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Chen LQ, Li X, Yao X, Li DZ, Barrett C, dePamphilis CW, Yu WB. Variations and reduction of plastome are associated with the evolution of parasitism in Convolvulaceae. PLANT MOLECULAR BIOLOGY 2024; 114:40. [PMID: 38622367 DOI: 10.1007/s11103-024-01440-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/09/2024] [Indexed: 04/17/2024]
Abstract
Parasitic lifestyle can often relax the constraint on the plastome, leading to gene pseudogenization and loss, and resulting in diverse genomic structures and rampant genome degradation. Although several plastomes of parasitic Cuscuta have been reported, the evolution of parasitism in the family Convolvulaceae which is linked to structural variations and reduction of plastome has not been well investigated. In this study, we assembled and collected 40 plastid genomes belonging to 23 species representing four subgenera of Cuscuta and ten species of autotrophic Convolvulaceae. Our findings revealed nine types of structural variations and six types of inverted repeat (IR) boundary variations in the plastome of Convolvulaceae spp. These structural variations were associated with the shift of parasitic lifestyle, and IR boundary shift, as well as the abundance of long repeats. Overall, the degradation of Cuscuta plastome proceeded gradually, with one clade exhibiting an accelerated degradation rate. We observed five stages of gene loss in Cuscuta, including NAD(P)H complex → PEP complex → Photosynthesis-related → Ribosomal protein subunits → ATP synthase complex. Based on our results, we speculated that the shift of parasitic lifestyle in early divergent time promoted relaxed selection on plastomes, leading to the accumulation of microvariations, which ultimately resulted in the plastome reduction. This study provides new evidence towards a better understanding of plastomic evolution, variation, and reduction in the genus Cuscuta.
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Affiliation(s)
- Li-Qiong Chen
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Xin Li
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Division of BiologicalScience, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Xin Yao
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Craig Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Claude W dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, State College, Pennsylvania, 16802, USA
| | - Wen-Bin Yu
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
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Chen Z, Zhou Z, Guo ZM, Van Do T, Sun H, Niu Y. Historical development of karst evergreen broadleaved forests in East Asia has shaped the evolution of a hemiparasitic genus Brandisia (Orobanchaceae). PLANT DIVERSITY 2023; 45:501-512. [PMID: 37936821 PMCID: PMC10625920 DOI: 10.1016/j.pld.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/14/2023] [Accepted: 03/17/2023] [Indexed: 11/09/2023]
Abstract
Brandisia is a shrubby genus of about eight species distributed basically in East Asian evergreen broadleaved forests (EBLFs), with distribution centers in the karst regions of Yunnan, Guizhou, and Guangxi in southwestern China. Based on the hemiparasitic and more or less liana habits of this genus, we hypothesized that its evolution and distribution were shaped by the development of EBLFs there. To test our hypothesis, the most comprehensive phylogenies of Brandisia hitherto were constructed based on plastome and nuclear loci (nrDNA, PHYA and PHYB); then divergence time and ancestral areas were inferred using the combined nuclear loci dataset. Phylogenetic analyses reconfirmed that Brandisia is a member of Orobanchaceae, with unstable placements caused by nuclear-plastid incongruences. Within Brandisia, three major clades were well supported, corresponding to the three subgenera based on morphology. Brandisia was inferred to have originated in the early Oligocene (32.69 Mya) in the Eastern Himalayas-SW China, followed by diversification in the early Miocene (19.45 Mya) in karst EBLFs. The differentiation dates of Brandisia were consistent with the origin of keystone species of EBLFs in this region (e.g., Fagaceae, Lauraceae, Theaceae, and Magnoliaceae) and the colonization of other characteristic groups (e.g., Gesneriaceae and Mahonia). These findings indicate that the distribution and evolution of Brandisia were facilitated by the rise of the karst EBLFs in East Asia. In addition, the woody and parasitic habits, and pollination characteristics of Brandisia may also be the important factors affecting its speciation and dispersal.
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Affiliation(s)
- Zhe Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
| | - Zhuo Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
| | - Ze-Min Guo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Truong Van Do
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay 10000, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay 10000, Hanoi, Vietnam
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
| | - Yang Niu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
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Gene Flow and Diversification in Himalopsyche martynovi Species Complex (Trichoptera: Rhyacophilidae) in the Hengduan Mountains. BIOLOGY 2021; 10:biology10080816. [PMID: 34440048 PMCID: PMC8389565 DOI: 10.3390/biology10080816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022]
Abstract
The Hengduan Mountains are one of the most species-rich mountainous areas in the world. The origin and evolution of such a remarkable biodiversity are likely to be associated with geological or climatic dynamics, as well as taxon-specific biotic processes (e.g., hybridization, polyploidization, etc.). Here, we investigate the mechanisms fostering the diversification of the endemic Himalopsyche martynovi complex, a poorly known group of aquatic insects. We used multiple allelic datasets generated from 691 AHE loci to reconstruct species and RaxML phylogenetic trees. We selected the most reliable phylogenetic tree to perform network and gene flow analyses. The phylogenetic reconstructions and network analysis identified three clades, including H. epikur, H. martynovi sensu stricto and H. cf. martynovi. Himalopsyche martynovi sensu stricto and H. cf. martynovi present an intermediate morphology between H. epikur and H. viteceki, the closest known relative to the H. martynovi-complex. The gene flow analysis revealed extensive gene flow among these lineages. Our results suggest that H. viteceki and H. epikur are likely to have contributed to the evolution of H. martynovi sensu stricto and H. cf. martynovi via gene flow, and thus, our study provides insights in the diversification process of a lesser-known ecological group, and hints at the potential role of gene flow in the emergence of biological novelty in the Hengduan Mountains.
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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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Zhang R, Xu B, Li J, Zhao Z, Han J, Lei Y, Yang Q, Peng F, Liu ZL. Transit From Autotrophism to Heterotrophism: Sequence Variation and Evolution of Chloroplast Genomes in Orobanchaceae Species. Front Genet 2020; 11:542017. [PMID: 33133143 PMCID: PMC7573133 DOI: 10.3389/fgene.2020.542017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/07/2020] [Indexed: 01/15/2023] Open
Abstract
The family Orobanchaceae including autotrophic, hemiparasitic, and holoparasitic species, is becoming a key taxa to study the evolution of chloroplast genomes in different lifestyles. But the early evolutionary trajectory in the transit from autotrophism to hemiparasitism still maintains unclear for the inadequate sampling. In this study, we compared 50 complete chloroplast genomes in Orobanchaceae, containing four newly sequenced plastomes from hemiparasitic Pedicularis, to elucidate the sequence variation patterns in the evolution of plastomes. Contrasted to the sequence and structural hypervariabilities in holoparasites, hemiparasitic plastomes exhibited high similarity to those of autotrophs in gene and GC contents. They are generally characterized with functional or physical loss of ndh/tRNA genes and the inverted small-single-copy region. Gene losses in Orobanchaceae were lineage-specific and convergent, possibly related to structural reconfiguration and expansion/contraction of the inverted region. Pseudogenization of ndh genes was unique in hemiparasites. At least in Pedicularis, the ndhF gene might be most sensitive to the environmental factors and easily pseudogenized when autotrophs transit to hemiparasites. And the changes in gene contents and structural variation potentially deeply rely on the feeding type. Selective pressure, together with mutational bias, was the dominant factor of shaping the codon usage patterns. The relaxed selective constraint, potentially with genome-based GC conversion (gBGC) and preferential codon usage, drive the fluctuation of GC contents among taxa with different lifestyles. Phylogenetic analysis in Orobanchaceae supported that parasitic species were single-originated while holoparasites were multiple-originated. Overall, the comparison of plastomes provided a good opportunity to understand the evolution process in Orobanchaceae with different lifestyles.
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Affiliation(s)
- Ruiting Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Bei Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Jianfang Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Zhe Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Jie Han
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Yunjing Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Qian Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Fangfang Peng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Zhan-Lin Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
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Kurotani KI, Wakatake T, Ichihashi Y, Okayasu K, Sawai Y, Ogawa S, Cui S, Suzuki T, Shirasu K, Notaguchi M. Host-parasite tissue adhesion by a secreted type of β-1,4-glucanase in the parasitic plant Phtheirospermum japonicum. Commun Biol 2020; 3:407. [PMID: 32733024 PMCID: PMC7393376 DOI: 10.1038/s42003-020-01143-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/10/2020] [Indexed: 01/10/2023] Open
Abstract
Tissue adhesion between plant species occurs both naturally and artificially. Parasitic plants establish intimate relationship with host plants by adhering tissues at roots or stems. Plant grafting, on the other hand, is a widely used technique in agriculture to adhere tissues of two stems. Here we found that the model Orobanchaceae parasitic plant Phtheirospermum japonicum can be grafted on to interfamily species. To understand molecular basis of tissue adhesion between distant plant species, we conducted comparative transcriptome analyses on both infection and grafting by P. japonicum on Arabidopsis. Despite different organs, we identified the shared gene expression profile, where cell proliferation- and cell wall modification-related genes are up-regulated. Among genes commonly induced in tissue adhesion between distant species, we showed a gene encoding a secreted type of β-1,4-glucanase plays an important role for plant parasitism. Our data provide insights into the molecular commonality between parasitism and grafting in plants.
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Affiliation(s)
- Ken-Ichi Kurotani
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Takanori Wakatake
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
- Center for Sustainable Resource Science, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Biocenter, Institute for Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, University of Würzburg, 97082, Würzburg, Germany
| | - Yasunori Ichihashi
- Center for Sustainable Resource Science, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Koji Okayasu
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Yu Sawai
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Satoshi Ogawa
- Center for Sustainable Resource Science, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Songkui Cui
- Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Matsumoto-cho, Kasugai, 487-8501, Japan
| | - Ken Shirasu
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Center for Sustainable Resource Science, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
| | - Michitaka Notaguchi
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
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Xia Z, Wen J, Gao Z. Does the Enigmatic Wightia Belong to Paulowniaceae (Lamiales)? FRONTIERS IN PLANT SCIENCE 2019; 10:528. [PMID: 31114599 PMCID: PMC6503002 DOI: 10.3389/fpls.2019.00528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
The familial placement of Wightia has been controversial in the Lamiales, and the genus is currently placed in Paulowniaceae in APG IV. Phylogenetic analyses of Wightia and its close relatives in Lamiales are conducted using sequences of the complete chloroplast genomes as well as sequence data from nine chloroplast DNA regions (atpB, matK, ndhF, psbBTNH, rbcL, rps4, rps16 intron, trnL-F, and trnV-atpE) and one mitochondrial gene rps3. The maximum likelihood and Bayesian analyses do not support a close relationship between Wightia and Paulownia of Paulowniaceae; instead the enigmatic Wightia is sister to Phrymaceae with strong support in all analyses. Hence Wightia should not be placed in Paulowniaceae. Because morphological data show Wightia's affinity to both Phrymaceae and Paulowniaceae and prior nrITS data suggest its sister relationship to Paulownia of Paulowniaceae, it is likely that Wightia may have had a hybrid origin between early lineages of Phrymaceae and Paulowniaceae. It is therefore the best to exclude Wightia from Paulowniaceae and place the genus as unassigned until further nuclear data to test the hybrid hypothesis. The seven species of Paulownia constitute a monophyletic group, and Paulowniaceae is supported to be a monogeneric family, consistent with a series of morphological and floral development characters. The genus Brandisia, which was sometimes regarded as a close relative of Wightia, is supported to be nested within Orobanchaceae, as sister to Pterygiella. This sister relationship can be corroborated by fruit, seed and pollen morphological characters.
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Affiliation(s)
- Zhi Xia
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Zhiming Gao
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
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Li X, Feng T, Randle C, Schneeweiss GM. Phylogenetic Relationships in Orobanchaceae Inferred From Low-Copy Nuclear Genes: Consolidation of Major Clades and Identification of a Novel Position of the Non-photosynthetic Orobanche Clade Sister to All Other Parasitic Orobanchaceae. FRONTIERS IN PLANT SCIENCE 2019; 10:902. [PMID: 31379896 PMCID: PMC6646720 DOI: 10.3389/fpls.2019.00902] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/26/2019] [Indexed: 05/18/2023]
Abstract
Molecular phylogenetic analyses have greatly advanced our understanding of phylogenetic relationships in Orobanchaceae, a model system to study parasitism in angiosperms. As members of this group may lack some genes widely used for phylogenetic analysis and exhibit varying degrees of accelerated base substitution in other genes, relationships among major clades identified previously remain contentious. To improve inferences of phylogenetic relationships in Orobanchaceae, we used two pentatricopeptide repeat (PPR) and three low-copy nuclear (LCN) genes, two of which have been developed for this study. Resolving power and level of support strongly differed among markers. Despite considerable incongruence among newly and previously sequenced markers, monophyly of major clades identified in previous studies was confirmed and, especially in analyses of concatenated data, strongly supported after the exclusion of a small group of East Asian genera (Pterygiella and Phtheirospermum) from the Euphrasia-Rhinanthus clade. The position of the Orobanche clade sister to all other parasitic Orobanchaceae may indicate that the shift to holoparasitism occurred early in the evolution of the family. Although well supported in analyses of concatenated data comprising ten loci (five newly and five previously sequenced), relationships among major clades, most prominently the Striga-Alectra clade, the Euphrasia-Rhinanthus clade, and the Castilleja-Pedicularis clade, were uncertain because of strongly supported incongruence also among well-resolving loci. Despite the limitations of using a few selected loci, congruence among markers with respect to circumscription of major clades of Orobanchaceae renders those frameworks for detailed, species-level, phylogenetic studies.
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Affiliation(s)
- Xi Li
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Tao Feng
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Chris Randle
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, United States
| | - Gerald M. Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- *Correspondence: Gerald M. Schneeweiss,
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