showed leaves of transgenic tobacco had obvious folds, more grooves and bulges on the lower leaf surface. Overall, we report a novel cold resistance R2R3-MYB gene, IlMYB306, in the flower of I. laevigata, which could improve tobacco cold stress tolerance by thickening the waxy layer, increasing antioxidant activity and the content of proline.
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Affiliation(s)
- J Yang
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - S Yu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, China
| | - G F Shi
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - L Yan
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - R T Lv
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Z Ma
- Department of Biology, Truman State University, Kirksville, MO, USA
| | - L Wang
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
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Perner H, Zhou R, Perner W, Jiang H, Lee YI. Cypripedium subtropicum embryo development and cytokinin requirements for asymbiotic germination. Bot Stud 2022; 63:28. [PMID: 36178517 PMCID: PMC9525480 DOI: 10.1186/s40529-022-00359-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/10/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Cypripedium subtropicum is a unique, endangered lady's slipper orchid with evergreen leaves on non-dormant shoots that is native to southwestern China. This study documents the major developmental events in C. subtropicum seed development from fertilization to seed maturity, determines the optimum period for seed collection, and examines the cytokinin requirements for asymbiotic germination and protocorm survival. RESULTS Structural studies revealed that embryo development proceeded after successful fertilization at 60 days after pollination (DAP). At 105 DAP, a globular embryo with the shrinking inner seed coat was observed, and seeds collected at this time point exhibited optimal germination. After 120 DAP, most seeds had a mature embryo within the capsule, and within the cells of the embryo proper, numerous proteins/lipid bodies were present as the main storage products. In addition, the inner seed coat had compressed into a thin layer that tightly enclosed the embryo, while the outer seed coat had progressively elongated, resulting in a hair-like appearance of the mature seed. Histochemical staining using Nile red and toluidine blue O (TBO) indicated that the lignified inner and outer seed coats may lead to coat-imposed dormancy. Seeds collected at this stage germinated poorly. Analyses of cytokinin preferences and optimal concentrations for germination and protocorm survival showed that both 6-(γ,γ-dimethylallylamino) purine (2iP) and 6-benzylaminopurine (BA) enhanced germination compared with the control, although higher concentrations of BA (4 and 8 μM) suppressed germination. The protocorm survival rate improved with increasing 2iP concentration. CONCLUSIONS This study provides a reproducible procedure for culturing immature seeds of C. subtropicum based on a defined time schedule of seed development. In addition, the cytokinin 2iP was shown to improve germination and protocorm survival. This study provides a scientific basis for seedling establishment through asymbiotic seed culture for further reintroduction efforts.
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Affiliation(s)
- Holger Perner
- Hengduan Mountains Biotechnology Ltd, Chengdu, 6100225, Sichuan, China
| | - Rong Zhou
- Hengduan Mountains Biotechnology Ltd, Chengdu, 6100225, Sichuan, China
| | - Wenqing Perner
- Hengduan Mountains Biotechnology Ltd, Chengdu, 6100225, Sichuan, China
| | - Hong Jiang
- Yunnan Laboratory for Conservation of Rare, Public Key Laboratory of the National Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Endangered & Endemic Forest Plants, Kunming, 650201, Yunnan, China.
| | - Yung-I Lee
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan.
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Song R, Zhang X, Wang H, Liu C. Polyoxometalate/Cellulose Nanofibrils Aerogels for Highly Efficient Oxidative Desulfurization. Molecules 2022; 27:2782. [PMID: 35566131 PMCID: PMC9101072 DOI: 10.3390/molecules27092782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/11/2022] [Accepted: 04/15/2022] [Indexed: 11/26/2022] Open
Abstract
Polyoxometalate (POM) presents great potential in oxidative desulfurization (ODS) reaction. However, the high dissolubility of POM in common solvents makes it difficult to recycle. Besides, the small specific surface area of POM also limits the interaction between them and the substrate. Depositing polyoxometalates onto three-dimensional (3D) network structured materials could largely expand the application of POM. Here, the surfaces of cellulose nanofibrils (CNFs) were modified with very few (3-Aminopropyl) trimethoxysilane (APTS) to endow positive charges on the surfaces of CNFs, and then phosphotungstic acid (PTA) was loaded to obtain the aerogel A-CNF/PTA as the ODS catalyst. FT-IR indicated the successful deposition of PTA onto aminosilane modified CNF surfaces. UV-VIS further suggested the stability of PTA in the aerogels. BET and SEM results suggested the increased specific surface area and the relatively uniform 3D network structure of the prepared aerogels. TGA analysis indicated that the thermal stability of the aerogel A-CNF/PTA50% was a little higher than that of the pure CNF aerogel. Most importantly, the aerogel A-CNF/PTA50% showed good catalytic performance for ODS. Catalysis results showed that the substrate conversion rate of the aerogel A-CNF/PTA50% reached 100% within 120 min at room temperature. Even after five cycles, the substrate conversion rate of the aerogel A-CNF/PTA50% still reached 91.2% during the dynamic catalytic process. This work provides a scalable and facile way to stably deposit POM onto 3D structured materials.
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Affiliation(s)
- Rui Song
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510006, China; (R.S.); (H.W.)
| | - Xueqin Zhang
- College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China;
| | - Huihui Wang
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510006, China; (R.S.); (H.W.)
| | - Chuanfu Liu
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510006, China; (R.S.); (H.W.)
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Mo X, Cai X, Hui Q, Sun H, Yu R, Bu R, Yan B, Ou Q, Li Q, He S, Jiang C. Whole genome sequencing and metabolomics analyses reveal the biosynthesis of nerol in a multi-stress-tolerant Meyerozyma guilliermondii GXDK6. Microb Cell Fact 2021; 20:4. [PMID: 33413399 PMCID: PMC7789178 DOI: 10.1186/s12934-020-01490-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/30/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Nerol (C10H18O), an acyclic monoterpene, naturally presents in plant essential oils, and is used widely in food, cosmetics and pharmaceuticals as the valuable fragrance. Meanwhile, chemical synthesis is the only strategy for large-scale production of nerol, and the disadvantages of chemical synthesis greatly limit the production and its application. These defects drive the interests of researchers shift to the production of nerol by eco-friendly methods known as biosynthesis methods. However, the main technical bottleneck restricting the biosynthesis of nerol is the lacking of corresponding natural aroma-producing microorganisms. RESULTS In this study, a novel multi-stress-tolerant probiotics Meyerozyma guilliermondii GXDK6 with aroma-producing properties was identified by whole genome sequencing and metabolomics technology. GXDK6 showed a broad pH tolerance in the range of 2.5-10.0. The species also showed salt tolerance with up to 12% NaCl and up to 18% of KCl or MgCl2. GXDK6 exhibited heavy-metal Mn2+ tolerance of up to 5494 ppm. GXDK6 could also ferment with a total of 21 kinds of single organic matter as the carbon source, and produce abundant aromatic metabolites. Results from the gas chromatography-mass spectrometry indicated the production of 8-14 types of aromatic metabolites (isopentanol, nerol, geraniol, phenylethanol, isobutanol, etc.) when GXDK6 was fermented up to 72 h with glucose, sucrose, fructose, or xylose as the single carbon source. Among them, nerol was found to be a novel aromatic metabolite from GXDK6 fermentation, and its biosynthesis mechanism had also been further revealed. CONCLUSION A novel aroma-producing M. guilliermondii GXDK6 was identified successfully by whole genome sequencing and metabolomics technology. GXDK6 showed high multi-stress-tolerant properties with acid-base, salty, and heavy-metal environments. The aroma-producing mechanism of nerol in GXDK6 had also been revealed. These findings indicated the aroma-producing M. guilliermondii GXDK6 with multi-stress-tolerant properties has great potential value in the fermentation industry.
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Affiliation(s)
- Xueyan Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Xinghua Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Qinyan Hui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Huijie Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Ran Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Ru Bu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Bing Yan
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai, 536000, China
| | - Qian Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Quanwen Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Sheng He
- Guangxi Birth Defects Prevention and Control Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530033, China.
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai, 536000, China.
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Mu DS, Liang QY, Wang XM, Lu DC, Shi MJ, Chen GJ, Du ZJ. Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing. Microbiome 2018; 6:230. [PMID: 30587241 PMCID: PMC6307301 DOI: 10.1186/s40168-018-0613-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/04/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND The pure culture of prokaryotes remains essential to elucidating the role of these organisms. Scientists have reasoned that hard to cultivate microorganisms might grow in pure culture if provided with the chemical components of their natural environment. However, most microbial species in the biosphere that would otherwise be "culturable" may fail to grow because of their growth state in nature, such as dormancy. That means even if scientist would provide microorganisms with the natural environment, such dormant microorganisms probably still remain in a dormant state. RESULTS We constructed an enrichment culture system for high-efficiency isolation of uncultured strains from marine sediment. Degree of enrichment analysis, dormant and active taxa calculation, viable but non-culturable bacteria resuscitation analysis, combined with metatranscriptomic and comparative genomic analyses of the interactions between microbial communications during enrichment culture showed that the so-called enrichment method could culture the "uncultured" not only through enriching the abundance of "uncultured," but also through the resuscitation mechanism. In addition, the enrichment culture was a complicated mixed culture system, which contains the competition, cooperation, or coordination among bacterial communities, compared with pure cultures. CONCLUSIONS Considering that cultivation techniques must evolve further-from axenic to mixed cultures-for us to fully understand the microbial world, we should redevelop an understanding of the classic enrichment culture method. Enrichment culture methods can be developed and used to construct a model for analyzing mixed cultures and exploring microbial dark matter. This study provides a new train of thought to mining marine microbial dark matter based on mixed cultures.
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Affiliation(s)
- Da-Shuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - Qi-Yun Liang
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - Xiao-Man Wang
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - De-Chen Lu
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - Ming-Jing Shi
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - Guan-Jun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China.
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Li Y, Guo XH, Dang YR, Sun LL, Zhang XY, Chen XL, Qin QL, Wang P. Complete genome sequence of Arcticibacterium luteifluviistationis SM1504 T, a cytophagaceae bacterium isolated from Arctic surface seawater. Stand Genomic Sci 2018; 13:33. [PMID: 30505389 PMCID: PMC6258284 DOI: 10.1186/s40793-018-0335-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/10/2018] [Indexed: 11/10/2022] Open
Abstract
Arcticibacterium luteifluviistationis SM1504T was isolated from Arctic surface seawater and classified as a novel genus of the phylum Bacteroides. To date, no Arcticibacterium genomes have been reported, their genomic compositions and metabolic features are still unknown. Here, we reported the complete genome sequence of A. luteifluviistationis SM1504T, which comprises 5,379,839 bp with an average GC content of 37.20%. Genes related to various stress (such as radiation, osmosis and antibiotics) resistance and gene clusters coding for carotenoid and flexirubin biosynthesis were detected in the genome. Moreover, the genome contained a 245-kb genomic island and a 15-kb incomplete prophage region. A great percentage of proteins belonging to carbohydrate metabolism especially in regard to polysaccharides utilization were found. These related genes and metabolic characteristics revealed genetic basis for adapting to the diverse extreme Arctic environments. The genome sequence of A. luteifluviistationis SM1504T also implied that the genus Arcticibacterium may act as a vital organic carbon matter decomposer in the Arctic seawater ecosystem.
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Affiliation(s)
- Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
| | - Xiao-Han Guo
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
| | - Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
| | - Lin-Lin Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, No.1, Wenhai Rd, Qingdao, 266237 China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, No.1, Wenhai Rd, Qingdao, 266237 China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, No.1, Wenhai Rd, Qingdao, 266237 China
| | - Peng Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
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