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Yu Q, Hu J, Hu X, Zhou Y, Wang F, Jiang S, Wang Y. Demographic patterns of two related desert shrubs with overlapping distributions in response to past climate changes. FRONTIERS IN PLANT SCIENCE 2024; 15:1345624. [PMID: 38450397 PMCID: PMC10915042 DOI: 10.3389/fpls.2024.1345624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024]
Abstract
Numerous studies have revealed that past geological events and climatic fluctuations had profoundly affected the genetic structure and demographic patterns of species. However, related species with overlapping ranges may have responded to such environmental changes in different ways. In this study, we compared the genetic structure and population dynamics of two typical desert shrubs with overlapping distributions in northern China, Nitraria tangutorum and Nitraria sphaerocarpa, based on chloroplast DNA (cpDNA) variations and species distribution models. We sequenced two cpDNA fragments (trnH-trnA and atpH-atpI) in 633 individuals sampled from 52 natural populations. Twenty-four chlorotypes, including eight rare chlorotypes, were identified, and a single dominant haplotype (H4) widely occurred in the entire geographical ranges of the two species. There were also a few distinctive chlorotypes fixed in different geographical regions. Population structure analyses suggested that the two species had significantly different levels of total genetic diversity and interpopulation differentiation, which was highly likely correlated with the special habitat preferences of the two species. A clear phylogeographic structure was identified to exist among populations of N. sphaerocarpa, but not exist for N. tangutorum. The neutral tests, together with the distribution of pairwise differences revealed that N. tangutorum experienced a sudden demographic expansion, and its expansion approximately occurred between 21 and 7 Kya before present, while a rapid range expansion was not identified for N. sphaerocarpa. The ecological niche modeling (ENM) analysis indicated that the potential ranges of two species apparently fluctuated during the past and present periods, with obvious contraction in the Last Glacial Maximum (LGM) and recolonization in the present, respectively, comparing to the Last Interglacial (LIG). These findings suggest that the two species extensively occurred in the Northwest of China before the Quaternary, and the current populations of them originated from a few separated glacial refugia following their habitat fragmentation in the Quarternary. Our results provide new insights on the impact of past geological and climatic fluctuations on the population dynamics of desert plants in northwestern China, and further enforce the hypothesis that there were several independent glacial refugia for these species during the Quaternary glaciations.
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Affiliation(s)
- Qiushi Yu
- Xinglongshan Forest Ecosystem National Positioning Observation and Research Station, Gansu Research Academy of Forestry Science and Technology, Lanzhou, China
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, China
| | - Jing Hu
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Xiaoke Hu
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Yongfeng Zhou
- Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fanglin Wang
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Shengxiu Jiang
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Yuqi Wang
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
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Banaev EV, Tomoshevich MA, Khozyaykina SA, Erst AA, Erst AS. Integrative Taxonomy of Nitraria (Nitrariaceae), Description of the New Enigmatic Species and Key to All Currently Known Species. PLANTS (BASEL, SWITZERLAND) 2023; 12:593. [PMID: 36771680 PMCID: PMC9921022 DOI: 10.3390/plants12030593] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/15/2023] [Accepted: 01/15/2023] [Indexed: 06/18/2023]
Abstract
A new species, Nitraria iliensis sp. nov., is described from the Ili basin, Almaty region, Kazakhstan. It belongs to section Nitraria ser. Sibiricae and is morphologically similar to N. sibirica Pall. An integrative taxonomic approach based on molecular, biochemical and morphological analyses, along with palynological data, was used to delimit this new species. The studied species of the genus are illustrated, and photographs of authentic specimens of the new species, as well as a distribution map of the new species and segregate taxa, are provided. Morphological characters were investigated, more important traits for identification were found, and a new key to distinguish between all species of the genus was prepared.
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Affiliation(s)
| | | | | | - Anna A. Erst
- Correspondence: (A.A.E.); (A.S.E.); Tel.: +7-(383)339-9842 (A.A.E.)
| | - Andrey S. Erst
- Correspondence: (A.A.E.); (A.S.E.); Tel.: +7-(383)339-9842 (A.A.E.)
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Lu L, Wu X, Tang Y, Zhu L, Hao Z, Zhang J, Li X, Shi J, Chen J, Cheng T. Halophyte Nitraria billardieri CIPK25 promotes photosynthesis in Arabidopsis under salt stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1052463. [PMID: 36589077 PMCID: PMC9800929 DOI: 10.3389/fpls.2022.1052463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
The calcineurin B-like (CBL)-interacting protein kinases (CIPKs), a type of plant-specific genes in the calcium signaling pathway, function in response to adverse environments. However, few halophyte derived CIPKs have been studied for their role in plant physiological and developmental adaptation during abiotic stresses, which inhibits the potential application of these genes to improve environmental adaptability of glycophytes. In this study, we constructed Nitraria billardieri CIPK25 overexpressing Arabidopsis and analyzed the seedling development under salt treatment. Our results show that Arabidopsis with NbCIPK25 expression exhibits more vigorous growth than wild type plants under salt condition. To gain insight into the molecular mechanisms underlying salt tolerance, we profiled the transcriptome of WT and transgenic plants via RNA-seq. GO and KEGG analyses revealed that upregulated genes in NbCIPK25 overexpressing seedlings under salt stress are enriched in photosynthesis related terms; Calvin-cycle genes including glyceraldehyde-3-phosphate dehydrogenases (GAPDHs) are significantly upregulated in transgenic plants, which is consistent with a decreased level of NADPH (GAPDH substrate) and increased level of NADP+. Accordingly, NbCIPK25 overexpressing plants exhibited more efficient photosynthesis; soluble sugar and proteins, as photosynthesis products, showed a higher accumulation in transgenic plants. These results provide molecular insight into how NbCIPK25 promotes the expression of genes involved in photosynthesis, thereby maintaining plant growth under salt stress. Our finding supports the potential application of halophyte-derived NbCIPK25 in genetic modification for better salt adaptation.
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Affiliation(s)
- Lu Lu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xinru Wu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yao Tang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Liming Zhu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jingbo Zhang
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou, Inner Mongolia, China
| | - Xinle Li
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou, Inner Mongolia, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Tielong Cheng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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Genetic Diversity in Marginal Populations of Nitraria schoberi L. from Romania. DIVERSITY 2022. [DOI: 10.3390/d14100882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Nitraria schoberi L. (Nitrariaceae) is a halophytic plant with a continuous range in Central Asia and with only two populations in the westernmost distribution limit of species, in Romania. Currently, there is no documented explanation for the species’ presence in Europe, outside the main distribution area. Considering that marginal populations genetics are important in establishing range limits and species adaptative potential, genetic diversity was assessed using Inter-simple sequence repeat markers (ISSR). Both the Shannon’s Information Index (I) and Expected Heterozygosity (He) suggested a relatively low level of genetic diversity within the two populations. However, the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram and Principal Coordinates Analysis clearly distinguished the two populations. Our presumptions, based on current results, are that the marginal westernmost population of N. schoberi was established due to the unique conditions from the “islands of desert” developed in a temperate continental climate. The European establishment of this species was likely accidental and probably due to ornithochory. Genetic relatedness between populations could be a consequence of their common origin, presumably from proximal Asian N. schoberi populations, while the separation can be explained by the lack of genetic material exchange between the two populations.
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Lu L, Wu X, Wang P, Zhu L, Liu Y, Tang Y, Hao Z, Lu Y, Zhang J, Shi J, Cheng T, Chen J. Halophyte Nitraria billardieri CIPK25 mitigates salinity-induced cell damage by alleviating H 2O 2 accumulation. FRONTIERS IN PLANT SCIENCE 2022; 13:961651. [PMID: 36003812 PMCID: PMC9393555 DOI: 10.3389/fpls.2022.961651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
The plant-specific module of calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs) play a crucial role in plant adaptation to different biotic and abiotic stresses in various plant species. Despite the importance of the CBL-CIPK module in regulating plant salt tolerance, few halophyte CIPK orthologs have been studied. We identified NbCIPK25 in the halophyte Nitraria billardieri as a salt-responsive gene that may improve salt tolerance in glycophytes. Sequence analyses indicated that NbCIPK25 is a typical CIPK family member with a conserved NAF motif, which contains the amino acids: asparagine, alanine, and phenylalanine. NbCIPK25 overexpression in salt-stressed transgenic Arabidopsis seedlings resulted in enhanced tolerance to salinity, a higher survival rate, longer newly grown roots, more root meristem cells, and less damaged root cells in comparison to wild-type (WT) plants. H2O2 accumulation and malondialdehyde (MDA) content were both deceased in NbCIPK25-transgenic plants under salt treatment. Furthermore, their proline content, an important factor for scavenging reactive oxygen species, accumulated at a significantly higher level. In concordance, the transcription of genes related to proline accumulation was positively regulated in transgenic plants under salt condition. Finally, we observed a stronger auxin response in salt-treated transgenic roots. These results provide evidence for NbCIPK25 improving salt tolerance by mediating scavenging of reactive oxygen species, thereby protecting cells from oxidation and maintaining plant development under salt stress. These findings suggest the potential application of salt-responsive NbCIPK25 for cultivating glycophytes with a higher salt tolerance through genetic engineering.
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Affiliation(s)
- Lu Lu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xinru Wu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Pengkai Wang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Liming Zhu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yuxin Liu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yao Tang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Ye Lu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jingbo Zhang
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Tielong Cheng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Banaev EV, Khozyaykina SA, Dorogina OV, Tomoshevich MA. Genetic Diversity of Nitraria sibirica Pall. (Nitrariaceae) in the Populations of Siberia and Kazakhstan Based on the Polymorphism of Intermicrosatellite Markers. CONTEMP PROBL ECOL+ 2022. [DOI: 10.1134/s1995425522040023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Song F, Feng Y. The complete chloroplast genome of the desert shrub Nitraria sphaerocarpa (Nitrariaceae) and phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1901-1903. [PMID: 34179469 PMCID: PMC8205073 DOI: 10.1080/23802359.2021.1934580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nitraria sphaerocarpa Maxim. is a typical desert shrub commonly used as a sand binder. Here, we sequenced and characterized the whole plastid genome of N. sphaerocarpa. It is 159,369 bp in length, containing two copies of inverted repeat (IR) regions (26,566 bp, each), a large single-copy (LSC) region (87,854 bp), and a small single-copy (SSC) region (18,383 bp). It has 114 unigenes, including 79 protein-coding genes, 30 tRNA genes, four rRNA genes, and one pseudogene (infA). Phylogenetic analysis shows that N. sphaerocarpa is located at a basal position of the genus Nitraria.
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Affiliation(s)
- Feng Song
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ying Feng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
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Yin H, Wang L, Shi Y, Qian C, Zhou H, Wang W, Ma XF, Tran LSP, Zhang B. The East Asian Winter Monsoon Acts as a Major Selective Factor in the Intraspecific Differentiation of Drought-Tolerant Nitraria tangutorum in Northwest China. PLANTS 2020; 9:plants9091100. [PMID: 32867062 PMCID: PMC7570063 DOI: 10.3390/plants9091100] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
The influence of Quaternary climate fluctuation on the geographical structure and genetic diversity of species distributed in the regions of the Qinghai–Tibet Plateau (QTP) has been well established. However, the underlying role of the East Asian monsoon system (EAMS) in shaping the genetic structure of the population and the demography of plants located in the arid northwest of China has not been explored. In the present study, Nitraria tangutorum, a drought-tolerant desert shrub that is distributed in the EAMS zone and has substantial ecological and economic value, was profiled to better understand the influence of EAMS evolution on its biogeographical patterns and demographic history. Thus, the phylogeographical structure and historical dynamics of this plant species were elucidated using its five chloroplast DNA (cpDNA) fragments. Hierarchical structure analysis revealed three distinct, divergent lineages: West, East-A, and East-B. The molecular dating was carried out using a Bayesian approach to estimate the time of intraspecies divergence. Notably, the eastern region, which included East-A and East-B lineages, was revealed to be the original center of distribution and was characterized by a high level of genetic diversity, with the intraspecific divergence time dated to be around 2.53 million years ago (Ma). These findings, combined with the data obtained by ecological niche modeling analysis, indicated that the East lineages have undergone population expansion and differentiation, which were closely correlated with the development of the EAMS, especially the East Asian winter monsoon (EAWM). The West lineage appears to have originated from the migration of N. tangutorum across the Hexi corridor at around 1.85 Ma, and subsequent colonization of the western region. These results suggest that the EAWM accelerated the population expansion of N. tangutorum and subsequent intraspecific differentiation. These findings collectively provide new information on the impact of the evolution of the EAMS on intraspecific diversification and population demography of drought-tolerant plant species in northwest China.
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Affiliation(s)
- Hengxia Yin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
| | - Lirong Wang
- College of Ecological Environment and Resources, Qinghai Nationalities University, Xining 810007, China;
| | - Yong Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
| | - Chaoju Qian
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, China; (C.Q.); (X.-F.M.)
| | - Huakun Zhou
- The Key Laboratory of Restoration Ecology in Cold Region of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Science, Xining 810008, China;
| | - Wenying Wang
- Department of Life Sciences, Qinghai Normal University, Xining 810008, China;
| | - Xiao-Fei Ma
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, China; (C.Q.); (X.-F.M.)
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang 550000, Vietnam
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-19 22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Correspondence: (L.-S.P.T.); (B.Z.)
| | - Benyin Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China
- Correspondence: (L.-S.P.T.); (B.Z.)
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Cusimano N, Renner SS. Sequential horizontal gene transfers from different hosts in a widespread Eurasian parasitic plant, Cynomorium coccineum. AMERICAN JOURNAL OF BOTANY 2019; 106:679-689. [PMID: 31081928 DOI: 10.1002/ajb2.1286] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
PREMISE Parasitic plants with large geographic ranges, and different hosts in parts of their range, may acquire horizontally transferred genes (HGTs), which might sometimes leave a footprint of gradual host and range expansion. Cynomorium coccineum, the only member of the Saxifragales family Cynomoriaceae, is a root holoparasite that occurs in water-stressed habitats from western China to the Canary Islands. It parasitizes at least 10 angiosperm families from different orders, some of them only in parts of its range. This parasite therefore offers an opportunity to trace HGTs as long as parasite-host pairs can be obtained and sequenced. METHODS By sequencing mitochondrial, plastid, and nuclear loci from parasite-host pairs from throughout the parasite's range and with prior information from completely assembled mitochondrial and plastid genomes, we detected 10 HGTs of five mitochondrial genes. RESULTS The 10 HGTs appear to have occurred sequentially as C. coccineum expanded from East to West. Molecular-clock models yield Cynomorium stem ages between 66 and 156 Myr, with relaxed clocks converging on 66-67 Myr. Chinese Sapindales, probably Nitraria, were the first source of transferred genes, followed by Iranian and Mediterranean Caryophyllales. The most recently acquired gene appears to come from a Tamarix host in the Iberian Peninsula. CONCLUSIONS Data on HGTs that have accumulated over the past 15 years, along with this discovery of multiple HGTs within a single widespread species, underline the need for more whole-genome data from parasite-host pairs to investigate whether and how transferred copies coexist with, or replace, native functional genes.
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Affiliation(s)
- Natalie Cusimano
- Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Munich, Germany
| | - Susanne S Renner
- Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Munich, Germany
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Zhu L, Song J, Zhou JL, Si J, Cui BK. Species Diversity, Phylogeny, Divergence Time, and Biogeography of the Genus Sanghuangporus (Basidiomycota). Front Microbiol 2019; 10:812. [PMID: 31057518 PMCID: PMC6478708 DOI: 10.3389/fmicb.2019.00812] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/01/2019] [Indexed: 11/17/2022] Open
Abstract
"Sanghuang" is a popular fungus used as a Chinese traditional medicine. In fact, it represents a group of fungi belonging to the genus Sanghuangporus, but little is known about its origin and biogeography. The aim of this study was to characterize the molecular relationships, origin and biogeographical distribution of Sanghuangporus. The multi-locus phylogenetic analyses were used to infer the phylogenetic relationships. In addition, based on Bayesian evolutionary analysis using sequences from the internal transcribed spacer (ITS), nuclear large subunit rDNA (nLSU), translation elongation factor 1-α (EF1-α), and the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2), we used a fungus fossil-based approach to gain insight into the divergence time of species in Sanghuangporus. The molecular phylogeny strongly supports the monophyly of Sanghuangporus (MP = 100%, ML = 100%, and BPP = 1.00), and 13 species are recognized in this genus. The Bayesian uncorrelated lognormal relaxed molecular clock using BEAST and reconstructed ancestral areas indicate that the maximum crown age of Sanghuangporus is approximately 30.85 million years. East Asia is the likely ancestral area (38%). Dispersal and differentiation to other continents then occurred during the late Middle Miocene and Pliocene. The ancestor of Sanghuangporus probably originated in palaeotropical Northeast Asia and covered Northeast Asia and East Africa during the Oligocene-Miocene, hosted by plants that expanded via the "Gomphotherium Landbridge." Six kinds of dispersal routes are proposed, including intercontinental dispersal events of three clades between Northeast Asia and East Africa, between East Asia and North America, and between Northeast Asia and Europe.
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Affiliation(s)
| | | | | | | | - Bao-Kai Cui
- Institute of Microbiology, Beijing Forestry University, Beijing, China
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Woutersen A, Jardine PE, Bogotá-Angel RG, Zhang HX, Silvestro D, Antonelli A, Gogna E, Erkens RH, Gosling WD, Dupont-Nivet G, Hoorn C. A novel approach to study the morphology and chemistry of pollen in a phylogenetic context, applied to the halophytic taxon Nitraria L.(Nitrariaceae). PeerJ 2018; 6:e5055. [PMID: 30038851 PMCID: PMC6054868 DOI: 10.7717/peerj.5055] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/01/2018] [Indexed: 11/23/2022] Open
Abstract
Nitraria is a halophytic taxon (i.e., adapted to saline environments) that belongs to the plant family Nitrariaceae and is distributed from the Mediterranean, across Asia into the south-eastern tip of Australia. This taxon is thought to have originated in Asia during the Paleogene (66-23 Ma), alongside the proto-Paratethys epicontinental sea. The evolutionary history of Nitraria might hold important clues on the links between climatic and biotic evolution but limited taxonomic documentation of this taxon has thus far hindered this line of research. Here we investigate if the pollen morphology and the chemical composition of the pollen wall are informative of the evolutionary history of Nitraria and could explain if origination along the proto-Paratethys and dispersal to the Tibetan Plateau was simultaneous or a secondary process. To answer these questions, we applied a novel approach consisting of a combination of Fourier Transform Infrared spectroscopy (FTIR), to determine the chemical composition of the pollen wall, and pollen morphological analyses using Light Microscopy (LM) and Scanning Electron Microscopy (SEM). We analysed our data using ordinations (principal components analysis and non-metric multidimensional scaling), and directly mapped it on the Nitrariaceae phylogeny to produce a phylomorphospace and a phylochemospace. Our LM, SEM and FTIR analyses show clear morphological and chemical differences between the sister groups Peganum and Nitraria. Differences in the morphological and chemical characteristics of highland species (Nitraria schoberi, N. sphaerocarpa, N. sibirica and N. tangutorum) and lowland species (Nitraria billardierei and N. retusa) are very subtle, with phylogenetic history appearing to be a more important control on Nitraria pollen than local environmental conditions. Our approach shows a compelling consistency between the chemical and morphological characteristics of the eight studied Nitrariaceae species, and these traits are in agreement with the phylogenetic tree. Taken together, this demonstrates how novel methods for studying fossil pollen can facilitate the evolutionary investigation of living and extinct taxa, and the environments they represent.
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Affiliation(s)
- Amber Woutersen
- University of Amsterdam, Institute for Biodiversity and Ecosystem Dynamics (IBED), Amsterdam, The Netherlands
| | - Phillip E. Jardine
- University of Potsdam, Institute of Earth and Environmental Science, Potsdam, Germany
- University of Münster, Institute of Geology and Palaeontology, Münster, Germany
| | - Raul Giovanni Bogotá-Angel
- University of Amsterdam, Institute for Biodiversity and Ecosystem Dynamics (IBED), Amsterdam, The Netherlands
- Universidad Distrital Francisco José de Caldas, Facultad del Medio Ambiente y Recursos Naturales, Bogotá, Colombia
| | - Hong-Xiang Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, China Academy of Sciences, Urumqi, China
| | | | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- University of Gothenburg, Department of Biological and Environmental Sciences, Göteborg, Sweden
- Gothenburg Botanical Garden, Göteborg, Sweden
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA, United States of America
| | - Elena Gogna
- Maastricht University, Maastricht Science Programme, Maastricht, The Netherlands
| | - Roy H.J. Erkens
- Maastricht University, Maastricht Science Programme, Maastricht, The Netherlands
| | - William D. Gosling
- University of Amsterdam, Institute for Biodiversity and Ecosystem Dynamics (IBED), Amsterdam, The Netherlands
| | - Guillaume Dupont-Nivet
- University of Potsdam, Institute of Earth and Environmental Science, Potsdam, Germany
- Université de Rennes, Geosciences Rennes UMR-CNRS, Rennes, France
| | - Carina Hoorn
- University of Amsterdam, Institute for Biodiversity and Ecosystem Dynamics (IBED), Amsterdam, The Netherlands
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12
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Zhou B, Tu T, Kong F, Wen J, Xu X. Revised phylogeny and historical biogeography of the cosmopolitan aquatic plant genus Typha (Typhaceae). Sci Rep 2018; 8:8813. [PMID: 29891978 PMCID: PMC5995854 DOI: 10.1038/s41598-018-27279-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/23/2018] [Indexed: 11/09/2022] Open
Abstract
Typha is a cosmopolitan aquatic plant genus that includes species with widespread distributions. It is a relatively ancient genus with an abundant fossil record dating back to the Paleogene. However, the details of its biogeographic history have remained unclear until now. In this study, we present a revised molecular phylogeny using sequences of seven chloroplast DNA markers from nine species sampled from various regions in order to infer the biogeographic history of the genus. Two clades were recovered with robust support. Typha minima and T. elephantina comprised one clade, and the other clade included the remaining seven species, which represented a polytomy of four robustly supported subclades. Two widespread species, T. angustifolia and T. domingensis, were revealed to be paraphyletic, indicating the need for taxonomic revision. Divergence time estimation suggested that Typha had a mid-Eocene crown origin, and its diversification occurred in the Middle and Late Miocene. Ancestral area reconstruction showed that Typha possibly originated from eastern Eurasia. Both dispersal via the Beringian Land Bridge and recent transoceanic dispersal may have influenced the intercontinental distribution of Typha species.
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Affiliation(s)
- Beibei Zhou
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Tieyao Tu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
| | - Fanjiao Kong
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA.
| | - Xinwei Xu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan, 430072, PR China.
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13
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Diversification dynamics and transoceanic Eurasian-Australian disjunction in the genus Picris (Compositae) induced by the interplay of shifts in intrinsic/extrinsic traits and paleoclimatic oscillations. Mol Phylogenet Evol 2018; 119:182-195. [DOI: 10.1016/j.ympev.2017.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 11/22/2022]
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14
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Bellot S, Cusimano N, Luo S, Sun G, Zarre S, Gröger A, Temsch E, Renner SS. Assembled Plastid and Mitochondrial Genomes, as well as Nuclear Genes, Place the Parasite Family Cynomoriaceae in the Saxifragales. Genome Biol Evol 2016; 8:2214-30. [PMID: 27358425 PMCID: PMC4987112 DOI: 10.1093/gbe/evw147] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cynomoriaceae, one of the last unplaced families of flowering plants, comprise one or two species or subspecies of root parasites that occur from the Mediterranean to the Gobi Desert. Using Illumina sequencing, we assembled the mitochondrial and plastid genomes as well as some nuclear genes of a
Cynomorium
specimen from Italy. Selected genes were also obtained by Sanger sequencing from individuals collected in China and Iran, resulting in matrices of 33 mitochondrial, 6 nuclear, and 14 plastid genes and rDNAs enlarged to include a representative angiosperm taxon sampling based on data available in GenBank. We also compiled a new geographic map to discern possible discontinuities in the parasites’ occurrence.
Cynomorium
has large genomes of 13.70–13.61 (Italy) to 13.95–13.76 pg (China). Its mitochondrial genome consists of up to 49 circular subgenomes and has an overall gene content similar to that of photosynthetic angiosperms, while its plastome retains only 27 of the normally 116 genes. Nuclear, plastid and mitochondrial phylogenies place Cynomoriaceae in Saxifragales, and we found evidence for several horizontal gene transfers from different hosts, as well as intracellular gene transfers.
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Affiliation(s)
- Sidonie Bellot
- Department of Plant Sciences, Plant Biodiversity Research, Technical University of Munich (TUM), Freising, Germany
| | - Natalie Cusimano
- Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Germany
| | - Shixiao Luo
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Guangzhou, China
| | - Guiling Sun
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, China
| | - Shahin Zarre
- Department of Plant Sciences, University of Tehran, Iran
| | | | - Eva Temsch
- Department of Systematic and Evolutionary Botany, University of Vienna, Austria
| | - Susanne S Renner
- Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Germany
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15
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Manafzadeh S, Staedler YM, Conti E. Visions of the past and dreams of the future in the Orient: the Irano-Turanian region from classical botany to evolutionary studies. Biol Rev Camb Philos Soc 2016; 92:1365-1388. [PMID: 27349491 DOI: 10.1111/brv.12287] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 01/20/2023]
Abstract
Ever since the 19th century, the immense arid lands of the Orient, now called the Irano-Turanian (IT) floristic region, attracted the interest of European naturalists with their tremendous plant biodiversity. Covering approximately 30% of the surface of Eurasia (16000000 km2 ), the IT region is one of the largest floristic regions of the world. The IT region represents one of the hotspots of evolutionary and biological diversity in the Old World, and serves as a source of xerophytic taxa for neighbouring regions. Moreover, it is the cradle of the numerous species domesticated in the Fertile Crescent. Over the last 200 years, naturalists outlined different borders for the IT region. Yet, the delimitation and evolutionary history of this area remain one of the least well-understood fields of global biogeography, even though it is crucial to explaining the distribution of life in Eurasia. No comprehensive review of the biogeographical delimitations nor of the role of geological and climatic changes in the evolution of the IT region is currently available. After considering the key role of floristic regions in biogeography, we review the history of evolving concepts about the borders and composition of the IT region over the past 200 years and outline a tentative circumscription for it. We also summarise current knowledge on the geological and climatic history of the IT region. We then use this knowledge to generate specific evolutionary hypotheses to explain how different geological, palaeoclimatic, and ecological factors contributed to range expansion and contraction, thus shaping patterns of speciation in the IT region over time and space. Both historical and ecological biogeography should be applied to understand better the floristic diversification of the region. This will ultimately require evolutionary comparative analyses based on integrative phylogenetic, geological, climatic, ecological, and species distribution studies on the region. Furthermore, an understanding of evolutionary and ecological processes will play a major role in regional planning for protecting biodiversity of the IT region in facing climatic change. With this review, we aim to introduce the IT floristic region to a broader audience of evolutionary, ecological and systematic biologists, thus promoting cutting-edge research on this area and raising awareness of this vast and diverse, yet understudied, part of the world.
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Affiliation(s)
- Sara Manafzadeh
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Yannick M Staedler
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Elena Conti
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
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