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Jian J, Wang Z, Chen C, Workman CT, Fang X, Larsen TO, Guo J, Sonnenschein EC. Two high-quality Prototheca zopfii genomes provide new insights into their evolution as obligate algal heterotrophs and their pathogenicity. Microbiol Spectr 2024:e0414823. [PMID: 38940543 DOI: 10.1128/spectrum.04148-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 05/24/2024] [Indexed: 06/29/2024] Open
Abstract
The majority of the nearly 10,000 described species of green algae are photoautotrophs; however, some species have lost their ability to photosynthesize and become obligate heterotrophs that rely on parasitism for survival. Two high-quality genomes of the heterotrophic algae Prototheca zopfii Pz20 and Pz23 were obtained using short- and long-read genomic as well as transcriptomic data. The genome sizes were 31.2 Mb and 31.3 Mb, respectively, and contig N50 values of 1.99 Mb and 1.26 Mb. Although P. zopfii maintained its plastid genome, the transition to heterotrophy led to a reduction in both plastid and nuclear genome size, including the loss of photosynthesis-related genes from both the nuclear and plastid genomes and the elimination of genes encoding for carotenoid oxygenase and pheophorbide an oxygenase. The loss of genes, including basic leucine-zipper (bZIP) transcription factors, flavin adenine dinucleotide-linked oxidase, and helicase, could have played a role in the transmission of autotrophy to heterotrophs and in the processes of abiotic stress resistance and pathogenicity. A total of 66 (1.37%) and 73 (1.49%) genes were identified as potential horizontal gene transfer events in the two P. zopfii genomes, respectively. Genes for malate synthase and isocitrate lyase, which are horizontally transferred from bacteria, may play a pivotal role in carbon and nitrogen metabolism as well as the pathogenicity of Prototheca and non-photosynthetic organisms. The two high-quality P. zopfii genomes provide new insights into their evolution as obligate heterotrophs and pathogenicity. IMPORTANCE The genus Prototheca, characterized by its heterotrophic nature and pathogenicity, serves as an exemplary model for investigating pathobiology. The limited understanding of the protothecosis infectious disease is attributed to the lack of genomic resources. Using HiFi long-read sequencing, both nuclear and plastid genomes were generated for two strains of P. zopfii. The findings revealed a concurrent reduction in both plastid and nuclear genome size, accompanied by the loss of genes associated with photosynthesis, carotenoid oxygenase, basic leucine-zipper (bZIP) transcription factors, and others. The analysis of horizontal gene transfer revealed the presence of 1.37% and 1.49% bacterial genes, including malate synthase and isocitrate lyase, which play crucial roles in carbon and nitrogen metabolism, as well as pathogenicity and obligate heterotrophy. The two high-quality P. zopfii genomes represent valuable resources for investigating their adaptation and evolution as obligate heterotrophs, as well as for developing future prevention and treatment strategies against protothecosis.
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Affiliation(s)
- Jianbo Jian
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- BGI Genomics, Shenzhen, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | | | | | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- Department of Biosciences, Swansea University, Swansea, United Kingdom
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Liu MJ, Fang JC, Ma Y, Chong GL, Huang CK, Takeuchi A, Takayanagi N, Ohtani M. Frontiers in plant RNA research in ICAR2023: from lab to innovative agriculture. PLANT MOLECULAR BIOLOGY 2024; 114:45. [PMID: 38630407 DOI: 10.1007/s11103-024-01436-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 04/19/2024]
Abstract
The recent growth in global warming, soil contamination, and climate instability have widely disturbed ecosystems, and will have a significant negative impact on the growth of plants that produce grains, fruits and woody biomass. To conquer this difficult situation, we need to understand the molecular bias of plant environmental responses and promote development of new technologies for sustainable maintenance of crop production. Accumulated molecular biological data have highlighted the importance of RNA-based mechanisms for plant stress responses. Here, we report the most advanced plant RNA research presented in the 33rd International Conference on Arabidopsis Research (ICAR2023), held as a hybrid event on June 5-9, 2023 in Chiba, Japan, and focused on "Arabidopsis for Sustainable Development Goals". Six workshops/concurrent sessions in ICAR2023 targeted plant RNA biology, and many RNA-related topics could be found in other sessions. In this meeting report, we focus on the workshops/concurrent sessions targeting RNA biology, to share what is happening now at the forefront of plant RNA research.
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Affiliation(s)
- Ming-Jung Liu
- Biotechnology Center in Southern Taiwan, Academia Sinica (AS-BCST), Tainan, Taiwan.
| | - Jhen-Cheng Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica (AS-BCST), Tainan, Taiwan
| | - Ya Ma
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 227-8562, Japan
| | - Geeng Loo Chong
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan
| | - Chun-Kai Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan
| | - Ami Takeuchi
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 227-8562, Japan
| | - Natsu Takayanagi
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 227-8562, Japan
| | - Misato Ohtani
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 227-8562, Japan.
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan.
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan.
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Ko I, Kranse OP, Senatori B, Eves-van den Akker S. A Critical Appraisal of DNA Transfer from Plants to Parasitic Cyst Nematodes. Mol Biol Evol 2024; 41:msae030. [PMID: 38366574 PMCID: PMC10899095 DOI: 10.1093/molbev/msae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/15/2023] [Accepted: 12/18/2023] [Indexed: 02/18/2024] Open
Abstract
Plant-parasitic nematodes are one of the most economically important pests of crops. It is widely accepted that horizontal gene transfer-the natural acquisition of foreign genes in parasitic nematodes-contributes to parasitism. However, an apparent paradox has emerged from horizontal gene transfer analyses: On the one hand, distantly related organisms with very dissimilar genetic structures (i.e. bacteria), and only transient interactions with nematodes as far as we know, dominate the list of putative donors, while on the other hand, considerably more closely related organisms (i.e. the host plant), with similar genetic structure (i.e. introns) and documented long-term associations with nematodes, are rare among the list of putative donors. Given that these nematodes ingest cytoplasm from a living plant cell for several weeks, there seems to be a conspicuous absence of plant-derived cases. Here, we used comparative genomic approaches to evaluate possible plant-derived horizontal gene transfer events in plant parasitic nematodes. Our evidence supports a cautionary message for plant-derived horizontal gene transfer cases in the sugar beet cyst nematode, Heterodera schachtii. We propose a 4-step model for horizontal gene transfer from plant to parasite in order to evaluate why the absence of plant-derived horizontal gene transfer cases is observed. We find that the plant genome is mobilized by the nematode during infection, but that uptake of the said "mobilome" is the first major barrier to horizontal gene transfer from host to nematode. These results provide new insight into our understanding of the prevalence/role of nucleic acid exchange in the arms race between plants and plant parasites.
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Affiliation(s)
- Itsuhiro Ko
- Department of Plant Sciences, The Crop Science Centre, University of Cambridge, Cambridge CB2 3EA, UK
- Present address: Department of Plant Pathology, Washington State University, Pullman 99163, USA
| | - Olaf Prosper Kranse
- Department of Plant Sciences, The Crop Science Centre, University of Cambridge, Cambridge CB2 3EA, UK
| | - Beatrice Senatori
- Department of Plant Sciences, The Crop Science Centre, University of Cambridge, Cambridge CB2 3EA, UK
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Sanchez-Puerta MV, Ceriotti LF, Gatica-Soria LM, Roulet ME, Garcia LE, Sato HA. Invited Review Beyond parasitic convergence: unravelling the evolution of the organellar genomes in holoparasites. ANNALS OF BOTANY 2023; 132:909-928. [PMID: 37503831 PMCID: PMC10808021 DOI: 10.1093/aob/mcad108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/27/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND The molecular evolution of organellar genomes in angiosperms has been studied extensively, with some lineages, such as parasitic ones, displaying unique characteristics. Parasitism has emerged 12 times independently in angiosperm evolution. Holoparasitism is the most severe form of parasitism, and is found in ~10 % of parasitic angiosperms. Although a few holoparasitic species have been examined at the molecular level, most reports involve plastomes instead of mitogenomes. Parasitic plants establish vascular connections with their hosts through haustoria to obtain water and nutrients, which facilitates the exchange of genetic information, making them more susceptible to horizontal gene transfer (HGT). HGT is more prevalent in the mitochondria than in the chloroplast or nuclear compartments. SCOPE This review summarizes current knowledge on the plastid and mitochondrial genomes of holoparasitic angiosperms, compares the genomic features across the different lineages, and discusses their convergent evolutionary trajectories and distinctive features. We focused on Balanophoraceae (Santalales), which exhibits extraordinary traits in both their organelles. CONCLUSIONS Apart from morphological similarities, plastid genomes of holoparasitic plants also display other convergent features, such as rampant gene loss, biased nucleotide composition and accelerated evolutionary rates. In addition, the plastomes of Balanophoraceae have extremely low GC and gene content, and two unexpected changes in the genetic code. Limited data on the mitochondrial genomes of holoparasitic plants preclude thorough comparisons. Nonetheless, no obvious genomic features distinguish them from the mitochondria of free-living angiosperms, except for a higher incidence of HGT. HGT appears to be predominant in holoparasitic angiosperms with a long-lasting endophytic stage. Among the Balanophoraceae, mitochondrial genomes exhibit disparate evolutionary paths with notable levels of heteroplasmy in Rhopalocnemis and unprecedented levels of HGT in Lophophytum. Despite their differences, these Balanophoraceae share a multichromosomal mitogenome, a feature also found in a few free-living angiosperms.
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Affiliation(s)
- M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - Luis F Ceriotti
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - Leonardo M Gatica-Soria
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - M Emilia Roulet
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
| | - Laura E Garcia
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - Hector A Sato
- Facultad de Ciencias Agrarias, Cátedra de Botánica General–Herbario JUA, Alberdi 47, Universidad Nacional de Jujuy, 4600 Jujuy, Argentina
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Chen X, Fang D, Xu Y, Duan K, Yoshida S, Yang S, Sahu SK, Fu H, Guang X, Liu M, Wu C, Liu Y, Mu W, Chen Y, Fan Y, Wang F, Peng S, Shi D, Wang Y, Yu R, Zhang W, Bai Y, Liu ZJ, Yan Q, Liu X, Xu X, Yang H, Wu J, Graham SW, Liu H. Balanophora genomes display massively convergent evolution with other extreme holoparasites and provide novel insights into parasite-host interactions. NATURE PLANTS 2023; 9:1627-1642. [PMID: 37735254 DOI: 10.1038/s41477-023-01517-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 08/18/2023] [Indexed: 09/23/2023]
Abstract
Parasitic plants have evolved to be subtly or severely dependent on host plants to complete their life cycle. To provide new insights into the biology of parasitic plants in general, we assembled genomes for members of the sandalwood order Santalales, including a stem hemiparasite (Scurrula) and two highly modified root holoparasites (Balanophora) that possess chimaeric host-parasite tubers. Comprehensive genome comparisons reveal that hemiparasitic Scurrula has experienced a relatively minor degree of gene loss compared with autotrophic plants, consistent with its moderate degree of parasitism. Nonetheless, patterns of gene loss appear to be substantially divergent across distantly related lineages of hemiparasites. In contrast, Balanophora has experienced substantial gene loss for the same sets of genes as an independently evolved holoparasite lineage, the endoparasitic Sapria (Malpighiales), and the two holoparasite lineages experienced convergent contraction of large gene families through loss of paralogues. This unprecedented convergence supports the idea that despite their extreme and strikingly divergent life histories and morphology, the evolution of these and other holoparasitic lineages can be shaped by highly predictable modes of genome reduction. We observe substantial evidence of relaxed selection in retained genes for both hemi- and holoparasitic species. Transcriptome data also document unusual and novel interactions between Balanophora and host plants at the host-parasite tuber interface tissues, with evidence of mRNA exchange, substantial and active hormone exchange and immune responses in parasite and host.
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Affiliation(s)
- Xiaoli Chen
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Yuxing Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Kunyu Duan
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Satoko Yoshida
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shuai Yang
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Hui Fu
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Xuanmin Guang
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Chenyu Wu
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Yang Liu
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China
| | - Weixue Mu
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Yewen Chen
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yannan Fan
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Fang Wang
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shufeng Peng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Dishen Shi
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Runxian Yu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wen Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yuqing Bai
- Administrative Office of Wutong Mountain National Park, Shenzhen, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiaoshun Yan
- Ailaoshan Station for Subtropical Forest Ecosystem Studies, Chinese Academy of Sciences, Jingdong, China
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jianqiang Wu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
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Longley R, Robinson A, Liber JA, Bryson AE, Morales DP, LaButti K, Riley R, Mondo SJ, Kuo A, Yoshinaga Y, Daum C, Barry K, Grigoriev IV, Desirò A, Chain PSG, Bonito G. Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi. Commun Biol 2023; 6:948. [PMID: 37723238 PMCID: PMC10507103 DOI: 10.1038/s42003-023-05299-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/29/2023] [Indexed: 09/20/2023] Open
Abstract
Diverse members of early-diverging Mucoromycota, including mycorrhizal taxa and soil-associated Mortierellaceae, are known to harbor Mollicutes-related endobacteria (MRE). It has been hypothesized that MRE were acquired by a common ancestor and transmitted vertically. Alternatively, MRE endosymbionts could have invaded after the divergence of Mucoromycota lineages and subsequently spread to new hosts horizontally. To better understand the evolutionary history of MRE symbionts, we generated and analyzed four complete MRE genomes from two Mortierellaceae genera: Linnemannia (MRE-L) and Benniella (MRE-B). These genomes include the smallest known of fungal endosymbionts and showed signals of a tight relationship with hosts including a reduced functional capacity and genes transferred from fungal hosts to MRE. Phylogenetic reconstruction including nine MRE from mycorrhizal fungi revealed that MRE-B genomes are more closely related to MRE from Glomeromycotina than MRE-L from the same host family. We posit that reductions in genome size, GC content, pseudogene content, and repeat content in MRE-L may reflect a longer-term relationship with their fungal hosts. These data indicate Linnemannia and Benniella MRE were likely acquired independently after their fungal hosts diverged from a common ancestor. This work expands upon foundational knowledge on minimal genomes and provides insights into the evolution of bacterial endosymbionts.
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Affiliation(s)
- Reid Longley
- Los Alamos National Laboratory, Los Alamos, NM, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Julian A Liber
- Department of Biology, Duke University, Durham, NC, 27704, USA
| | - Abigail E Bryson
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Kurt LaButti
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robert Riley
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Stephen J Mondo
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80521, USA
| | - Alan Kuo
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Gregory Bonito
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA.
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7
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Lesica P, Lavin M. Will molecular phylogenetics help decrease nomenclatural instability? AMERICAN JOURNAL OF BOTANY 2023; 110:e16219. [PMID: 37561649 DOI: 10.1002/ajb2.16219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 08/12/2023]
Affiliation(s)
- Peter Lesica
- Division of Biological Sciences, University of Montana, Missoula, 59812, Montana, USA
| | - Matt Lavin
- Plant Sciences and Plant Pathology Department, Montana State University, Bozeman, 59717, Montana, USA
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8
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Zhang J, Zhang C, Zan T, Nan P, Li L, Song Z, Zhang W, Yang J, Wang Y. Host shift promotes divergent evolution between closely related holoparasitic species. Mol Phylogenet Evol 2023:107842. [PMID: 37321361 DOI: 10.1016/j.ympev.2023.107842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/27/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023]
Abstract
Distinct hosts have been hypothesized to possess the potential for affecting species differentiation and genome evolution of parasitic organisms. However, what host shift history is experienced by the closely related parasites and whether disparate evolution of their genomes occur remain largely unknown. Here, we screened horizontal gene transfer (HGT) events in a pair of sister species of holoparasitic Boschniakia (Orobanchaceae) having obligate hosts from distinct families to recall the former host-parasite associations and performed a comparative analysis to investigate the difference of their organelle genomes. Except those from the current hosts (Ericaceae and Betulaceae), we identified a number of HGTs from Rosaceae supporting the occurrence of unexpected ancient host shifts. Different hosts transfer functional genes which changed nuclear genomes of this sister species. Likewise, different donors transferred sequences to their mitogenomes, which vary in size due to foreign and repetitive elements rather than other factors found in other parasites. The plastomes are both severely reduced, and the degree of difference in reduction syndrome reaches the intergeneric level. Our findings provide new insights into the genome evolution of parasites adapting to different hosts and extend the mechanism of host shift promoting species differentiation to parasitic plant lineages.
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Affiliation(s)
- Jiayin Zhang
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Chi Zhang
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Ting Zan
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Peng Nan
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Linfeng Li
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Zhiping Song
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Wenju Zhang
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Ji Yang
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Yuguo Wang
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
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9
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Guo X, Hu X, Li J, Shao B, Wang Y, Wang L, Li K, Lin D, Wang H, Gao Z, Jiao Y, Wen Y, Ji H, Ma C, Ge S, Jiang W, Jin X. The Sapria himalayana genome provides new insights into the lifestyle of endoparasitic plants. BMC Biol 2023; 21:134. [PMID: 37280593 DOI: 10.1186/s12915-023-01620-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Sapria himalayana (Rafflesiaceae) is an endoparasitic plant characterized by a greatly reduced vegetative body and giant flowers; however, the mechanisms underlying its special lifestyle and greatly altered plant form remain unknown. To illustrate the evolution and adaptation of S. himalayasna, we report its de novo assembled genome and key insights into the molecular basis of its floral development, flowering time, fatty acid biosynthesis, and defense responses. RESULTS The genome of S. himalayana is ~ 1.92 Gb with 13,670 protein-coding genes, indicating remarkable gene loss (~ 54%), especially genes involved in photosynthesis, plant body, nutrients, and defense response. Genes specifying floral organ identity and controlling organ size were identified in S. himalayana and Rafflesia cantleyi, and showed analogous spatiotemporal expression patterns in both plant species. Although the plastid genome had been lost, plastids likely biosynthesize essential fatty acids and amino acids (aromatic amino acids and lysine). A set of credible and functional horizontal gene transfer (HGT) events (involving genes and mRNAs) were identified in the nuclear and mitochondrial genomes of S. himalayana, most of which were under purifying selection. Convergent HGTs in Cuscuta, Orobanchaceae, and S. himalayana were mainly expressed at the parasite-host interface. Together, these results suggest that HGTs act as a bridge between the parasite and host, assisting the parasite in acquiring nutrients from the host. CONCLUSIONS Our results provide new insights into the flower development process and endoparasitic lifestyle of Rafflesiaceae plants. The amount of gene loss in S. himalayana is consistent with the degree of reduction in its body plan. HGT events are common among endoparasites and play an important role in their lifestyle adaptation.
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Affiliation(s)
- Xuelian Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Xiaodi Hu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Jianwu Li
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun Township, Mengla County, Yunnan, 666303, China
| | - Bingyi Shao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Yajun Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Long Wang
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Kui Li
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Dongliang Lin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Hanchen Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Zhiyuan Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Yingying Wen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Hongyu Ji
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Chongbo Ma
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing, 100083, China.
| | - Xiaohua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China.
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10
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Hudzik C, Maguire S, Guan S, Held J, Axtell MJ. Trans-species microRNA loci in the parasitic plant Cuscuta campestris have a U6-like snRNA promoter. THE PLANT CELL 2023; 35:1834-1847. [PMID: 36896651 PMCID: PMC10226579 DOI: 10.1093/plcell/koad076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/09/2023] [Accepted: 02/12/2023] [Indexed: 05/30/2023]
Abstract
Small regulatory RNAs can move between organisms and regulate gene expression in the recipient. Whether the trans-species small RNAs being exported are distinguished from the normal endogenous small RNAs of the source organism is not known. The parasitic plant Cuscuta campestris (dodder) produces many microRNAs that specifically accumulate at the host-parasite interface, several of which have trans-species activity. We found that induction of C. campestris interface-induced microRNAs is similar regardless of host species and occurs in C. campestris haustoria produced in the absence of any host. The loci-encoding C. campestris interface-induced microRNAs are distinguished by a common cis-regulatory element. This element is identical to a conserved upstream sequence element (USE) used by plant small nuclear RNA loci. The properties of the interface-induced microRNA primary transcripts strongly suggest that they are produced via U6-like transcription by RNA polymerase III. The USE promotes accumulation of interface-induced miRNAs (IIMs) in a heterologous system. This promoter element distinguishes C. campestris IIM loci from other plant small RNAs. Our data suggest that C. campestris IIMs are produced in a manner distinct from canonical miRNAs. All confirmed C. campestris microRNAs with documented trans-species activity are interface-induced and possess these features. We speculate that RNA polymerase III transcription of IIMs may allow these miRNAs to be exported to hosts.
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Affiliation(s)
- Collin Hudzik
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sean Maguire
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Shengxi Guan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Jeremy Held
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michael J Axtell
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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11
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Hartenstein M, Albert M, Krause K. The plant vampire diaries: a historic perspective on Cuscuta research. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2944-2955. [PMID: 36882965 DOI: 10.1093/jxb/erad082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/01/2023] [Indexed: 05/21/2023]
Abstract
The angiosperm genus Cuscuta lives as an almost achlorophyllous root- and leafless holoparasite and has therefore occupied scientists for more than a century. The 'evolution' of Cuscuta research started with early studies that established the phylogenetic framework for this unusual genus. It continued to produce groundbreaking cytological, morphological, and physiological insight throughout the second half of the 20th century and culminated in the last two decades in exciting discoveries regarding the molecular basis of Cuscuta parasitism that were facilitated by the modern 'omics' tools and traceable fluorescent marker technologies of the 21st century. This review will show how present activities are inspired by those past breakthroughs. It will describe significant milestones and recurring themes of Cuscuta research and connect these to the remaining as well as newly evolving questions and future directions in this research field that is expected to sustain its strong growth in the future.
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Affiliation(s)
- Maleen Hartenstein
- Department of Biology, Molecular Plant Physiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058 Erlangen, Germany
| | - Markus Albert
- Department of Biology, Molecular Plant Physiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058 Erlangen, Germany
| | - Kirsten Krause
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
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12
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Cai L. Rethinking convergence in plant parasitism through the lens of molecular and population genetic processes. AMERICAN JOURNAL OF BOTANY 2023; 110:e16174. [PMID: 37154532 DOI: 10.1002/ajb2.16174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 05/10/2023]
Abstract
The autotrophic lifestyle of photosynthetic plants has profoundly shaped their body plan, physiology, and gene repertoire. Shifts to parasitism and heterotrophy have evolved at least 12 times in more than 4000 species, and this transition has consequently left major evolutionary footprints among these parasitic lineages. Features that are otherwise rare at the molecular level and beyond have evolved repetitively, including reduced vegetative bodies, carrion-mimicking during reproduction, and the incorporation of alien genetic material. Here, I propose an integrated conceptual model, referred to as the funnel model, to define the general evolutionary trajectory of parasitic plants and provide a mechanistic explanation for their convergent evolution. This model connects our empirical understanding of gene regulatory networks in flowering plants with classical theories of molecular and population genetics. It emphasizes that the cascading effects brought about by the loss of photosynthesis may be a major force constraining the physiological capacity of parasitic plants and shaping their genomic landscapes. Here I review recent studies on the anatomy, physiology, and genetics of parasitic plants that lend support to this photosynthesis-centered funnel model. Focusing on nonphotosynthetic holoparasites, I elucidate how they may inevitably reach an evolutionary terminal status (i.e., extinction) and highlight the utility of a general, explicitly described and falsifiable model for future studies of parasitic plants.
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Affiliation(s)
- Liming Cai
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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13
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Wang D, Fletcher GC, Gagic D, On SLW, Palmer JS, Flint SH. Comparative genome identification of accessory genes associated with strong biofilm formation in Vibrio parahaemolyticus. Food Res Int 2023; 166:112605. [PMID: 36914349 DOI: 10.1016/j.foodres.2023.112605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/04/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
Vibrio parahaemolyticus biofilms on the seafood processing plant surfaces are a potential source of seafood contamination and subsequent food poisoning. Strains differ in their ability to form biofilm, but little is known about the genetic characteristics responsible for biofilm development. In this study, pangenome and comparative genome analysis of V. parahaemolyticus strains reveals genetic attributes and gene repertoire that contribute to robust biofilm formation. The study identified 136 accessory genes that were exclusively present in strong biofilm forming strains and these were functionally assigned to the Gene Ontology (GO) pathways of cellulose biosynthesis, rhamnose metabolic and catabolic processes, UDP-glucose processes and O antigen biosynthesis (p < 0.05). Strategies of CRISPR-Cas defence and MSHA pilus-led attachment were implicated via Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. Higher levels of horizontal gene transfer (HGT) were inferred to confer more putatively novel properties on biofilm-forming V. parahaemolyticus. Furthermore, cellulose biosynthesis, a neglected potential virulence factor, was identified as being acquired from within the order Vibrionales. The cellulose synthase operons in V. parahaemolyticus were examined for their prevalence (22/138, 15.94 %) and were found to consist of the genes bcsG, bcsE, bcsQ, bcsA, bcsB, bcsZ, bcsC. This study provides insights into robust biofilm formation of V. parahaemolyticus at the genomic level and facilitates: identification of key attributes for robust biofilm formation, elucidation of biofilm formation mechanisms and development of potential targets for novel control strategies of persistent V. parahaemolyticus.
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Affiliation(s)
- Dan Wang
- School of Food and Advanced Technology, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Graham C Fletcher
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Dragana Gagic
- School of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Stephen L W On
- Faculty of Agriculture and Life Sciences, Lincoln University, Private Bag 85084, Canterbury, New Zealand
| | - Jon S Palmer
- School of Food and Advanced Technology, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Steve H Flint
- School of Food and Advanced Technology, Massey University, Private Bag 11222, Palmerston North, New Zealand.
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14
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Hu Y, Wang X, Xu Y, Yang H, Tong Z, Tian R, Xu S, Yu L, Guo Y, Shi P, Huang S, Yang G, Shi S, Wei F. Molecular mechanisms of adaptive evolution in wild animals and plants. SCIENCE CHINA. LIFE SCIENCES 2023; 66:453-495. [PMID: 36648611 PMCID: PMC9843154 DOI: 10.1007/s11427-022-2233-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/30/2022] [Indexed: 01/18/2023]
Abstract
Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.
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Affiliation(s)
- Yibo Hu
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiaoping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yongchao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zeyu Tong
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ran Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Shuangquan Huang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Fuwen Wei
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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15
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Genomic and Epigenomic Mechanisms of the Interaction between Parasitic and Host Plants. Int J Mol Sci 2023; 24:ijms24032647. [PMID: 36768970 PMCID: PMC9917227 DOI: 10.3390/ijms24032647] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/22/2023] [Indexed: 02/01/2023] Open
Abstract
Parasitic plants extract nutrients from the other plants to finish their life cycle and reproduce. The control of parasitic weeds is notoriously difficult due to their tight physical association and their close biological relationship to their hosts. Parasitic plants differ in their susceptible host ranges, and the host species differ in their susceptibility to parasitic plants. Current data show that adaptations of parasitic plants to various hosts are largely genetically determined. However, multiple cases of rapid adaptation in genetically homogenous parasitic weed populations to new hosts strongly suggest the involvement of epigenetic mechanisms. Recent progress in genome-wide analyses of gene expression and epigenetic features revealed many new molecular details of the parasitic plants' interactions with their host plants. The experimental data obtained in the last several years show that multiple common features have independently evolved in different lines of the parasitic plants. In this review we discuss the most interesting new details in the interaction between parasitic and host plants.
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16
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Wang Y, Shahid MQ. Genome sequencing and resequencing identified three horizontal gene transfers and uncovered the genetic mechanism on the intraspecies adaptive evolution of Gastrodia elata Blume. FRONTIERS IN PLANT SCIENCE 2023; 13:1035157. [PMID: 36684780 PMCID: PMC9848658 DOI: 10.3389/fpls.2022.1035157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Horizontal gene transfer is a rare and useful genetic mechanism in higher plants. Gastrodia elata Blume (GE) (Orchidaceae), well known as traditional medicinal material in East Asia, adopts a heterotrophic lifestyle, thus being considered to be more prone to horizontal gene transfer (HGT). GE is a "polytypic species" that currently comprised of five recognized forms according to the plant morphology. G. elata Blume forma elata (GEE) and G. elata Bl.f.glauca (GEG) are two common forms that naturally grow in different habitats with difference in altitude and latitude. G. elata Bl.f.viridis (GEV) often occurs sporadically in cultivated populations of GEE and GEG. However, the genetic relationships and genetic mechanism underpinned the divergent ecological adaptations of GEE and GEG have not been revealed. Here, we assembled a chromosome-level draft genome of GEE with 1.04 Gb. Among predicted 17,895 protein coding genes, we identified three HGTs. Meanwhile, we resequenced 10 GEE accessions, nine GEG accessions, and 10 GEV accessions, and identified two independent genetic lineages: GEG_pedigree (GEG individuals and GEV individuals collected from GEG populations) and GEE_pedigree (GEE individuals and GEV individuals collected from GEE populations), which strongly support the taxonomic status of GEE and GEG as subspecies, not as different forms. In highly differentiated genomic regions of GEE_pedigree and GEG_pedigree, three chalcone synthase-encoding genes and one Phox/Bem1p (PB1) domain of encoding Auxin (AUX)/Indoleacetic acid (IAA) were identified in selection sweeping genome regions, which suggested that differentiation between GEE_pedigree and GEG_pedigree was promoted by the selection of genes related to photoresponse and growth and development. Overall, this new genome would be helpful for breeding and utilization of GE and the new findings would deepen the understanding about ecological adaptation and evolution of GE.
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Affiliation(s)
- Yunsheng Wang
- School of Health and Life Science, Kaili University, Kaili, Guizhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
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17
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Detecting macroevolutionary genotype-phenotype associations using error-corrected rates of protein convergence. Nat Ecol Evol 2023; 7:155-170. [PMID: 36604553 PMCID: PMC9834058 DOI: 10.1038/s41559-022-01932-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/12/2022] [Indexed: 01/07/2023]
Abstract
On macroevolutionary timescales, extensive mutations and phylogenetic uncertainty mask the signals of genotype-phenotype associations underlying convergent evolution. To overcome this problem, we extended the widely used framework of non-synonymous to synonymous substitution rate ratios and developed the novel metric ωC, which measures the error-corrected convergence rate of protein evolution. While ωC distinguishes natural selection from genetic noise and phylogenetic errors in simulation and real examples, its accuracy allows an exploratory genome-wide search of adaptive molecular convergence without phenotypic hypothesis or candidate genes. Using gene expression data, we explored over 20 million branch combinations in vertebrate genes and identified the joint convergence of expression patterns and protein sequences with amino acid substitutions in functionally important sites, providing hypotheses on undiscovered phenotypes. We further extended our method with a heuristic algorithm to detect highly repetitive convergence among computationally non-trivial higher-order phylogenetic combinations. Our approach allows bidirectional searches for genotype-phenotype associations, even in lineages that diverged for hundreds of millions of years.
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18
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Jhu MY, Sinha NR. Cuscuta species: Model organisms for haustorium development in stem holoparasitic plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1086384. [PMID: 36578337 PMCID: PMC9792094 DOI: 10.3389/fpls.2022.1086384] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Parasitic plants are notorious for causing serious agricultural losses in many countries. Specialized intrusive organs, haustoria, confer on parasitic plants the ability to acquire water and nutrients from their host plants. Investigating the mechanism involved in haustorium development not only reveals the fascinating mystery of how autotrophic plants evolved parasitism but also provides the foundation for developing more effective methods to control the agricultural damage caused by parasitic plants. Cuscuta species, also known as dodders, are one of the most well-known and widely spread stem holoparasitic plants. Although progress has been made recently in understanding the evolution and development of haustoria in root parasitic plants, more and more studies indicate that the behaviors between root and stem haustorium formation are distinct, and the mechanisms involved in the formation of these organs remain largely unknown. Unlike most endoparasites and root holoparasitic plants, which have high host-specificity and self- or kin-recognition to avoid forming haustoria on themselves or closely related species, auto-parasitism and hyper-parasitism are commonly observed among Cuscuta species. In this review, we summarize the current understanding of haustorium development in dodders and the unique characteristics of their parasitizing behaviors. We also outline the advantages of using Cuscuta species as model organisms for haustorium development in stem holoparasitic plants, the current unknown mysteries and limitations in the Cuscuta system, and potential future research directions to overcome these challenges.
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Affiliation(s)
- Min-Yao Jhu
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Neelima R. Sinha
- Department of Plant Biology, University of California, Davis, CA, United States
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19
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Yan Y. Insights into Mobile Small-RNAs Mediated Signaling in Plants. PLANTS (BASEL, SWITZERLAND) 2022; 11:3155. [PMID: 36432884 PMCID: PMC9698838 DOI: 10.3390/plants11223155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
In higher plants, small RNA (sRNA)-mediated RNA interfering (RNAi) is involved in a broad range of biological processes. Growing evidence supports the model that sRNAs are mobile signaling agents that move intercellularly, systemically and cross-species. Recently, considerable progress has been made in terms of characterization of the mobile sRNAs population and their function. In this review, recent progress in identification of new mobile sRNAs is assessed. Here, critical questions related to the function of these mobile sRNAs in coordinating developmental, physiological and defense-related processes is discussed. The forms of mobile sRNAs and the underlying mechanisms mediating sRNA trafficking are discussed next. A concerted effort has been made to integrate these new findings into a comprehensive overview of mobile sRNAs signaling in plants. Finally, potential important areas for both basic science and potential applications are highlighted for future research.
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Affiliation(s)
- Yan Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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20
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Li L, Peng S, Wang Z, Zhang T, Li H, Xiao Y, Li J, Liu Y, Yin H. Genome mining reveals abiotic stress resistance genes in plant genomes acquired from microbes via HGT. FRONTIERS IN PLANT SCIENCE 2022; 13:1025122. [PMID: 36407614 PMCID: PMC9667741 DOI: 10.3389/fpls.2022.1025122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Colonization by beneficial microbes can enhance plant tolerance to abiotic stresses. However, there are still many unknown fields regarding the beneficial plant-microbe interactions. In this study, we have assessed the amount or impact of horizontal gene transfer (HGT)-derived genes in plants that have potentials to confer abiotic stress resistance. We have identified a total of 235 gene entries in fourteen high-quality plant genomes belonging to phyla Chlorophyta and Streptophyta that confer resistance against a wide range of abiotic pressures acquired from microbes through independent HGTs. These genes encode proteins contributed to toxic metal resistance (e.g., ChrA, CopA, CorA), osmotic and drought stress resistance (e.g., Na+/proline symporter, potassium/proton antiporter), acid resistance (e.g., PcxA, ArcA, YhdG), heat and cold stress resistance (e.g., DnaJ, Hsp20, CspA), oxidative stress resistance (e.g., GST, PoxA, glutaredoxin), DNA damage resistance (e.g., Rad25, Rad51, UvrD), and organic pollutant resistance (e.g., CytP450, laccase, CbbY). Phylogenetic analyses have supported the HGT inferences as the plant lineages are all clustering closely with distant microbial lineages. Deep-learning-based protein structure prediction and analyses, in combination with expression assessment based on codon adaption index (CAI) further corroborated the functionality and expressivity of the HGT genes in plant genomes. A case-study applying fold comparison and molecular dynamics (MD) of the HGT-driven CytP450 gave a more detailed illustration on the resemblance and evolutionary linkage between the plant recipient and microbial donor sequences. Together, the microbe-originated HGT genes identified in plant genomes and their participation in abiotic pressures resistance indicate a more profound impact of HGT on the adaptive evolution of plants.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | | | - Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Teng Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
- Hunan Urban and Rural Environmental Construction Co., Ltd, Changsha, China
| | - Hongguang Li
- Hunan Tobacco Science Institute, Changsha, China
| | - Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Chenzhou, China
| | - Jingjun Li
- Chenzhou Tobacco Company of Hunan Province, Chenzhou, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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21
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Kong X, Yang M, Le BH, He W, Hou Y. The master role of siRNAs in plant immunity. MOLECULAR PLANT PATHOLOGY 2022; 23:1565-1574. [PMID: 35869407 PMCID: PMC9452763 DOI: 10.1111/mpp.13250] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 06/01/2023]
Abstract
Gene silencing mediated by small noncoding RNAs (sRNAs) is a fundamental gene regulation mechanism in eukaryotes that broadly governs cellular processes. It has been established that sRNAs are critical regulators of plant growth, development, and antiviral defence, while accumulating studies support positive roles of sRNAs in plant defence against bacteria and eukaryotic pathogens such as fungi and oomycetes. Emerging evidence suggests that plant sRNAs move between species and function as antimicrobial agents against nonviral parasites. Multiple plant pathosystems have been shown to involve a similar exchange of small RNAs between species. Recent analysis about extracellular sRNAs shed light on the understanding of the selection and transportation of sRNAs moving from plant to parasites. In this review, we summarize current advances regarding the function and regulatory mechanism of plant endogenous small interfering RNAs (siRNAs) in mediating plant defence against pathogen intruders including viruses, bacteria, fungi, oomycetes, and parasitic plants. Beyond that, we propose potential mechanisms behind the sorting of sRNAs moving between species and the idea that engineering siRNA-producing loci could be a useful strategy to improve disease resistance of crops.
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Affiliation(s)
- Xiuzhen Kong
- Shanghai Collaborative Innovation Center of Agri‐Seeds/School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Meng Yang
- Shanghai Collaborative Innovation Center of Agri‐Seeds/School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Brandon H. Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome BiologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - Wenrong He
- Plant Molecular and Cellular Biology LaboratorySalk Institute for Biological StudiesLa JollaCaliforniaUSA
| | - Yingnan Hou
- Shanghai Collaborative Innovation Center of Agri‐Seeds/School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
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22
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Zangishei Z, Annacondia ML, Gundlach H, Didriksen A, Bruckmüller J, Salari H, Krause K, Martinez G. Parasitic plant small RNA analyses unveil parasite-specific signatures of microRNA retention, loss, and gain. PLANT PHYSIOLOGY 2022; 190:1242-1259. [PMID: 35861439 PMCID: PMC9516757 DOI: 10.1093/plphys/kiac331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/12/2022] [Indexed: 05/29/2023]
Abstract
Parasitism is a successful life strategy that has evolved independently in several families of vascular plants. The genera Cuscuta and Orobanche represent examples of the two profoundly different groups of parasites: one parasitizing host shoots and the other infecting host roots. In this study, we sequenced and described the overall repertoire of small RNAs from Cuscuta campestris and Orobanche aegyptiaca. We showed that C. campestris contains a number of novel microRNAs (miRNAs) in addition to a conspicuous retention of miRNAs that are typically lacking in other Solanales, while several typically conserved miRNAs seem to have become obsolete in the parasite. One new miRNA appears to be derived from a horizontal gene transfer event. The exploratory analysis of the miRNA population (exploratory due to the absence of a full genomic sequence for reference) from the root parasitic O. aegyptiaca also revealed a loss of a number of miRNAs compared to photosynthetic species from the same order. In summary, our study shows partly similar evolutionary signatures in the RNA silencing machinery in both parasites. Our data bear proof for the dynamism of this regulatory mechanism in parasitic plants.
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Affiliation(s)
| | | | - Heidrun Gundlach
- Helmholtz Zentrum München (HMGU), Plant Genome and Systems Biology (PGSB), Neuherberg 85764, Germany
| | - Alena Didriksen
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø 9019, Norway
| | | | - Hooman Salari
- Department of Production Engineering and Plant Genetics, Faculty of Science and Agricultural Engineering, Razi University, Kermanshah 67155, Iran
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23
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Philips JG, Martin-Avila E, Robold AV. Horizontal gene transfer from genetically modified plants - Regulatory considerations. Front Bioeng Biotechnol 2022; 10:971402. [PMID: 36118580 PMCID: PMC9471246 DOI: 10.3389/fbioe.2022.971402] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Gene technology regulators receive applications seeking permission for the environmental release of genetically modified (GM) plants, many of which possess beneficial traits such as improved production, enhanced nutrition and resistance to drought, pests and diseases. The regulators must assess the risks to human and animal health and to the environment from releasing these GM plants. One such consideration, of many, is the likelihood and potential consequence of the introduced or modified DNA being transferred to other organisms, including people. While such gene transfer is most likely to occur to sexually compatible relatives (vertical gene transfer), horizontal gene transfer (HGT), which is the acquisition of genetic material that has not been inherited from a parent, is also a possibility considered during these assessments. Advances in HGT detection, aided by next generation sequencing, have demonstrated that HGT occurrence may have been previously underestimated. In this review, we provide updated evidence on the likelihood, factors and the barriers for the introduced or modified DNA in GM plants to be horizontally transferred into a variety of recipients. We present the legislation and frameworks the Australian Gene Technology Regulator adheres to with respect to the consideration of risks posed by HGT. Such a perspective may generally be applicable to regulators in other jurisdictions as well as to commercial and research organisations who develop GM plants.
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24
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Bartha L, Mandáková T, Kovařík A, Bulzu PA, Rodde N, Mahelka V, Lysak MA, Fustier MA, Šafář J, Cápal P, Keresztes L, Banciu HL. Intact ribosomal DNA arrays of Potentilla origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer. THE NEW PHYTOLOGIST 2022; 235:1246-1259. [PMID: 35460285 DOI: 10.1111/nph.18171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
During our initial phylogenetic study of the monocot genus Erythronium (Liliaceae), we observed peculiar eudicot-type internal transcribed spacer (ITS) sequences in a dataset derived from genomic DNA of Erythronium dens-canis. This raised the possibility of horizontal transfer of a eudicot alien ribosomal DNA (rDNA) into the Erythronium genome. In this work we aimed to support this hypothesis by carrying out genomic, molecular, and cytogenetic analyses. Genome skimming coupled by PacBio HiFi sequencing of a bacterial artificial chromosome clone derived from flow-sorted nuclei was used to characterise the alien 45S rDNA. Integration of alien rDNA in the recipient genome was further proved by Southern blotting and fluorescence in situ hybridization using specific probes. Alien rDNA, nested among Potentilla species in phylogenetic analysis, likely entered the Erythronium lineage in the common ancestor of E. dens-canis and E. caucasicum. Transferred eudicot-type rDNA preserved its tandemly arrayed feature on a single chromosome and was found to be transcribed in the monocot host, albeit much less efficiently than the native counterpart. This study adds a new example to the rarely documented nuclear-to-nuclear jumps of DNA between eudicots and monocots while holding the scientific community continually in suspense about the mode of DNA transfer.
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Affiliation(s)
- László Bartha
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeş-Bolyai University, 400271, Cluj-Napoca, Romania
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
| | - Aleš Kovařík
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265, Brno, Czech Republic
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, 370 05, České Budějovice, Czech Republic
| | - Nathalie Rodde
- French Plant Genomic Resource Center, INRAE-CNRGV, 31320, Castanet Tolosan, France
| | - Václav Mahelka
- Institute of Botany, Czech Academy of Sciences, 25243, Průhonice, Czech Republic
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
| | | | - Jan Šafář
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, 779 00, Olomouc, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, 779 00, Olomouc, Czech Republic
| | - Lujza Keresztes
- Hungarian Department of Biology and Ecology, Babeş-Bolyai University, 400006, Cluj-Napoca, Romania
- Centre of Systems Biology, Biodiversity and Bioresources (3B), Babeş-Bolyai University, 400006, Cluj-Napoca, Romania
| | - Horia L Banciu
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeş-Bolyai University, 400271, Cluj-Napoca, Romania
- Centre of Systems Biology, Biodiversity and Bioresources (3B), Babeş-Bolyai University, 400006, Cluj-Napoca, Romania
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 400006, Cluj-Napoca, Romania
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25
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Ceriotti LF, Gatica-Soria L, Sanchez-Puerta MV. Cytonuclear coevolution in a holoparasitic plant with highly disparate organellar genomes. PLANT MOLECULAR BIOLOGY 2022; 109:673-688. [PMID: 35359176 DOI: 10.1007/s11103-022-01266-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Contrasting substitution rates in the organellar genomes of Lophophytum agree with the DNA repair, replication, and recombination gene content. Plastid and nuclear genes whose products form multisubunit complexes co-evolve. The organellar genomes of the holoparasitic plant Lophophytum (Balanophoraceae) show disparate evolution. In the plastid, the genome has been severely reduced and presents a > 85% AT content, while in the mitochondria most protein-coding genes have been replaced by homologs acquired by horizontal gene transfer (HGT) from their hosts (Fabaceae). Both genomes carry genes whose products form multisubunit complexes with those of nuclear genes, creating a possible hotspot of cytonuclear coevolution. In this study, we assessed the evolutionary rates of plastid, mitochondrial and nuclear genes, and their impact on cytonuclear evolution of genes involved in multisubunit complexes related to lipid biosynthesis and proteolysis in the plastid and those in charge of the oxidative phosphorylation in the mitochondria. Genes from the plastid and the mitochondria (both native and foreign) of Lophophytum showed extremely high and ordinary substitution rates, respectively. These results agree with the biased loss of plastid-targeted proteins involved in angiosperm organellar repair, replication, and recombination machinery. Consistent with the high rate of evolution of plastid genes, nuclear-encoded subunits of plastid complexes showed disproportionate increases in non-synonymous substitution rates, while those of the mitochondrial complexes did not show different rates than the control (i.e. non-organellar nuclear genes). Moreover, the increases in the nuclear-encoded subunits of plastid complexes were positively correlated with the level of physical interaction they possess with the plastid-encoded ones. Overall, these results suggest that a structurally-mediated compensatory factor may be driving plastid-nuclear coevolution in Lophophytum, and that mito-nuclear coevolution was not altered by HGT.
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Affiliation(s)
- Luis F Ceriotti
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - Leonardo Gatica-Soria
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - M Virginia Sanchez-Puerta
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina.
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina.
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26
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Yan Y, Ham BK. The Mobile Small RNAs: Important Messengers for Long-Distance Communication in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:928729. [PMID: 35783973 PMCID: PMC9247610 DOI: 10.3389/fpls.2022.928729] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/25/2022] [Indexed: 06/06/2023]
Abstract
Various species of small RNAs (sRNAs), notably microRNAs and small interfering RNAs (siRNAs), have been characterized as the major effectors of RNA interference in plants. Growing evidence supports a model in which sRNAs move, intercellularly, systemically, and between cross-species. These non-coding sRNAs can traffic cell-to-cell through plasmodesmata (PD), in a symplasmic manner, as well as from source to sink tissues, via the phloem, to trigger gene silencing in their target cells. Such mobile sRNAs function in non-cell-autonomous communication pathways, to regulate various biological processes, such as plant development, reproduction, and plant defense. In this review, we summarize recent progress supporting the roles of mobile sRNA in plants, and discuss mechanisms of sRNA transport, signal amplification, and the plant's response, in terms of RNAi activity, within the recipient tissues. We also discuss potential research directions and their likely impact on engineering of crops with traits for achieving food security.
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Affiliation(s)
- Yan Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Byung-Kook Ham
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
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27
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Lin Q, Banerjee A, Stefanović S. Mitochondrial phylogenomics of Cuscuta (Convolvulaceae) reveals a potentially functional horizontal gene transfer from the host. Genome Biol Evol 2022; 14:evac091. [PMID: 35700229 PMCID: PMC9234195 DOI: 10.1093/gbe/evac091] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 11/14/2022] Open
Abstract
Horizontal gene transfers (HGTs) from host or other organisms have been reported in mitochondrial genomes of parasitic plants. Genes transferred in this fashion have usually been found non-functional. Several examples of HGT from the mitochondrial genome of parasitic Cuscuta (Convolvulaceae) to its hosts have been reported, but not vice versa. Here we used 31 protein-coding mitochondrial genes to infer the phylogeny of Cuscuta, and compared it with previous nuclear and plastid phylogenetic estimates. We also investigated the presence of HGTs within these lineages. Unlike in plastid genomes, we did not find extensive gene loss in their mitochondrial counterparts. Our results reveal the first example of organellar HGT from host to Cuscuta. Mitochondrial atp1 genes of South African subgenus Pachystigma were inferred to be transferred from Lamiales, with high support. Moreover, the horizontally transferred atp1 gene has functionally replaced the native, vertically transmitted copy, has an intact open reading frame, and is under strong purifying selection, all of which suggests that this xenolog remains functional. The mitochondrial phylogeny of Cuscuta is generally consistent with previous plastid and nuclear phylogenies, except for the misplacement of Pachystigma when atp1 is included. This incongruence may be caused by the HGT mentioned above. No example of HGT was found within mitochondrial genes of three other, independently evolved parasitic lineages we sampled: Cassytha/Laurales, Krameria/Zygophyllales, and Lennooideae/Boraginales.
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Affiliation(s)
- Qianshi Lin
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 2Z9, Canada
| | - Arjan Banerjee
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 2Z9, Canada
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
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28
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Mau M, Mandáková TM, Ma X, Ebersbach J, Zou L, Lysak MA, Sharbel TF. Evolution of an Apomixis-Specific Allele Class in Supernumerary Chromatin of Apomictic Boechera. FRONTIERS IN PLANT SCIENCE 2022; 13:890038. [PMID: 35720540 PMCID: PMC9198585 DOI: 10.3389/fpls.2022.890038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/03/2022] [Indexed: 06/06/2023]
Abstract
Asexual reproduction through seeds in plants (i.e., apomixis) is a heritable trait, and apomixis- linked loci have been identified in multiple species. However, direct identification of genomic elements is typically hindered as apomixis-linked loci and are commonly found in recombination-suppressed and repetitive regions. Heterochromatinized elements, such as B chromosomes and other supernumerary chromosomal DNA fragments have long been known to be associated with asexuality in both plants and animals and are prime candidate regions for the evolution of multiple apomixis factors controlling the individual elements of apomixis. Here, we examined molecular evolution, gene regulation, and chromosomal location of a male apomeiosis factor (UPG2), a long noncoding RNA gene, in sexual and apomictic Boechera with and without male apomeiosis (i.e., balanced and unbalanced apomicts). We revealed the origin of the gene in the apomixis genome on an apomixis-specific, supernumerary heterochromatic Boechera chromosome (Boe1). The UPG2 is active in the tapetum at male meiosis. We found allele classes specific to apomictic and sexual Boechera accessions and a third class that shares the features of both and points to a convergent transition state. Sex alleles are found only in some of the sexual accessions and have higher nucleotide divergence and lower transcriptional activity compared to apo alleles. These data demonstrate selective pressure to maintain the function of UPG2 for unreduced pollen formation in apomicts as the occasional transmission of the allele from unbalanced apomicts into sexual organisms that lead to pseudogenization and functional decay of copies in sexual organisms.
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Affiliation(s)
- Martin Mau
- Apomixis Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Xingliang Ma
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jana Ebersbach
- Saskatoon Research and Development Centre, Saskatoon, SK, Canada
| | - Lifang Zou
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
| | - Martin A. Lysak
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Timothy F. Sharbel
- Apomixis Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
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29
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Li W, Chen S, Liu Y, Wang L, Jiang J, Zhao S, Fang W, Chen F, Guan Z. Long-distance transport RNAs between rootstocks and scions and graft hybridization. PLANTA 2022; 255:96. [PMID: 35348893 DOI: 10.1007/s00425-022-03863-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
The present review addresses the advances of the identification methods, functions, and transportation mechanism of long-distance transport RNAs between rootstock and scion. In addition, we highlight the cognitive processes and potential mechanisms of graft hybridization. Phloem, the main transport channel of higher plants, plays an important role in the growth and development of plants. Numerous studies have identified a large number of RNAs, including mRNAs, miRNAs, siRNAs, and lncRNAs, in the plant phloem. They can not only be transported to long distances across the grafting junction in the phloem, but also act as signal molecules to regulate the growth, development, and stress resistance of remote cells or tissues, resulting in changes in the traits of rootstocks and scions. Many mobile RNAs have been discovered, but their detection methods, functions, and long-distance transport mechanisms remain to be elucidated. In addition, grafting hybridization, a phenomenon that has been questioned before, and which has an important role in selecting for superior traits, is gradually being recognized with the emergence of new evidence and the prevalence of horizontal gene transfer between parasitic plants. In this review, we outline the species, functions, identification methods, and potential mechanisms of long-distance transport RNAs between rootstocks and scions after grafting. In addition, we summarize the process of recognition and the potential mechanisms of graft hybridization. This study aimed to emphasize the role of grafting in the study of long-distance signals and selection for superior traits and to provide ideas and clues for further research on long-distance transport RNAs and graft hybridization.
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Affiliation(s)
- Wenjie Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ye Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Likai Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuang Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weimin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhiyong Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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30
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Wu Y, Luo D, Fang L, Zhou Q, Liu W, Liu Z. Bidirectional lncRNA Transfer between Cuscuta Parasites and Their Host Plant. Int J Mol Sci 2022; 23:561. [PMID: 35008986 PMCID: PMC8745499 DOI: 10.3390/ijms23010561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/28/2021] [Accepted: 01/02/2022] [Indexed: 02/01/2023] Open
Abstract
Dodder species (Cuscuta spp.) are holoparasites that have extensive material exchange with their host plants through vascular connections. Recent studies on cross-species transfer have provided breakthrough insights, but little is known about the interaction mechanisms of the inter-plant mobile substances in parasitic systems. We sequenced the transcriptomes of dodder growing on soybean hosts to characterize the long non-coding RNA (lncRNA) transfer between the two species, and found that lncRNAs can move in high numbers (365 dodder lncRNAs and 14 soybean lncRNAs) in a bidirectional manner. Reverse transcription-polymerase chain reaction further confirmed that individual lncRNAs were trafficked in the dodder-soybean parasitic system. To reveal the potential functions of mobile transcripts, the Gene Ontology terms of mobile lncRNA target genes were predicted, and mobile dodder target genes were found to be mainly enriched in "metabolic process", "catalytic activity", "signaling", and "response to stimulus" categories, whereas mobile soybean target genes were enriched in organelle-related categories, indicating that specific mobile lncRNAs may be important in regulating dodder parasitism. Our findings reveal that lncRNAs are transferred between dodder and its host soybean plants, which may act as critical regulators to coordinate the host-dodder interaction at the whole parasitic level.
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Affiliation(s)
| | | | | | | | | | - Zhipeng Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (Y.W.); (D.L.); (L.F.); (Q.Z.); (W.L.)
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31
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Wafula EK, Zhang H, Von Kuster G, Leebens-Mack JH, Honaas LA, dePamphilis CW. PlantTribes2: Tools for comparative gene family analysis in plant genomics. FRONTIERS IN PLANT SCIENCE 2022; 13:1011199. [PMID: 36798801 PMCID: PMC9928214 DOI: 10.3389/fpls.2022.1011199] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/02/2022] [Indexed: 05/12/2023]
Abstract
Plant genome-scale resources are being generated at an increasing rate as sequencing technologies continue to improve and raw data costs continue to fall; however, the cost of downstream analyses remains large. This has resulted in a considerable range of genome assembly and annotation qualities across plant genomes due to their varying sizes, complexity, and the technology used for the assembly and annotation. To effectively work across genomes, researchers increasingly rely on comparative genomic approaches that integrate across plant community resources and data types. Such efforts have aided the genome annotation process and yielded novel insights into the evolutionary history of genomes and gene families, including complex non-model organisms. The essential tools to achieve these insights rely on gene family analysis at a genome-scale, but they are not well integrated for rapid analysis of new data, and the learning curve can be steep. Here we present PlantTribes2, a scalable, easily accessible, highly customizable, and broadly applicable gene family analysis framework with multiple entry points including user provided data. It uses objective classifications of annotated protein sequences from existing, high-quality plant genomes for comparative and evolutionary studies. PlantTribes2 can improve transcript models and then sort them, either genome-scale annotations or individual gene coding sequences, into pre-computed orthologous gene family clusters with rich functional annotation information. Then, for gene families of interest, PlantTribes2 performs downstream analyses and customizable visualizations including, (1) multiple sequence alignment, (2) gene family phylogeny, (3) estimation of synonymous and non-synonymous substitution rates among homologous sequences, and (4) inference of large-scale duplication events. We give examples of PlantTribes2 applications in functional genomic studies of economically important plant families, namely transcriptomics in the weedy Orobanchaceae and a core orthogroup analysis (CROG) in Rosaceae. PlantTribes2 is freely available for use within the main public Galaxy instance and can be downloaded from GitHub or Bioconda. Importantly, PlantTribes2 can be readily adapted for use with genomic and transcriptomic data from any kind of organism.
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Affiliation(s)
- Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Huiting Zhang
- Tree Fruit Research Laboratory, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Wenatchee, WA, United States
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Gregory Von Kuster
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | | | - Loren A Honaas
- Tree Fruit Research Laboratory, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Wenatchee, WA, United States
| | - Claude W dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
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Park SY, Shimizu K, Brown J, Aoki K, Westwood JH. Mobile Host mRNAs Are Translated to Protein in the Associated Parasitic Plant Cuscuta campestris. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010093. [PMID: 35009096 PMCID: PMC8747733 DOI: 10.3390/plants11010093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 05/03/2023]
Abstract
Cuscuta spp. are obligate parasites that connect to host vascular tissue using a haustorium. In addition to water, nutrients, and metabolites, a large number of mRNAs are bidirectionally exchanged between Cuscuta spp. and their hosts. This trans-specific movement of mRNAs raises questions about whether these molecules function in the recipient species. To address the possibility that mobile mRNAs are ultimately translated, we built upon recent studies that demonstrate a role for transfer RNA (tRNA)-like structures (TLSs) in enhancing mRNA systemic movement. C. campestris was grown on Arabidopsis that expressed a β-glucuronidase (GUS) reporter transgene either alone or in GUS-tRNA fusions. Histochemical staining revealed localization in tissue of C. campestris grown on Arabidopsis with GUS-tRNA fusions, but not in C. campestris grown on Arabidopsis with GUS alone. This corresponded with detection of GUS transcripts in Cuscuta on Arabidopsis with GUS-tRNA, but not in C. campestris on Arabidopsis with GUS alone. Similar results were obtained with Arabidopsis host plants expressing the same constructs containing an endoplasmic reticulum localization signal. In C. campestris, GUS activity was localized in the companion cells or phloem parenchyma cells adjacent to sieve tubes. We conclude that host-derived GUS mRNAs are translated in C. campestris and that the TLS fusion enhances RNA mobility in the host-parasite interactions.
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Affiliation(s)
- So-Yon Park
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (S.-Y.P.); (J.B.)
| | - Kohki Shimizu
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Japan;
| | - Jocelyn Brown
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (S.-Y.P.); (J.B.)
| | - Koh Aoki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Japan;
- Correspondence: (K.A.); (J.H.W.)
| | - James H. Westwood
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (S.-Y.P.); (J.B.)
- Correspondence: (K.A.); (J.H.W.)
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Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmF C genes. BMC Genomics 2021; 22:816. [PMID: 34772334 PMCID: PMC8588681 DOI: 10.1186/s12864-021-08105-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/19/2021] [Indexed: 01/30/2023] Open
Abstract
Background The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus. Results The mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmFC gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT. Conclusions The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08105-z.
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Yu R, Sun C, Liu Y, Zhou R. Shifts from cis-to trans-splicing of five mitochondrial introns in Tolypanthus maclurei. PeerJ 2021; 9:e12260. [PMID: 34703675 PMCID: PMC8489412 DOI: 10.7717/peerj.12260] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/15/2021] [Indexed: 01/20/2023] Open
Abstract
Shifts from cis-to trans-splicing of mitochondrial introns tend to correlate with relative genome rearrangement rates during vascular plant evolution, as is particularly apparent in some lineages of gymnosperms. However, although many angiosperms have also relatively high mitogenomic rearrangement rates, very few cis-to trans-splicing shifts except for five trans-spliced introns shared in seed plants have been reported. In this study, we sequenced and characterized the mitogenome of Tolypanthus maclurei, a hemiparasitic plant from the family Loranthaceae (Santalales). The mitogenome was assembled into a circular chromosome of 256,961 bp long, relatively small compared with its relatives from Santalales. It possessed a gene content of typical angiosperm mitogenomes, including 33 protein-coding genes, three rRNA genes and ten tRNA genes. Plastid-derived DNA fragments took up 9.1% of the mitogenome. The mitogenome contained one group I intron (cox1i729) and 23 group II introns. We found shifts from cis-to trans-splicing of five additional introns in its mitogenome, of which two are specific in T. maclurei. Moreover, atp1 is a chimeric gene and phylogenetic analysis indicated that a 356 bp region near the 3′ end of atp1 of T. maclurei was acquired from Lamiales via horizontal gene transfer. Our results suggest that shifts to trans-splicing of mitochondrial introns may not be uncommon among angiosperms.
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Affiliation(s)
- Runxian Yu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Chenyu Sun
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
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Aubin E, El Baidouri M, Panaud O. Horizontal Gene Transfers in Plants. Life (Basel) 2021; 11:life11080857. [PMID: 34440601 PMCID: PMC8401529 DOI: 10.3390/life11080857] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022] Open
Abstract
In plants, as in all eukaryotes, the vertical transmission of genetic information through reproduction ensures the maintenance of the integrity of species. However, many reports over the past few years have clearly shown that horizontal gene transfers, referred to as HGTs (the interspecific transmission of genetic information across reproductive barriers) are very common in nature and concern all living organisms including plants. The advent of next-generation sequencing technologies (NGS) has opened new perspectives for the study of HGTs through comparative genomic approaches. In this review, we provide an up-to-date view of our current knowledge of HGTs in plants.
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Yoshida S, Kee YJ. Large-scale sequencing paves the way for genomic and genetic analyses in parasitic plants. Curr Opin Biotechnol 2021; 70:248-254. [PMID: 34242992 DOI: 10.1016/j.copbio.2021.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023]
Abstract
Parasitic plants pose a serious agricultural threat, but are also precious resources for valuable metabolites. The heterotrophic nature of these plants has resulted in the development of several morphological and physiological features that are of evolutionary significance. Recent advances in large-scale sequencing technology have provided insights into the evolutionary and molecular mechanisms of plant parasitism. Genome sequencing has revealed gene losses and horizontal gene transfers in parasitic plants. Mobile signals traveling between the parasite and host may have contributed to the increased fitness of parasitic life styles. Transcriptome analyses implicate shared processes among various parasitic species and the establishment of functional analysis is beginning to reveal molecular mechanisms during host and parasite interactions.
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Affiliation(s)
- Satoko Yoshida
- Nara Institute of Science and Technology, Grad. School Sci. Tech., Ikoma, Nara, Japan; JST, PRESTO, Japan.
| | - Yee Jia Kee
- Nara Institute of Science and Technology, Grad. School Sci. Tech., Ikoma, Nara, Japan
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Lyko P, Wicke S. Genomic reconfiguration in parasitic plants involves considerable gene losses alongside global genome size inflation and gene births. PLANT PHYSIOLOGY 2021; 186:1412-1423. [PMID: 33909907 PMCID: PMC8260112 DOI: 10.1093/plphys/kiab192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/13/2021] [Indexed: 05/02/2023]
Abstract
Parasitic plant genomes and transcriptomes reveal numerous genetic innovations, the functional-evolutionary relevance and roles of which open unprecedented research avenues.
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Affiliation(s)
- Peter Lyko
- Institute for Biology, Humboldt-University of Berlin, Germany
| | - Susann Wicke
- Institute for Biology, Humboldt-University of Berlin, Germany
- Author for communication:
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Hibdige SGS, Raimondeau P, Christin PA, Dunning LT. Widespread lateral gene transfer among grasses. THE NEW PHYTOLOGIST 2021; 230:2474-2486. [PMID: 33887801 DOI: 10.1111/nph.17328] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
Lateral gene transfer (LGT) occurs in a broad range of prokaryotes and eukaryotes, occasionally promoting adaptation. LGT of functional nuclear genes has been reported among some plants, but systematic studies are needed to assess the frequency and facilitators of LGT. We scanned the genomes of a diverse set of 17 grass species that span more than 50 Ma of divergence and include major crops to identify grass-to-grass protein-coding LGT. We identified LGTs in 13 species, with significant variation in the amount each received. Rhizomatous species acquired statistically more genes, probably because this growth habit boosts opportunities for transfer into the germline. In addition, the amount of LGT increases with phylogenetic relatedness, which might reflect genomic compatibility among close relatives facilitating successful transfers. However, genetic exchanges among highly divergent species indicates that transfers can occur across almost the entire family. Overall, we showed that LGT is a widespread phenomenon in grasses that has moved functional genes across the grass family into domesticated and wild species alike. Successful LGTs appear to increase with both opportunity and compatibility.
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Affiliation(s)
- Samuel G S Hibdige
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Pauline Raimondeau
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | | | - Luke T Dunning
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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Sacristán S, Goss EM, Eves-van den Akker S. How Do Pathogens Evolve Novel Virulence Activities? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:576-586. [PMID: 33522842 DOI: 10.1094/mpmi-09-20-0258-ia] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This article is part of the Top 10 Unanswered Questions in MPMI invited review series.We consider the state of knowledge on pathogen evolution of novel virulence activities, broadly defined as anything that increases pathogen fitness with the consequence of causing disease in either the qualitative or quantitative senses, including adaptation of pathogens to host immunity and physiology, host species, genotypes, or tissues, or the environment. The evolution of novel virulence activities as an adaptive trait is based on the selection exerted by hosts on variants that have been generated de novo or arrived from elsewhere. In addition, the biotic and abiotic environment a pathogen experiences beyond the host may influence pathogen virulence activities. We consider host-pathogen evolution, host range expansion, and external factors that can mediate pathogen evolution. We then discuss the mechanisms by which pathogens generate and recombine the genetic variation that leads to novel virulence activities, including DNA point mutation, transposable element activity, gene duplication and neofunctionalization, and genetic exchange. In summary, if there is an (epi)genetic mechanism that can create variation in the genome, it will be used by pathogens to evolve virulence factors. Our knowledge of virulence evolution has been biased by pathogen evolution in response to major gene resistance, leaving other virulence activities underexplored. Understanding the key driving forces that give rise to novel virulence activities and the integration of evolutionary concepts and methods with mechanistic research on plant-microbe interactions can help inform crop protection.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040-Madrid, Spain
| | - Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, U.S.A
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Zilber-Rosenberg I, Rosenberg E. Microbial driven genetic variation in holobionts. FEMS Microbiol Rev 2021; 45:6261188. [PMID: 33930136 DOI: 10.1093/femsre/fuab022] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Genetic variation in holobionts, (host and microbiome), occurring by changes in both host and microbiome genomes, can be observed from two perspectives: observable variations and the processes that bring about the variation. The observable includes the enormous genetic diversity of prokaryotes, which gave rise to eukaryotic organisms. Holobionts then evolved a rich microbiome with a stable core containing essential genes, less so common taxa, and a more diverse non-core enabling considerable genetic variation. The result being that, the human gut microbiome, for example, contains 1,000 times more unique genes than are present in the human genome. Microbial driven genetic variation processes in holobionts include: (1) Acquisition of novel microbes from the environment, which bring in multiple genes in one step, (2) amplification/reduction of certain microbes in the microbiome, that contribute to holobiont` s adaptation to changing conditions, (3) horizontal gene transfer between microbes and between microbes and host, (4) mutation, which plays an important role in optimizing interactions between different microbiota and between microbiota and host. We suggest that invertebrates and plants, where microbes can live intracellularly, have a greater chance of genetic exchange between microbiota and host, thus a greater chance of vertical transmission and a greater effect of microbiome on evolution of host than vertebrates. However, even in vertebrates the microbiome can aid in environmental fluctuations by amplification/reduction and by acquisition of novel microorganisms.
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Affiliation(s)
- Ilana Zilber-Rosenberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv Israel
| | - Eugene Rosenberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv Israel
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Mutuku JM, Cui S, Yoshida S, Shirasu K. Orobanchaceae parasite-host interactions. THE NEW PHYTOLOGIST 2021; 230:46-59. [PMID: 33202061 DOI: 10.1111/nph.17083] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Parasitic plants in the family Orobanchaceae, such as Striga, Orobanche and Phelipanche, often cause significant damage to agricultural crops. The Orobanchaceae family comprises more than 2000 species in about 100 genera, providing an excellent system for studying the molecular basis of parasitism and its evolution. Notably, the establishment of model Orobanchaceae parasites, such as Triphysaria versicolor and Phtheirospermum japonicum, that can infect the model host Arabidopsis, has greatly facilitated transgenic analyses of genes important for parasitism. In addition, recent genomic and transcriptomic analyses of several Orobanchaceae parasites have revealed fascinating molecular insights into the evolution of parasitism and strategies for adaptation in this family. This review highlights recent progress in understanding how Orobanchaceae parasites attack their hosts and how the hosts mount a defense against the threats.
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Affiliation(s)
- J Musembi Mutuku
- The Central and West African Virus Epidemiology (WAVE). Pôle Scientifique et d'Innovation de Bingerville, Université Félix Houphouët-Boigny, BP V34, Abidjan, 01, Côte d'Ivoire
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Songkui Cui
- Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Satoko Yoshida
- Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
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Meitha K, Esyanti RR, Iriawati, Hanisia RH, Rohyani. Green pesticide: Tapping to the promising roles of plant secreted small RNAs and responses towards extracellular DNA. Noncoding RNA Res 2021; 6:42-50. [PMID: 33778217 PMCID: PMC7970063 DOI: 10.1016/j.ncrna.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/02/2021] [Accepted: 02/07/2021] [Indexed: 12/19/2022] Open
Abstract
The diverse roles of non-coding RNA and DNA in cross-species communication is yet to be revealed. Once thought to only involve intra-specifically in regulating gene expression, the evidence that these genetic materials can also modulate gene expression between species that belong to different kingdoms is accumulating. Plants send small RNAs to the pathogen or parasite when they are being attacked, targeting essential mRNAs for infection or parasitism of the hosts. However, the same survival mechanism is also deployed by the pathogen or parasite to destabilize plant immune responses. In plants, it is suggested that exposure to extracellular self-DNA impedes growth, while to extracellular non-self-DNA induces the modulation of reactive oxygen species, expression of resistance related genes, epigenetic mechanism, or suppression of disease severity. Exploring the potential of secreted RNA and extracellular DNA as a green pesticide could be a promising alternative if we are to provide food for the future global population without further damaging the environment. Hence, some studies on plant secreted RNA and responses towards extracellular DNA are discussed in this review. The precise mode of action of entry and the following cascade of signaling once the plant cell is exposed to secreted RNA or extracellular DNA could be an interesting topic for future research.
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Affiliation(s)
- Karlia Meitha
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Rizkita Rachmi Esyanti
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Iriawati
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Ristag Hamida Hanisia
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Rohyani
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
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Abstract
The genome of the parasitic plant Sapria himalayana reveals extraordinary changes that reflect its endoparasitic lifestyle. The genome has lost many genes, including the entire chloroplast genome, but has gained genes through horizontal gene transfer and repeated transposable elements.
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Affiliation(s)
- James H Westwood
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA.
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Cai L, Arnold BJ, Xi Z, Khost DE, Patel N, Hartmann CB, Manickam S, Sasirat S, Nikolov LA, Mathews S, Sackton TB, Davis CC. Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae). Curr Biol 2021; 31:1002-1011.e9. [DOI: 10.1016/j.cub.2020.12.045] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/11/2020] [Accepted: 12/23/2020] [Indexed: 12/18/2022]
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Mahelka V, Krak K, Fehrer J, Caklová P, Nagy Nejedlá M, Čegan R, Kopecký D, Šafář J. A Panicum-derived chromosomal segment captured by Hordeum a few million years ago preserves a set of stress-related genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1141-1164. [PMID: 33484020 DOI: 10.1111/tpj.15167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Intra-specific variability is a cornerstone of evolutionary success of species. Acquiring genetic material from distant sources is an important adaptive mechanism in bacteria, but it can also play a role in eukaryotes. In this paper, we investigate the nature and evolution of a chromosomal segment of panicoid (Poaceae, Panicoideae) origin occurring in the nuclear genomes of species of the barley genus Hordeum (Pooideae). The segment, spanning over 440 kb in the Asian Hordeum bogdanii and 219 kb in the South American Hordeum pubiflorum, resides on a pair of nucleolar organizer region (NOR)-bearing chromosomes. Conserved synteny and micro-collinearity of the segment in both species indicate a common origin of the segment, which was acquired before the split of the respective barley lineages 5-1.7 million years ago. A major part of the foreign DNA consists of several approximately 68 kb long repeated blocks containing five stress-related protein-coding genes and transposable elements (TEs). Whereas outside these repeats, the locus was invaded by multiple TEs from the host genome, the repeated blocks are rather intact and appear to be preserved. The protein-coding genes remained partly functional, as indicated by conserved reading frames, a low amount of non-synonymous mutations, and expression of mRNA. A screen across Hordeum species targeting the panicoid protein-coding genes revealed the presence of the genes in all species of the section Stenostachys. In summary, our study shows that grass genomes can contain large genomic segments obtained from distantly related species. These segments usually remain undetected, but they may play an important role in the evolution and adaptation of species.
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Affiliation(s)
- Václav Mahelka
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
| | - Karol Krak
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague 6, 16500, Czech Republic
| | - Judith Fehrer
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
| | - Petra Caklová
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
| | | | - Radim Čegan
- Institute of Biophysics, Czech Academy of Sciences, Brno, 61265, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, 77900, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, 77900, Czech Republic
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46
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Whole-genome sequencing, genome mining, metabolic reconstruction and evolution of pentachlorophenol and other xenobiotic degradation pathways in Bacillus tropicus strain AOA-CPS1. Funct Integr Genomics 2021; 21:171-193. [PMID: 33547987 DOI: 10.1007/s10142-021-00768-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 09/30/2020] [Accepted: 01/19/2021] [Indexed: 12/11/2022]
Abstract
A pentachlorophenol degrading bacterium was isolated from effluent of a wastewater treatment plant in Durban, South Africa, and identified as Bacillus tropicus strain AOA-CPS1 (BtAOA). The isolate degraded 29% of pentachlorophenol (PCP) within 9 days at an initial PCP concentration of 100 mg L-1 and 62% of PCP when the initial concentration was set at 350 mg L-1. The whole-genome of BtAOA was sequenced using Pacific Biosciences RS II sequencer with the Single Molecule, Real-Time (SMRT) Link (version 7.0.1.66975) and analysed using the HGAP4-de-novo assembly application. The contigs were annotated at NCBI, RASTtk and PROKKA prokaryotic genome annotation pipelines. The BtAOA genome is comprised of a 5,246,860-bp chromosome and a 58,449-bp plasmid with a GC content of 35.4%. The metabolic reconstruction for BtAOA showed that the organism has been naturally exposed to various chlorophenolic compounds including PCP and other xenobiotics. The chromosome encodes genes for core processes, stress response and PCP catabolic genes. Analogues of PCP catabolic gene (cpsBDCAE, and p450) sequences were identified from the NCBI annotation data, PCR-amplified from the whole genome of BtAOA, cloned into pET15b expression vector, overexpressed in E. coli BL21 (DE3) expression host, purified and characterized. Sequence mining and comparative analysis of the metabolic reconstruction of the BtAOA genome with closely related strains suggests that the operon encoding the first two enzymes in the PCP degradation pathway were acquired from a pre-existing pterin-carbinolamine dehydratase subsystem. The other two enzymes were recruited via horizontal gene transfer (HGT) from the pool of hypothetical proteins with no previous specific function, while the last enzyme was recruited from pre-existing enzymes from the TCA or serine-glyoxalase cycle via HGT events. This study provides a comprehensive understanding of the role of BtAOA in PCP degradation and its potential exploitation for bioremediation of other xenobiotic compounds.
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Neumann P, Oliveira L, Čížková J, Jang TS, Klemme S, Novák P, Stelmach K, Koblížková A, Doležel J, Macas J. Impact of parasitic lifestyle and different types of centromere organization on chromosome and genome evolution in the plant genus Cuscuta. THE NEW PHYTOLOGIST 2021; 229:2365-2377. [PMID: 33090498 DOI: 10.1111/nph.17003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/01/2020] [Indexed: 05/06/2023]
Abstract
The parasitic genus Cuscuta (Convolvulaceae) is exceptional among plants with respect to centromere organization, including both monocentric and holocentric chromosomes, and substantial variation in genome size and chromosome number. We investigated 12 species representing the diversity of the genus in a phylogenetic context to reveal the molecular and evolutionary processes leading to diversification of their genomes. We measured genome sizes and investigated karyotypes and centromere organization using molecular cytogenetic techniques. We also performed low-pass whole genome sequencing and comparative analysis of repetitive DNA composition. A remarkable 102-fold variation in genome sizes (342-34 734 Mbp/1C) was detected for monocentric Cuscuta species, while genomes of holocentric species were of moderate sizes (533-1545 Mbp/1C). The genome size variation was primarily driven by the differential accumulation of LTR-retrotransposons and satellite DNA. The transition to holocentric chromosomes in the subgenus Cuscuta was associated with loss of histone H2A phosphorylation and elimination of centromeric retrotransposons. In addition, basic chromosome number of holocentric species (x = 7) was smaller than in monocentrics (x = 15 or 16). We demonstrated that the transition to holocentricity in Cuscuta was accompanied by significant changes in epigenetic marks, chromosome number and the repetitive DNA sequence composition.
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Affiliation(s)
- Pavel Neumann
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Ludmila Oliveira
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-779 00, Czech Republic
| | - Tae-Soo Jang
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sonja Klemme
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Katarzyna Stelmach
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
- Department of Plant Biology and Biotechnology, University of Agriculture in Krakow, 29 Listopada 54, Krakow, 31-425, Poland
| | - Andrea Koblížková
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-779 00, Czech Republic
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
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48
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Hu L, Wang J, Yang C, Islam F, Bouwmeester HJ, Muños S, Zhou W. The Effect of Virulence and Resistance Mechanisms on the Interactions between Parasitic Plants and Their Hosts. Int J Mol Sci 2020; 21:E9013. [PMID: 33260931 PMCID: PMC7730841 DOI: 10.3390/ijms21239013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/26/2020] [Accepted: 10/31/2020] [Indexed: 01/06/2023] Open
Abstract
Parasitic plants have a unique heterotrophic lifestyle based on the extraction of water and nutrients from host plants. Some parasitic plant species, particularly those of the family Orobanchaceae, attack crops and cause substantial yield losses. The breeding of resistant crop varieties is an inexpensive way to control parasitic weeds, but often does not provide a long-lasting solution because the parasites rapidly evolve to overcome resistance. Understanding mechanisms underlying naturally occurring parasitic plant resistance is of great interest and could help to develop methods to control parasitic plants. In this review, we describe the virulence mechanisms of parasitic plants and resistance mechanisms in their hosts, focusing on obligate root parasites of the genera Orobanche and Striga. We noticed that the resistance (R) genes in the host genome often encode proteins with nucleotide-binding and leucine-rich repeat domains (NLR proteins), hence we proposed a mechanism by which host plants use NLR proteins to activate downstream resistance gene expression. We speculated how parasitic plants and their hosts co-evolved and discussed what drives the evolution of virulence effectors in parasitic plants by considering concepts from similar studies of plant-microbe interaction. Most previous studies have focused on the host rather than the parasite, so we also provided an updated summary of genomic resources for parasitic plants and parasitic genes for further research to test our hypotheses. Finally, we discussed new approaches such as CRISPR/Cas9-mediated genome editing and RNAi silencing that can provide deeper insight into the intriguing life cycle of parasitic plants and could potentially contribute to the development of novel strategies for controlling parasitic weeds, thereby enhancing crop productivity and food security globally.
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Affiliation(s)
- Luyang Hu
- Institute of Crop Science and Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China; (L.H.); (J.W.); (F.I.)
| | - Jiansu Wang
- Institute of Crop Science and Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China; (L.H.); (J.W.); (F.I.)
| | - Chong Yang
- Bioengineering Research Laboratory, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou 510316, China;
| | - Faisal Islam
- Institute of Crop Science and Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China; (L.H.); (J.W.); (F.I.)
| | - Harro J. Bouwmeester
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1000 BE Amsterdam, The Netherlands;
| | - Stéphane Muños
- LIPM, Université de Toulouse, INRAE, CNRS, 31326 Castanet-Tolosan, France;
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou 310058, China; (L.H.); (J.W.); (F.I.)
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49
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Chen R, Huangfu L, Lu Y, Fang H, Xu Y, Li P, Zhou Y, Xu C, Huang J, Yang Z. Adaptive innovation of green plants by horizontal gene transfer. Biotechnol Adv 2020; 46:107671. [PMID: 33242576 DOI: 10.1016/j.biotechadv.2020.107671] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022]
Abstract
Horizontal gene transfer (HGT) refers to the movement of genetic material between distinct species by means other than sexual reproduction. HGT has contributed tremendously to the genome plasticity and adaptive evolution of prokaryotes and certain unicellular eukaryotes. The evolution of green plants from chlorophyte algae to angiosperms and from water to land represents a process of adaptation to diverse environments, which has been facilitated by acquisition of genetic material from other organisms. In this article, we review the occurrence of HGT in major lineages of green plants, including chlorophyte and charophyte green algae, bryophytes, lycophytes, ferns, and seed plants. In addition, we discuss the significance of horizontally acquired genes in the adaptive innovations of green plants and their potential applications to crop breeding and improvement.
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Affiliation(s)
- Rujia Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Liexiang Huangfu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yue Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Huimin Fang
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yang Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Pengcheng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC 28590, USA; State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
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50
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Li Y, Mohanty S, Nilsson D, Hansson B, Mao K, Irbäck A. When a foreign gene meets its native counterpart: computational biophysics analysis of two PgiC loci in the grass Festuca ovina. Sci Rep 2020; 10:18752. [PMID: 33127989 PMCID: PMC7599235 DOI: 10.1038/s41598-020-75650-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/16/2020] [Indexed: 11/14/2022] Open
Abstract
Duplicative horizontal gene transfer may bring two previously separated homologous genes together, which may raise questions about the interplay between the gene products. One such gene pair is the “native” PgiC1 and “foreign” PgiC2 in the perennial grass Festuca ovina. Both PgiC1 and PgiC2 encode cytosolic phosphoglucose isomerase, a dimeric enzyme whose proper binding is functionally essential. Here, we use biophysical simulations to explore the inter-monomer binding of the two homodimers and the heterodimer that can be produced by PgiC1 and PgiC2 in F. ovina. Using simulated native-state ensembles, we examine the structural properties and binding tightness of the dimers. In addition, we investigate their ability to withstand dissociation when pulled by a force. Our results suggest that the inter-monomer binding is tighter in the PgiC2 than the PgiC1 homodimer, which could explain the more frequent occurrence of the foreign PgiC2 homodimer in dry habitats. We further find that the PgiC1 and PgiC2 monomers are compatible with heterodimer formation; the computed binding tightness is comparable to that of the PgiC1 homodimer. Enhanced homodimer stability and capability of heterodimer formation with PgiC1 are properties of PgiC2 that may contribute to the retaining of the otherwise redundant PgiC2 gene.
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Affiliation(s)
- Yuan Li
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, 223 62, Lund, Sweden
| | - Sandipan Mohanty
- Institute for Advanced Simulation, Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Daniel Nilsson
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, 223 62, Lund, Sweden
| | - Bengt Hansson
- Department of Biology, Lund University, 223 62, Lund, Sweden
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Anders Irbäck
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, 223 62, Lund, Sweden.
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