1
|
Ma Y, López‐Pujol J, Yan D, Zhou Z, Deng Z, Niu J. Complete chloroplast genomes of the hemiparasitic genus Cymbaria: Insights into comparative analysis, development of molecular markers, and phylogenetic relationships. Ecol Evol 2024; 14:e11677. [PMID: 38962021 PMCID: PMC11221886 DOI: 10.1002/ece3.11677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 05/18/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024] Open
Abstract
The hemiparasitic tribe Cymbarieae (Orobanchaceae) plays a crucial role in elucidating the initial stage of the transition from autotrophism to heterotrophism. However, the complete chloroplast genome of the type genus Cymbaria has yet to be reported. In addition, the traditional Mongolian medicine Cymbaria daurica is frequently subjected to adulteration or substitution because of the minor morphological differences with Cymbaria mongolica. In this study, the complete chloroplast genomes of the two Cymbaria species were assembled and annotated, and those of other published 52 Orobanchaceae species were retrieved for comparative analyses. We found that the Cymbaria chloroplast genomes are characterized by pseudogenization or loss of stress-relevant genes (ndh) and a unique rbcL-matK inversion. Unlike the high variability observed in holoparasites, Cymbaria and other hemiparasites exhibit high similarity to autotrophs in genome size, guanine-cytosine (GC) content, and intact genes. Notably, four pairs of specific DNA barcodes were developed and validated to distinguish the medicinal herb from its adulterants. Phylogenetic analyses revealed that the genus Cymbaria and the Schwalbea-Siphonostegia clade are grouped into the tribe Cymbarieae, which forms a sister clade to the remaining Orobanchaceae parasitic lineages. Moreover, the diversification of monophyletic Cymbaria occurred during the late Miocene (6.72 Mya) in the Mongol-Chinese steppe region. Our findings provide valuable genetic resources for studying the phylogeny of Orobanchaceae and plant parasitism, and genetic tools to validate the authenticity of the traditional Mongolian medicine "Xinba.".
Collapse
Affiliation(s)
- Yang Ma
- School of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
| | - Jordi López‐Pujol
- Botanic Institute of Barcelona (IBB)CSIC‐CMCNBBarcelonaSpain
- Escuela de Ciencias AmbientalesUniversidad Espíritu Santo (UEES)SamborondónEcuador
| | - Dongqing Yan
- School of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
| | - Zhen Zhou
- School of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
| | - Zekun Deng
- School of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
| | - Jianming Niu
- School of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian PlateauHohhotChina
- Inner Mongolia Key Laboratory of Grassland Ecology and the Candidate State Key Laboratory of Ministry of Science and TechnologyHohhotChina
| |
Collapse
|
2
|
Barrett CF, Pace MC, Corbett CW. Plastid genome evolution in leafless members of the orchid subfamily Orchidoideae, with a focus on Degranvillea dermaptera. AMERICAN JOURNAL OF BOTANY 2024; 111:e16370. [PMID: 38989916 DOI: 10.1002/ajb2.16370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 07/12/2024]
Abstract
PREMISE Leafless, heterotrophic plants are prime examples of organismal modification, the genomic consequences of which have received considerable interest. In particular, plastid genomes (plastomes) are being sequenced at a high rate, allowing continual refinement of conceptual models of reductive evolution in heterotrophs. However, numerous sampling gaps exist, hindering the ability to conduct comprehensive phylogenomic analyses in these plants. METHODS Using floral tissue from an herbarium specimen, we sequenced and analyzed the plastome of Degranvillea dermaptera, a rarely collected, leafless orchid species from South America about which little is known, including its phylogenetic affinities. RESULTS The plastome is the most reduced of those sequenced among the orchid subfamily Orchidoideae. In Degranvillea, it has lost the majority of genes found in leafy autotrophic species, is structurally rearranged, and has similar gene content to the most reduced plastomes among the orchids. We found strong evidence for the placement of Degranvillea within the subtribe Spiranthinae using models that explicitly account for heterotachy, or lineage-specific evolutionary rate variation over time. We further found evidence of relaxed selection on several genes and of correlations among substitution rates and several other "traits" of the plastome among leafless members of orchid subfamily Orchidoideae. CONCLUSIONS Our findings advance knowledge on the phylogenetic relationships and paths of plastid genome evolution among the orchids, which have experienced more independent transitions to heterotrophy than any other plant family. This study demonstrates the importance of herbarium collections in comparative genomics of poorly known species of conservation concern.
Collapse
Affiliation(s)
- Craig F Barrett
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, 26506, WV, USA
| | - Matthew C Pace
- New York Botanical Garden, 2900 Southern Boulevard, Bronx, 10458, NY, USA
| | - Cameron W Corbett
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, 26506, WV, USA
| |
Collapse
|
3
|
Giannakis K, Richards L, Dauda KA, Johnston IG. Connecting Species-Specific Extents of Genome Reduction in Mitochondria and Plastids. Mol Biol Evol 2024; 41:msae097. [PMID: 38758976 PMCID: PMC11144018 DOI: 10.1093/molbev/msae097] [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: 03/11/2024] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024] Open
Abstract
Mitochondria and plastids have both dramatically reduced their genomes since the endosymbiotic events that created them. The similarities and differences in the evolution of the two organelle genome types have been the target of discussion and investigation for decades. Ongoing work has suggested that similar mechanisms may modulate the reductive evolution of the two organelles in a given species, but quantitative data and statistical analyses exploring this picture remain limited outside of some specific cases like parasitism. Here, we use cross-eukaryote organelle genome data to explore evidence for coevolution of mitochondrial and plastid genome reduction. Controlling for differences between clades and pseudoreplication due to relatedness, we find that extents of mtDNA and ptDNA gene retention are related to each other across taxa, in a generally positive correlation that appears to differ quantitatively across eukaryotes, for example, between algal and nonalgal species. We find limited evidence for coevolution of specific mtDNA and ptDNA gene pairs, suggesting that the similarities between the two organelle types may be due mainly to independent responses to consistent evolutionary drivers.
Collapse
Affiliation(s)
| | - Luke Richards
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Kazeem A Dauda
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
| |
Collapse
|
4
|
Tang L, Wang T, Hou L, Zhang G, Deng M, Guo X, Ji Y. Comparative and phylogenetic analyses of Loranthaceae plastomes provide insights into the evolutionary trajectories of plastome degradation in hemiparasitic plants. BMC PLANT BIOLOGY 2024; 24:406. [PMID: 38750463 PMCID: PMC11097404 DOI: 10.1186/s12870-024-05094-5] [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: 03/05/2024] [Accepted: 05/02/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND The lifestyle transition from autotrophy to heterotrophy often leads to extensive degradation of plastomes in parasitic plants, while the evolutionary trajectories of plastome degradation associated with parasitism in hemiparasitic plants remain poorly understood. In this study, phylogeny-oriented comparative analyses were conducted to investigate whether obligate Loranthaceae stem-parasites experienced higher degrees of plastome degradation than closely related facultative root-parasites and to explore the potential evolutionary events that triggered the 'domino effect' in plastome degradation of hemiparasitic plants. RESULTS Through phylogeny-oriented comparative analyses, the results indicate that Loranthaceae hemiparasites have undergone varying degrees of plastome degradation as they evolved towards a heterotrophic lifestyle. Compared to closely related facultative root-parasites, all obligate stem-parasites exhibited an elevated degree plastome degradation, characterized by increased downsizing, gene loss, and pseudogenization, thereby providing empirical evidence supporting the theoretical expectation that evolution from facultative parasitism to obligate parasitism may result in a higher degree of plastome degradation in hemiparasites. Along with infra-familial divergence in Loranthaceae, several lineage-specific gene loss/pseudogenization events occurred at deep nodes, whereas further independent gene loss/pseudogenization events were observed in shallow branches. CONCLUSIONS The findings suggest that in addition to the increasing levels of nutritional reliance on host plants, cladogenesis can be considered as another pivotal evolutionary event triggering the 'domino effect' in plastome degradation of hemiparasitic plants. These findings provide new insights into the evolutionary trajectory of plastome degradation in hemiparasitic plants.
Collapse
Affiliation(s)
- Lilei Tang
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Tinglu Wang
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Luxiao Hou
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
| | - Guangfei Zhang
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Institute of Biodiversity, Yunnan University, Kunming, Yunnan, 650504, China
| | - Min Deng
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China.
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Institute of Biodiversity, Yunnan University, Kunming, Yunnan, 650504, China.
| | - Xiaorong Guo
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China.
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Institute of Biodiversity, Yunnan University, Kunming, Yunnan, 650504, China.
| | - Yunheng Ji
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| |
Collapse
|
5
|
Fu CN, Wicke S, Zhu AD, Li DZ, Gao LM. Distinctive plastome evolution in carnivorous angiosperms. BMC PLANT BIOLOGY 2023; 23:660. [PMID: 38124058 PMCID: PMC10731798 DOI: 10.1186/s12870-023-04682-1] [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: 07/14/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Independent origins of carnivory in multiple angiosperm families are fabulous examples of convergent evolution using a diverse array of life forms and habitats. Previous studies have indicated that carnivorous plants have distinct evolutionary trajectories of plastid genome (plastome) compared to their non-carnivorous relatives, yet the extent and general characteristics remain elusive. RESULTS We compared plastomes from 9 out of 13 carnivorous families and their non-carnivorous relatives to assess carnivory-associated evolutionary patterns. We identified inversions in all sampled Droseraceae species and four species of Utricularia, Pinguicula, Darlingtonia and Triphyophyllum. A few carnivores showed distinct shifts in inverted repeat boundaries and the overall repeat contents. Many ndh genes, along with some other genes, were independently lost in several carnivorous lineages. We detected significant substitution rate variations in most sampled carnivorous lineages. A significant overall substitution rate acceleration characterizes the two largest carnivorous lineages of Droseraceae and Lentibulariaceae. We also observe moderate substitution rates acceleration in many genes of Cephalotus follicularis, Roridula gorgonias, and Drosophyllum lusitanicum. However, only a few genes exhibit significant relaxed selection. CONCLUSION Our results indicate that the carnivory of plants have different effects on plastome evolution across carnivorous lineages. The complex mechanism under carnivorous habitats may have resulted in distinctive plastome evolution with conserved plastome in the Brocchinia hechtioides to strongly reconfigured plastomes structures in Droseraceae. Organic carbon obtained from prey and the efficiency of utilizing prey-derived nutrients might constitute possible explanation.
Collapse
Affiliation(s)
- Chao-Nan Fu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, Yunnan, China
| | - Susann Wicke
- Institute for Biology, Humboldt-University Berlin, Berlin, Germany
- Späth-Arboretum of the Humboldt-University Berlin, Berlin, Germany
| | - An-Dan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - De-Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, Yunnan, China.
| |
Collapse
|
6
|
Preuss M, Díaz-Tapia P, Verbruggen H, Zuccarello GC. Gene-rich plastid genomes of two parasitic red algal species, Laurencia australis and L. verruciformis (Rhodomelaceae, Ceramiales), and a taxonomic revision of Janczewskia. JOURNAL OF PHYCOLOGY 2023; 59:950-962. [PMID: 37638497 DOI: 10.1111/jpy.13373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 08/29/2023]
Abstract
Parasitic red algae are an interesting system for investigating the genetic changes that occur in parasites. These parasites have evolved independently multiple times within the red algae. The functional loss of plastid genomes can be investigated in these multiple independent examples, and fine-scale patterns may be discerned. The only plastid genomes from red algal parasites known so far are highly reduced and missing almost all photosynthetic genes. Our study assembled and annotated plastid genomes from the parasites Janczewskia tasmanica and its two Laurencia host species (Laurencia elata and one unidentified Laurencia sp. A25) from Australia and Janczewskia verruciformis, its host species (Laurencia catarinensis), and the closest known free-living relative (Laurencia obtusa) from the Canary Islands (Spain). For the first time we show parasitic red algal plastid genomes that are similar in size and gene content to free-living host species without any gene loss or genome reduction. The only exception was two pseudogenes (moeB and ycf46) found in the plastid genome of both isolates of J. tasmanica, indicating potential for future loss of these genes. Further comparative analyses with the three highly reduced plastid genomes showed possible gene loss patterns, in which photosynthetic gene categories were lost followed by other gene categories. Phylogenetic analyses did not confirm monophyly of Janczewskia, and the genus was subsumed into Laurencia. Further investigations will determine if any convergent small-scale patterns of gene loss exist in parasitic red algae and how these are applicable to other parasitic systems.
Collapse
Affiliation(s)
- Maren Preuss
- National Institute of Water and Atmosphere Research, Wellington, New Zealand
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Pilar Díaz-Tapia
- Coastal Biology Research Group, Faculty of Sciences and Centre for Advanced Scientific Research, University of A Coruña, A Coruña, Spain
- Instituto Español de Oceanografía (IEO-CSIC), Centro Oceanográfico de A Coruña, A Coruña, Spain
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| | - Giuseppe C Zuccarello
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| |
Collapse
|
7
|
Mkala EM, Jost M, Dong X, Mwachala G, Musili PM, Wanke S, Hu GW, Wang QF. Phylogenetic and comparative analyses of Hydnora abyssinica plastomes provide evidence for hidden diversity within Hydnoraceae. BMC Ecol Evol 2023; 23:34. [PMID: 37464315 PMCID: PMC10353213 DOI: 10.1186/s12862-023-02142-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND To date, plastid genomes have been published for all but two holoparasitic angiosperm families. However, only a single or a few plastomes represent most of these families. Of the approximately 40 genera of holoparasitic angiosperms, a complete plastid genome sequence is available for only about half. In addition, less than 15 species are currently represented with more than one published plastid genome, most of which belong to the Orobanchaceae. Therefore, a significant portion of the holoparasitic plant plastome diversity remains unexplored. This limited information could hinder potential evolutionary pattern recognition as well as the exploration of inter- and intra-species plastid genome diversity in the most extreme holoparasitic angiosperms. RESULTS Here, we report the first plastomes of Kenyan Hydnora abyssinica accessions. The plastomes have a typical quadripartite structure and encode 24 unique genes. Phylogenetic tree reconstruction recovers the Kenyan accessions as monophyletic and together in a clade with the Namibian H. abyssinica accession and the recently published H. arabica from Oman. Hydnora abyssinica as a whole however is recovered as non-monophyletic, with H. arabica nested within. This result is supported by distinct structural plastome synapomorphies as well as pairwise distance estimates that reveal hidden diversity within the Hydnora species in Africa. CONCLUSION We propose to increase efforts to sample widespread holoparasitic species for their plastid genomes, as is the case with H. abyssinica, which is widely distributed in Africa. Morphological reinvestigation and further molecular data are needed to fully investigate the diversity of H. abyssinica along the entire range of distribution, as well as the diversity of currently synonymized taxa.
Collapse
Affiliation(s)
- Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China
- University of Chinese Academy of Sciences, Beijing, CN-100049, China
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, 01062, Dresden, Germany
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China
- University of Chinese Academy of Sciences, Beijing, CN-100049, China
| | - Geoffrey Mwachala
- East African Herbarium, National Museums of Kenya, P. O. Box 451660-0100, Nairobi, Kenya
| | - Paul Mutuku Musili
- East African Herbarium, National Museums of Kenya, P. O. Box 451660-0100, Nairobi, Kenya
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, 01062, Dresden, Germany
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China.
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Shao BY, Wang MZ, Chen SS, Ya JD, Jin XH. Habitat-related plastome evolution in the mycoheterotrophic Neottia listeroides complex (Orchidaceae, Neottieae). BMC PLANT BIOLOGY 2023; 23:282. [PMID: 37244988 DOI: 10.1186/s12870-023-04302-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Abstract
BACKGROUND Mycoheterotrophs, acquiring organic carbon and other nutrients from mycorrhizal fungi, have evolved repeatedly with substantial plastid genome (plastome) variations. To date, the fine-scale evolution of mycoheterotrophic plastomes at the intraspecific level is not well-characterized. A few studies have revealed unexpected plastome divergence among species complex members, possibly driven by various biotic/abiotic factors. To illustrate evolutionary mechanisms underlying such divergence, we analyzed plastome features and molecular evolution of 15 plastomes of Neottia listeroides complex from different forest habitats. RESULTS These 15 samples of Neottia listeroides complex split into three clades according to their habitats approximately 6 million years ago: Pine Clade, including ten samples from pine-broadleaf mixed forests, Fir Clade, including four samples from alpine fir forests and Fir-willow Clade with one sample. Compared with those of Pine Clade members, plastomes of Fir Clade members show smaller size and higher substitution rates. Plastome size, substitution rates, loss and retention of plastid-encoded genes are clade-specific. We propose to recognized six species in N. listeroides complex and slightly modify the path of plastome degradation. CONCLUSIONS Our results provide insight into the evolutionary dynamics and discrepancy of closely related mycoheterotrophic orchid lineages at a high phylogenetic resolution.
Collapse
Affiliation(s)
- Bing-Yi Shao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mo-Zhu Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Si-Si Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ji-Dong Ya
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
10
|
Garrett N, Viruel J, Klimpert N, Soto Gomez M, Lam VKY, Merckx VSFT, Graham SW. Plastid phylogenomics and molecular evolution of Thismiaceae (Dioscoreales). AMERICAN JOURNAL OF BOTANY 2023; 110:e16141. [PMID: 36779918 DOI: 10.1002/ajb2.16141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Species in Thismiaceae can no longer photosynthesize and instead obtain carbon from soil fungi. Here we infer Thismiaceae phylogeny using plastid genome data and characterize the molecular evolution of this genome. METHODS We assembled five Thismiaceae plastid genomes from genome skimming data, adding to previously published data for phylogenomic inference. We investigated plastid-genome structural changes, considering locally colinear blocks (LCBs). We also characterized possible shifts in selection pressure in retained genes by considering changes in the ratio of nonsynonymous to synonymous changes (ω). RESULTS Thismiaceae experienced two major pulses of gene loss around the early diversification of the family, with subsequent scattered gene losses across descendent lineages. In addition to massive size reduction, Thismiaceae plastid genomes experienced occasional inversions, and there were likely two independent losses of the plastid inverted repeat (IR) region. Retained plastid genes remain under generally strong purifying selection (ω << 1), with significant and sporadic weakening or strengthening in several instances. The bifunctional trnE-UUC gene of Thismia huangii may retain a secondary role in heme biosynthesis, despite a probable loss of functionality in protein translation. Several cis-spliced group IIA introns have been retained, despite the loss of the plastid intron maturase, matK. CONCLUSIONS We infer that most gene losses in Thismiaceae occurred early and rapidly, following the initial loss of photosynthesis in its stem lineage. As a species-rich, fully mycoheterotrophic lineage, Thismiaceae provide a model system for uncovering the unique and divergent ways in which plastid genomes evolve in heterotrophic plants.
Collapse
Affiliation(s)
- Natalie Garrett
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Juan Viruel
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - Nathaniel Klimpert
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | | | - Vivienne K Y Lam
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Vincent S F T Merckx
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Sciencepark 904, 1098, XH, Amsterdam, The Netherlands
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
11
|
Zhou L, Chen T, Qiu X, Liu J, Guo S. Evolutionary differences in gene loss and pseudogenization among mycoheterotrophic orchids in the tribe Vanilleae (subfamily Vanilloideae). FRONTIERS IN PLANT SCIENCE 2023; 14:1160446. [PMID: 37035052 PMCID: PMC10073425 DOI: 10.3389/fpls.2023.1160446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Galeola lindleyana is a mycoheterotrophic orchid belonging to the tribe Vanilleae within the subfamily Vanilloideae. METHODS In this study, the G. lindleyana plastome was assembled and annotated, and compared with other Vanilleae orchids, revealing the evolutionary variations between the photoautotrophic and mycoheterotrophic plastomes. RESULTS The G. lindleyana plastome was found to include 32 protein-coding genes, 16 tRNA genes and four ribosomal RNA genes, including 11 pseudogenes. Almost all of the genes encoding photosynthesis have been lost physically or functionally, with the exception of six genes encoding ATP synthase and psaJ in photosystem I. The length of the G. lindleyana plastome has decreased to 100,749 bp, while still retaining its typical quadripartite structure. Compared with the photoautotrophic Vanilloideae plastomes, the inverted repeat (IR) regions and the large single copy (LSC) region of the mycoheterotrophic orchid's plastome have contracted, while the small single copy (SSC) region has expanded significantly. Moreover, the difference in length between the two ndhB genes was found to be 682 bp, with one of them spanning the IRb/SSC boundary. The Vanilloideae plastomes were varied in their structural organization, gene arrangement, and gene content. Even the Cyrtosia septentrionalis plastome which was found to be closest in length to the G. lindleyana plastome, differed in terms of its gene arrangement and gene content. In the LSC region, the psbA, psbK, atpA and psaB retained in the G. lindleyana plastome were missing in the C. septentrionalis plastome, while, the matK, rps16, and atpF were incomplete in the C. septentrionalis plastome, yet still complete in that of the G. lindleyana. Lastly, compared with the G. lindleyana plastome, a 15 kb region located in the SSC area between ndhB-rrn16S was found to be inverted in the C. septentrionalis plastome. These changes in gene content, gene arrangment and gene structure shed light on the polyphyletic evolution of photoautotrophic orchid plastomes to mycoheterotrophic orchid plastomes. DISCUSSION Thus, this study's decoding of the mycoheterotrophic G. lindleyana plastome provides valuable resource data for future research and conservation of endangered orchids.
Collapse
Affiliation(s)
| | | | | | - Jinxin Liu
- *Correspondence: Jinxin Liu, ; Shunxing Guo,
| | | |
Collapse
|
12
|
Banerjee A, Stefanović S. A comparative study across the parasitic plants of Cuscuta subgenus Grammica (Convolvulaceae) reveals a possible loss of the plastid genome in its section Subulatae. PLANTA 2023; 257:66. [PMID: 36826697 DOI: 10.1007/s00425-023-04099-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Most species in Cuscuta subgenus Grammica retain many photosynthesis-related plastid genes, generally under purifying selection. A group of holoparasitic species in section Subulatae may have lost their plastid genomes entirely. The c. 153 species of plants belonging to Cuscuta subgenus Grammica are all obligate stem parasites. However, some have completely lost the ability to conduct photosynthesis while others retain photosynthetic machinery and genes. The plastid genome that primarily encodes key photosynthesis genes functions as a bellwether for how reliant plants are on primary production. This research assembles and analyses 17 plastomes across Cuscuta subgenus Grammica with the aim of characterizing the state of the plastome in each of its sections. By comparing the structure and content of plastid genomes across the subgenus, as well as by quantifying the selection acting upon each gene, we reconstructed the patterns of plastome change within the phylogenetic context for this group. We found that species in 13 of the 15 sections that comprise Grammica retain the bulk of plastid photosynthesis genes and are thus hemiparasitic. The complete loss of photosynthesis can be traced to two clades: the entire section Subulatae and a complex of three species within section Ceratophorae. We were unable to recover any significant plastome sequences from section Subulatae, suggesting that plastomes in these species are either drastically reduced or lost entirely.
Collapse
Affiliation(s)
- 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
| |
Collapse
|
13
|
Kamra K, Jung J, Kim JH. A phylogenomic study of Iridaceae Juss. based on complete plastid genome sequences. FRONTIERS IN PLANT SCIENCE 2023; 14:1066708. [PMID: 36844099 PMCID: PMC9948625 DOI: 10.3389/fpls.2023.1066708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
The plastid genome has proven to be an effective tool for examining deep correlations in plant phylogenetics, owing to its highly conserved structure, uniparental inheritance, and limited variation in evolutionary rates. Iridaceae, comprising more than 2,000 species, includes numerous economically significant taxa that are frequently utilized in food industries and medicines and for ornamental and horticulture purposes. Molecular studies on chloroplast DNA have confirmed the position of this family in the order Asparagales with non-asparagoids. The current subfamilial classification of Iridaceae recognizes seven subfamilies-Isophysioideae, Nivenioideae, Iridoideae, Crocoideae, Geosiridaceae, Aristeoideae, and Patersonioideae-which are supported by limited plastid DNA regions. To date, no comparative phylogenomic studies have been conducted on the family Iridaceae. We assembled and annotated (de novo) the plastid genomes of 24 taxa together with seven published species representing all the seven subfamilies of Iridaceae and performed comparative genomics using the Illumina MiSeq platform. The plastomes of the autotrophic Iridaceae represent 79 protein-coding, 30 tRNA, and four rRNA genes, with lengths ranging from 150,062 to 164,622 bp. The phylogenetic analysis of the plastome sequences based on maximum parsimony, maximum likelihood, and Bayesian inference analyses suggested that Watsonia and Gladiolus were closely related, supported by strong support values, which differed considerably from recent phylogenetic studies. In addition, we identified genomic events, such as sequence inversions, deletions, mutations, and pseudogenization, in some species. Furthermore, the largest nucleotide variability was found in the seven plastome regions, which can be used in future phylogenetic studies. Notably, three subfamilies-Crocoideae, Nivenioideae, and Aristeoideae-shared a common ycf2 gene locus deletion. Our study is a preliminary report of a comparative study of the complete plastid genomes of 7/7 subfamilies and 9/10 tribes, elucidating the structural characteristics and shedding light on plastome evolution and phylogenetic relationships within Iridaceae. Additionally, further research is required to update the relative position of Watsonia within the tribal classification of the subfamily Crocoideae.
Collapse
|
14
|
Wang Y, Xie Y, Jin J, Li J, Qiu X, Tong Y, Li Z, Zhang Z, Lai W. Comparison of the chloroplast genomes and phylogenomic analysis of Elaeocarpaceae. PeerJ 2023; 11:e15322. [PMID: 37187516 PMCID: PMC10178313 DOI: 10.7717/peerj.15322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Background Elaeocarpaceae is a vital family in tropical and subtropical forests. Compared with the important position of Elaeocarpaceae species in forest ecosystem and the concern of medicinal value, the most research on Elaeocarpaceae are classification and taxonomy. Molecular systematics has corrected the morphological misjudgment, and it belongs to Oxalidales. Phylogenetic and divergence time estimates of Elaeocarpaceae is mostly constructed by using chloroplast gene fragments. At present, although there are reports on the chloroplast structure of Elaeocarpaceae, a comprehensive analysis of the chloroplast structure of Elaeocarpaceae is lacking. Methods To understand the variation in chloroplast sequence size and structure in Elaeocarpaceae, the chloroplast genomes of nine species were sequenced using the Illumina HiSeq 2500 platform and further assembled and annotated with Elaeocarpus japonicus and Sloanea sinensis (family Elaeocarpaceae) as references. A phylogenomic tree was constructed based on the complete chloroplast genomes of the 11 species representing five genera of Elaeocarpaceae. Chloroplast genome characteristics were examined by using Circoletto and IRscope software. Results The results revealed the following: (a) The 11 sequenced chloroplast genomes ranged in size from 157,546 to 159,400 bp. (b) The chloroplast genomes of Elaeocarpus, Sloanea, Crinodendron and Vallea lacked the rpl32 gene in the small single-copy (SSC) region. The large single-copy (LSC) region of the chloroplast genomes lacked the ndhK gene in Elaeocarpus, Vallea stipularis, and Aristotelia fruticosa. The LSC region of the chloroplast genomes lacked the infA gene in genus Elaeocarpus and Crinodendron patagua. (c) Through inverted repeat (IR) expansion and contraction analysis, a significant difference was found between the LSC/IRB and IRA/LSC boundaries among these species. Rps3 was detected in the neighboring regions of the LSC and IRb regions in Elaeocarpus. (d) Phylogenomic analysis revealed that the genus Elaeocarpus is closely related to Crinodendron patagua on an independent branch and Aristotelia fruticosa is closely related to Vallea stipularis, forming a clade with the genus Sloanea. Structural comparisons showed that Elaeocarpaceae diverged at 60 Mya, the genus Elaeocarpus diverged 53 Mya and that the genus Sloanea diverged 0.44 Mya. These results provide new insight into the evolution of the Elaeocarpaceae.
Collapse
Affiliation(s)
- Yihui Wang
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
- School of Landscape Architecture, Beijing Forestry University, Beijing, P.R. China
| | - Yifei Xie
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
- Key Laboratory of Nanling Plant Resources Conservation and Utilization, Ganzhou, P.R. China
| | - Jiayi Jin
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
| | - Jinyue Li
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xishuangbanna, P.R. China
| | - Xiangdong Qiu
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
| | - Yang Tong
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
| | - Zhongyang Li
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
- Key Laboratory of Nanling Plant Resources Conservation and Utilization, Ganzhou, P.R. China
| | - Zhixiang Zhang
- School of Ecology and Nature conservation, Beijing Forestry University, Beijing, P.R. China
| | - Wenling Lai
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
- Key Laboratory of Nanling Plant Resources Conservation and Utilization, Ganzhou, P.R. China
| |
Collapse
|
15
|
Klimpert NJ, Mayer JLS, Sarzi DS, Prosdocimi F, Pinheiro F, Graham SW. Phylogenomics and plastome evolution of a Brazilian mycoheterotrophic orchid, Pogoniopsis schenckii. AMERICAN JOURNAL OF BOTANY 2022; 109:2030-2050. [PMID: 36254561 DOI: 10.1002/ajb2.16084] [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: 04/14/2022] [Revised: 09/23/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Pogoniopsis likely represents an independent photosynthesis loss in orchids. We use phylogenomic data to better identify the phylogenetic placement of this fully mycoheterotrophic taxon, and investigate its molecular evolution. METHODS We performed likelihood analysis of plastid and mitochondrial phylogenomic data to localize the position of Pogoniopsis schenckii in orchid phylogeny, and investigated the evolution of its plastid genome. RESULTS All analyses place Pogoniopsis in subfamily Epidendroideae, with strongest support from mitochondrial data, which also place it near tribe Sobralieae with moderately strong support. Extreme rate elevation in Pogoniopsis plastid genes broadly depresses branch support; in contrast, mitochondrial genes are only mildly rate elevated and display very modest and localized reductions in bootstrap support. Despite considerable genome reduction, including loss of photosynthesis genes and multiple translation apparatus genes, gene order in Pogoniopsis plastomes is identical to related autotrophs, apart from moderately shifted inverted repeat (IR) boundaries. All cis-spliced introns have been lost in retained genes. Two plastid genes (accD, rpl2) show significant strengthening of purifying selection. A retained plastid tRNA gene (trnE-UUC) of Pogoniopsis lacks an anticodon; we predict that it no longer functions in translation but retains a secondary role in heme biosynthesis. CONCLUSIONS Slowly evolving mitochondrial genes clarify the placement of Pogoniopsis in orchid phylogeny, a strong contrast with analysis of rate-elevated plastome data. We documented the effects of the novel loss of photosynthesis: for example, despite massive gene loss, its plastome is fully colinear with other orchids, and it displays only moderate shifts in selective pressure in retained genes.
Collapse
Affiliation(s)
- Nathaniel J Klimpert
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Juliana Lischka Sampaio Mayer
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Deise Schroder Sarzi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, UFRJ/CCS/Bloco B33, Rio de Janeiro, RJ, 21.941-902, Brazil
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, UFRJ/CCS/Bloco B33, Rio de Janeiro, RJ, 21.941-902, Brazil
| | - Fábio Pinheiro
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| |
Collapse
|
16
|
Lin Q, Braukmann TWA, Soto Gomez M, Mayer JLS, Pinheiro F, Merckx VSFT, Stefanović S, Graham SW. Mitochondrial genomic data are effective at placing mycoheterotrophic lineages in plant phylogeny. THE NEW PHYTOLOGIST 2022; 236:1908-1921. [PMID: 35731179 DOI: 10.1111/nph.18335] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/13/2022] [Indexed: 05/03/2023]
Abstract
Fully mycoheterotrophic plants can be difficult to place in plant phylogeny due to elevated substitution rates associated with photosynthesis loss. This potentially limits the effectiveness of downstream analyses of mycoheterotrophy that depend on accurate phylogenetic inference. Although mitochondrial genomic data sets are rarely used in plant phylogenetics, theory predicts that they should be resilient to long-branch artefacts, thanks to their generally slow evolution, coupled with limited rate elevation in heterotrophs. We examined the utility of mitochondrial genomes for resolving contentious higher-order placements of mycoheterotrophic lineages in two test cases: monocots (focusing on Dioscoreales) and Ericaceae. We find Thismiaceae to be distantly related to Burmanniaceae in the monocot order Dioscoreales, conflicting with current classification schemes based on few gene data sets. We confirm that the unusual Afrothismia is related to Taccaceae-Thismiaceae, with a corresponding independent loss of photosynthesis. In Ericaceae we recovered the first well supported relationships among its five major lineages: mycoheterotrophic Ericaceae are not monophyletic, as pyroloids are inferred to be sister to core Ericaceae, and monotropoids to arbutoids. Genes recovered from mitochondrial genomes collectively resolved previously ambiguous mycoheterotroph higher-order relationships. We propose that mitochondrial genomic data should be considered in standardised gene panels for inferring overall plant phylogeny.
Collapse
Affiliation(s)
- Qianshi Lin
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 2Z9, Canada
| | - Thomas W A Braukmann
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 2Z9, Canada
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Juliana Lischka Sampaio Mayer
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Fábio Pinheiro
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Vincent S F T Merckx
- Naturalis Biodiversity Center, Vondellaan 55, 2332 AA, Leiden, the Netherlands
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, the Netherlands
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 2Z9, Canada
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| |
Collapse
|
17
|
Zhang C, Lin Q, Zhang J, Huang Z, Nan P, Li L, Song Z, Zhang W, Yang J, Wang Y. Comparing complete organelle genomes of holoparasitic Christisonia kwangtungensis (Orabanchaceae) with its close relatives: how different are they? BMC PLANT BIOLOGY 2022; 22:444. [PMID: 36114450 PMCID: PMC9482287 DOI: 10.1186/s12870-022-03814-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Orobanchaceae is the only flowering plant family with species from free-living nonparasite, hemi-parasite to holoparasite, making it an ideal system for studying the evolution of parasitism. However, both plastid and mitochondrial genome have been sequenced in only few parasitic species in Orobanchaceae. Therefore, further comparative study is wanted to investigate the impact of holoparasitism on organelle genomes evolution between close relatives. Here, we sequenced organelle genomes and transcriptome of holoparasitic Christisonia kwangtungensis and compared it with its closely related groups to analyze similarities and differences in adaption strategies to the holoparasitic lifestyle. RESULTS The plastid genome of C. kwangtungensis has undergone extensive pseudogenization and gene loss, but its reduction pattern is different from that of Aeginetia indica, the close relative of C. kwangtungensis. Similarly, the gene expression detected in the photosynthetic pathway of these two genera is different. In Orobanchaceae, holoparasites in Buchnereae have more plastid gene loss than Rhinantheae, which reflects their longer history of holoparasitism. Distinct from severe degradation of the plastome, protein-coding genes in the mitochondrial genome of C. kwangtungensis are relatively conserved. Interestingly, besides intracellularly transferred genes which are still retained in its plastid genome, we also found several horizontally transferred genes of plastid origin from diverse donors other than their current hosts in the mitochondrial genome, which probably indicate historical hosts. CONCLUSION Even though C. kwangtungensis and A. indica are closely related and share severe degradation of plastome, they adapt organelle genomes to the parasitic lifestyle in different ways. The difference between their gene loss and gene expression shows they ultimately lost photosynthetic genes but through different pathways. Our study exemplifies how parasites part company after achieving holoparasitism.
Collapse
Affiliation(s)
- Chi Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai, 200433 China
| | - Qianshi Lin
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 2Z9 Canada
| | - Jiayin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai, 200433 China
| | - Zihao Huang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai, 200433 China
| | - Peng Nan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai, 200433 China
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai, 200433 China
| | - Zhiping Song
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai, 200433 China
| | - Wenju Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai, 200433 China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai, 200433 China
| | - Yuguo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai, 200433 China
- Tibet University-Fudan University Joint Laboratory for Biodiversity and Global Change, College of Science, Tibet University, Lhasa, 850012 China
| |
Collapse
|
18
|
Mkala EM, Jost M, Wanke S, Ngarega BK, Hughes A, Mutinda ES, Waswa EN, Mwanzia VM, Oulo MA, Wanga VO, Ngumbau VM, Mwachala G, Hu GW, Wang QF. How vulnerable are holoparasitic plants with obligate hosts to negative climate change impacts? ECOL INFORM 2022; 69:101636. [DOI: https:/doi.org/10.1016/j.ecoinf.2022.101636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
|
19
|
Mkala EM, Jost M, Wanke S, Ngarega BK, Hughes A, Mutinda ES, Waswa EN, Mwanzia VM, Oulo MA, Wanga VO, Ngumbau VM, Mwachala G, Hu GW, Wang QF. How vulnerable are holoparasitic plants with obligate hosts to negative climate change impacts? ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2022.101636] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
20
|
Jost M, Naumann J, Bolin JF, Martel C, Rocamundi N, Cocucci AA, Lupton D, Neinhuis C, Wanke S. Structural plastome evolution in holoparasitic Hydnoraceae with special focus on inverted and direct repeats. Genome Biol Evol 2022; 14:6602284. [PMID: 35660863 PMCID: PMC9168662 DOI: 10.1093/gbe/evac077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 11/14/2022] Open
Abstract
Plastome condensation during adaptation to a heterotrophic lifestyle is generally well understood and lineage-independent models have been derived. However, understanding the evolutionary trajectories of comparatively old heterotrophic lineages, that are on the cusp of a minimal plastomes, is essential to complement and expand current knowledge. We study Hydnoraceae, one of the oldest and least investigated parasitic angiosperm lineages. Plastome comparative genomics, using seven out of eight known species of the genus Hydnora and three species of Prosopanche, reveal a high degree of structural similarity and shared gene content; contrasted by striking dissimilarities with respect to repeat content (inverted and direct repeats). We identified varying IR content and positions, likely resulting from multiple, independent evolutionary events and a direct repeat gain in Prosopanche. Considering different evolutionary trajectories and based on a fully resolved and supported species-level phylogenetic hypothesis, we describe three possible, distinct models to explain the Hydnoraceae plastome states. For comparative purposes we also report the first plastid genomes for the closely related autotrophic genera Lactoris (Lactoridaceae) and Thottea (Aristolochiaceae).
Collapse
Affiliation(s)
- Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Germany
| | - Julia Naumann
- Institut für Botanik, Technische Universität Dresden, Germany
| | | | - Carlos Martel
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK.,Instituto de Ciencias Ómicas y Biotecnología Aplicada, Pontificia Universidad Católica del Perú, Peru
| | - Nicolás Rocamundi
- Laboratorio de Ecología Evolutiva y Biología Floral, IMBIV, CONICET and Universidad Nacional de Córdoba, Argentina
| | - Andrea A Cocucci
- Laboratorio de Ecología Evolutiva y Biología Floral, IMBIV, CONICET and Universidad Nacional de Córdoba, Argentina
| | - Darach Lupton
- Oman Botanic Garden, Sultanate of Oman.,National Botanic Gardens, Glasnevin, Ireland
| | | | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Germany.,Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
21
|
Schelkunov MI, Nuraliev MS, Logacheva MD. Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives. PeerJ 2021; 9:e12106. [PMID: 34540375 PMCID: PMC8415285 DOI: 10.7717/peerj.12106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 08/11/2021] [Indexed: 12/02/2022] Open
Abstract
The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have revealed that plastid genomes of Balanophoraceae exhibit a number of interesting features, one of the most prominent of those being a highly elevated AT content of nearly 90%. Additionally, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is an order of magnitude greater than that of their photosynthetic relatives without signs of relaxed selection. Currently, there are no definitive explanations for these features. Given these unusual features, we hypothesised that the nuclear genomes of Balanophoraceae may also provide valuable information in regard to understanding the evolution of non-photosynthetic plants. To gain insight into these genomes, in the present study we analysed the transcriptomes of two Balanophoraceae species (Rhopalocnemis phalloides and Balanophora fungosa) and compared them to the transcriptomes of their close photosynthetic relatives (Daenikera sp., Dendropemon caribaeus, and Malania oleifera). Our analysis revealed that the AT content of the nuclear genes of Balanophoraceae did not markedly differ from that of the photosynthetic relatives. The nucleotide substitution rate in the genes of Balanophoraceae is, for an unknown reason, several-fold larger than in the genes of photosynthetic Santalales; however, the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in the Balanophoraceae family members. Additionally, we did not observe transcripts of several genes whose products function in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.
Collapse
Affiliation(s)
- Mikhail I Schelkunov
- Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute for Information Transmission Problems, Moscow, Russia
| | - Maxim S Nuraliev
- Faculty of Biology, Moscow State University, Moscow, Russia.,Joint Russian-Vietnamese Tropical Scientific and Technological Center, Hanoi, Vietnam
| | | |
Collapse
|
22
|
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.
Collapse
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:
| |
Collapse
|
23
|
Ceriotti LF, Roulet ME, Sanchez-Puerta MV. Plastomes in the holoparasitic family Balanophoraceae: Extremely high AT content, severe gene content reduction, and two independent genetic code changes. Mol Phylogenet Evol 2021; 162:107208. [PMID: 34029719 DOI: 10.1016/j.ympev.2021.107208] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 05/11/2021] [Accepted: 05/19/2021] [Indexed: 12/29/2022]
Abstract
The transition to a heterotrophic lifestyle in angiosperms is characterized by convergent evolutionary changes. Plastid genome remodeling includes dramatic functional and physical reductions with the highest degrees observed in fully heterotrophic plants. Genes related to photosynthesis are generally absent or pseudogenized, while a few genes related to other metabolic processes that take place within the plastid are almost invariably maintained. The family Balanophoraceae consists of root holoparasites that present reduced plastid genomes with an extraordinarily elevated AT content and the single genetic code change ever documented in land plant plastomes (the stop codon TAG now codes for tryptophan). Here, we studied the plastomes of Lophophytum leandri and Ombrophytum subterraneum (Balanophoraceae) that showed the remarkable absence of the gene trnE, a highly biased nucleotide composition, and an independent genetic code change (the standard stop codon TGA codes for tryptophan). This is the second genetic code change identified in land plant plastomes. Analysis of the transcriptome of Lophophytum indicated that the entire C5 pathway typical of plants is conserved despite the lack of trnE in its plastome. A hypothetical model of plastome evolution in the Balanophoraceae is presented.
Collapse
Affiliation(s)
- Luis Federico Ceriotti
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB Chacras de Coria, 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, M5528AHB Chacras de Coria, Argentina
| | - M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB Chacras de Coria, Argentina; Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA Mendoza, Argentina.
| |
Collapse
|
24
|
Jost M, Samain MS, Marques I, Graham SW, Wanke S. Discordant Phylogenomic Placement of Hydnoraceae and Lactoridaceae Within Piperales Using Data From All Three Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:642598. [PMID: 33912209 PMCID: PMC8072514 DOI: 10.3389/fpls.2021.642598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/17/2021] [Indexed: 05/08/2023]
Abstract
Phylogenetic relationships within the magnoliid order Piperales have been studied extensively, yet the relationships of the monotypic family Lactoridaceae and the holoparasitic Hydnoraceae to the remainder of the order remain a matter of debate. Since the first confident molecular phylogenetic placement of Hydnoraceae among Piperales, different studies have recovered various contradictory topologies. Most phylogenetic hypotheses were inferred using only a few loci and have had incomplete taxon sampling at the genus level. Based on these results and an online survey of taxonomic opinion, the Angiosperm Phylogeny Group lumped both Hydnoraceae and Lactoridaceae in Aristolochiaceae; however, the latter family continues to have unclear relationships to the aforementioned taxa. Here we present extensive phylogenomic tree reconstructions based on up to 137 loci from all three subcellular genomes for all genera of Piperales. We infer relationships based on a variety of phylogenetic methods, explore instances of phylogenomic discordance between the subcellular genomes, and test alternative topologies. Consistent with these phylogenomic results and a consideration of the principles of phylogenetic classification, we propose to exclude Hydnoraceae and Lactoridaceae from the broad circumscription of Aristolochiaceae, and instead favor recognition of four monophyletic and morphologically well circumscribed families in the perianth-bearing Piperales: Aristolochiaceae, Asaraceae, Hydnoraceae, and Lactoridaceae, with a total of six families in the order.
Collapse
Affiliation(s)
- Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Marie-Stéphanie Samain
- Instituto de Ecología, A.C., Red de Diversidad Biológica del Occidente Mexicano, Pátzcuaro, Mexico
| | - Isabel Marques
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- Plant-Environment Interactions and Biodiversity Lab, Forest Research Centre, Instituto Superior de Agronomia, Universidadede Lisboa, Lisbon, Portugal
| | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| |
Collapse
|
25
|
Mkala EM, Mutungi MM, Mutinda ES, Oulo MA, Wanga VO, Mwachala G, Hu GW. Understanding the Ethnobotany, Chemistry, Pharmacology, and Distribution of Genus Hydnora (Aristolochiaceae). PLANTS (BASEL, SWITZERLAND) 2021; 10:494. [PMID: 33807757 PMCID: PMC8001087 DOI: 10.3390/plants10030494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022]
Abstract
The genus Hydnora (Hydnoraceae) is one of the basal angiosperms in the order Piperales, found in the semi-arid regions of Africa, and the Southern Arabian Peninsula. Plants in this genus play essential roles in communities around the world as revealed by various studies. Currently, there are eight species of the genus Hydnora; seven in Africa and one in the Arabian Peninsula. Notably, Hydnora abyssinica A.Br. and Hydnora africana Thunb. are widely distributed compared to other species. They are widely used for their medicinal and nutritional values. The information on ethnobotany, chemistry, pharmacology, and distribution of genus Hydnora was gathered using phytochemical and ethnobotanical books, electronic sources, and published articles. Preliminary phytochemical screening shows that flavonoids, phenolics, proanthocyanidins, and tannins are the main compounds in H. abyssinica and H. africana. Furthermore, 11 compounds have been isolated from H. abyssinica. The biological activities of H. abyssinica and H. africana have been reported. They include antibacterial, antiproliferative, antioxidant, antidiarrhea, and antifungal potentials. Despite the Hydnora species being practiced in ancient folkloric medicine, their traditional uses and pharmacological value are poorly documented. Based on the available information on ethnobotany, phytochemistry, pharmacology, and distribution, we aim to provide research gaps and challenges for a better understanding of this genus. This may be resourceful in the development of effective phytomedicines, and aid in conservation. The available studies on this genus on some aspects such as phytochemistry, pharmacological activities, and distribution are under-reported hence the need for further research.
Collapse
Affiliation(s)
- Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.M.M.); (M.M.M.); (E.S.M.); (M.A.O.); (V.O.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- East African Herbarium, National Museums of Kenya, P.O. Box 451660-0100 Nairobi, Kenya;
| | - Moses Mutuse Mutungi
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.M.M.); (M.M.M.); (E.S.M.); (M.A.O.); (V.O.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Elizabeth Syowai Mutinda
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.M.M.); (M.M.M.); (E.S.M.); (M.A.O.); (V.O.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Millicent Akinyi Oulo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.M.M.); (M.M.M.); (E.S.M.); (M.A.O.); (V.O.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.M.M.); (M.M.M.); (E.S.M.); (M.A.O.); (V.O.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Geoffrey Mwachala
- East African Herbarium, National Museums of Kenya, P.O. Box 451660-0100 Nairobi, Kenya;
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.M.M.); (M.M.M.); (E.S.M.); (M.A.O.); (V.O.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
26
|
Allio R, Nabholz B, Wanke S, Chomicki G, Pérez-Escobar OA, Cotton AM, Clamens AL, Kergoat GJ, Sperling FAH, Condamine FL. Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants. Nat Commun 2021; 12:354. [PMID: 33441560 PMCID: PMC7806994 DOI: 10.1038/s41467-020-20507-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/03/2020] [Indexed: 01/29/2023] Open
Abstract
The mega-diversity of herbivorous insects is attributed to their co-evolutionary associations with plants. Despite abundant studies on insect-plant interactions, we do not know whether host-plant shifts have impacted both genomic adaptation and species diversification over geological times. We show that the antagonistic insect-plant interaction between swallowtail butterflies and the highly toxic birthworts began 55 million years ago in Beringia, followed by several major ancient host-plant shifts. This evolutionary framework provides a valuable opportunity for repeated tests of genomic signatures of macroevolutionary changes and estimation of diversification rates across their phylogeny. We find that host-plant shifts in butterflies are associated with both genome-wide adaptive molecular evolution (more genes under positive selection) and repeated bursts of speciation rates, contributing to an increase in global diversification through time. Our study links ecological changes, genome-wide adaptations and macroevolutionary consequences, lending support to the importance of ecological interactions as evolutionary drivers over long time periods.
Collapse
Affiliation(s)
- Rémi Allio
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
| | - Benoit Nabholz
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany
| | - Guillaume Chomicki
- Department of Bioscience, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | | | - Adam M Cotton
- 86/2 Moo 5, Tambon Nong Kwai, Hang Dong, Chiang Mai, Thailand
| | - Anne-Laure Clamens
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | - Gaël J Kergoat
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, AB, Canada
| | - Fabien L Condamine
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, AB, Canada.
| |
Collapse
|
27
|
Yuan C, Sha X, Xiong M, Zhong W, Wei Y, Li M, Tao S, Mou F, Peng F, Zhang C. Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications. Sci Rep 2021; 11:988. [PMID: 33441833 PMCID: PMC7806627 DOI: 10.1038/s41598-020-80225-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/16/2020] [Indexed: 12/02/2022] Open
Abstract
Ligusticum L., one of the largest members in Apiaceae, encompasses medicinally important plants, the taxonomic statuses of which have been proved to be difficult to resolve. In the current study, the complete chloroplast genomes of seven crucial plants of the best-known herbs in Ligusticum were presented. The seven genomes ranged from 148,275 to 148,564 bp in length with a highly conserved gene content, gene order and genomic arrangement. A shared dramatic decrease in genome size resulted from a lineage-specific inverted repeat (IR) contraction, which could potentially be a promising diagnostic character for taxonomic investigation of Ligusticum, was discovered, without affecting the synonymous rate. Although a higher variability was uncovered in hotspot divergence regions that were unevenly distributed across the chloroplast genome, a concatenated strategy for rapid species identification was proposed because separate fragments inadequately provided variation for fine resolution. Phylogenetic inference using plastid genome-scale data produced a concordant topology receiving a robust support value, which revealed that L. chuanxiong had a closer relationship with L. jeholense than L. sinense, and L. sinense cv. Fuxiong had a closer relationship to L. sinense than L. chuanxiong, for the first time. Our results not only furnish concrete evidence for clarifying Ligusticum taxonomy but also provide a solid foundation for further pharmaphylogenetic investigation.
Collapse
Affiliation(s)
- Can Yuan
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Xiufen Sha
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Miao Xiong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Wenjuan Zhong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Yu Wei
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mingqian Li
- Cancer Institute of Integrated Traditional Chinese and Western Medicine, Zhejiang Academy of Traditional Chinese Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, 310012, Zhejiang, China
| | - Shan Tao
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China
| | - Fangsheng Mou
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China
| | - Fang Peng
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China. .,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China.
| | - Chao Zhang
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China. .,Comprehensive Experimental Station of Cheng Du, Chinese Materia Medica of China Agriculture Research System, Chengdu, 610300, China.
| |
Collapse
|
28
|
Wei N, Pérez-Escobar OA, Musili PM, Huang WC, Yang JB, Hu AQ, Hu GW, Grace OM, Wang QF. Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region. FRONTIERS IN PLANT SCIENCE 2021; 12:712064. [PMID: 34421963 PMCID: PMC8372406 DOI: 10.3389/fpls.2021.712064] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/05/2021] [Indexed: 05/09/2023]
Abstract
With c. 2,000 species, Euphorbia is one of the largest angiosperm genera, yet a lack of chloroplast genome (plastome) resources impedes a better understanding of its evolution. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, of which 15 were newly sequenced. Phylogenomic and comparative analyses of 22 plastome sequences from all four recognized subgenera within Euphorbia revealed that plastome length in Euphorbia is labile, presenting a range of variation c. 42 kb. Large-scale expansions of the inverted repeat (IR) region were identified, and at the extreme opposite, the near-complete loss of the IR region (with only 355 bp left) was detected for the first time in Euphorbiaceae. Other structural variations, including gene inversion and duplication, and gene loss/pseudogenization, were also observed. We screened the most promising molecular markers from both intergenic and coding regions for phylogeny-based utilities, and estimated maximum likelihood and Bayesian phylogenies from four datasets including whole plastome sequences. The monophyly of Euphorbia is supported, and its four subgenera are recovered in a successive sister relationship. Our study constitutes the first comprehensive investigation on the plastome structural variation in Euphorbia and it provides resources for phylogenetic research in the genus, facilitating further studies on its taxonomy, evolution, and conservation.
Collapse
Affiliation(s)
- Neng Wei
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Paul M. Musili
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Wei-Chang Huang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ai-Qun Hu
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Olwen M. Grace
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- *Correspondence: Olwen M. Grace,
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Qing-Feng Wang,
| |
Collapse
|
29
|
Guo X, Liu C, Wang H, Zhang G, Yan H, Jin L, Su W, Ji Y. The complete plastomes of two flowering epiparasites (Phacellaria glomerata and P. compressa): Gene content, organization, and plastome degradation. Genomics 2020; 113:447-455. [PMID: 33370586 DOI: 10.1016/j.ygeno.2020.12.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 03/10/2020] [Accepted: 12/22/2020] [Indexed: 11/28/2022]
Abstract
A plant parasite obligately parasitizing another plant parasite is referred to as epiparasite, which is extremely rare in angiosperms, and their complete plastome sequences have not been characterized to date. In this study, the complete plastomes of two flowering epiparasites: Phacellaria compressa and P. glomerata (Amphorogynaceae, Santalales) were sequenced. The plastomes of both species are of similar size, structure, gene content, and arrangement of genes to other hemiparasites in Santalales. Their plastomes were characterized by the functional loss of plastid-encoded NAD(P)H-dehydrogenase and infA genes, which strongly coincides with the general pattern of plastome degradation observed in Santalales hemiparasites. Our study demonstrates that the relatively higher level of nutritional reliance on the host plants and the reduced vegetative bodies of P. compressa and P. glomerata do not appear to cause any unique plastome degradation compared with their closely related hemiparasites.
Collapse
Affiliation(s)
- Xiaorong Guo
- Institute of Ecology and Geobotany, Yunnan University, Kunming, Yunnan, China
| | - Changkun Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Guangfei Zhang
- Institute of Ecology and Geobotany, Yunnan University, Kunming, Yunnan, China
| | - Hanjing Yan
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Lei Jin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China; School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Wenhua Su
- Institute of Ecology and Geobotany, Yunnan University, Kunming, Yunnan, China
| | - Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China; Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
| |
Collapse
|
30
|
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.
Collapse
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.)
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
Preuss M, Verbruggen H, Zuccarello GC. The Organelle Genomes in the Photosynthetic Red Algal Parasite Pterocladiophila hemisphaerica (Florideophyceae, Rhodophyta) Have Elevated Substitution Rates and Extreme Gene Loss in the Plastid Genome. JOURNAL OF PHYCOLOGY 2020; 56:1006-1018. [PMID: 32215918 DOI: 10.1111/jpy.12996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 03/06/2020] [Indexed: 06/10/2023]
Abstract
Comparative organelle genome studies of parasites can highlight genetic changes that occur during the transition from a free-living to a parasitic state. Our study focuses on a poorly studied group of red algal parasites, which are often closely related to their red algal hosts and from which they presumably evolved. Most of these parasites are pigmented and some show photosynthetic capacity. Here, we assembled and annotated the complete organelle genomes of the photosynthetic red algal parasite, Pterocladiophila hemisphaerica. The plastid genome is the smallest known red algal plastid genome at 68,701 bp. The plastid genome has many genes missing, including all photosynthesis-related genes. In contrast, the mitochondrial genome is similar in architecture to that of other free-living red algae. Both organelle genomes show elevated mutation rates and significant changes in patterns of selection, measured as dN/dS ratios. This caused phylogenetic analyses, even of multiple aligned proteins, to be unresolved or give contradictory relationships. Full plastid datasets interfered by selected best gene evolution models showed the supported relationship of P. hemisphaerica within the Ceramiales, but the parasite was grouped with support as sister to the Gracilariales when interfered under the GHOST model. Nuclear rDNA showed a supported grouping of the parasite within a clade containing several red algal orders including the Gelidiales. This photosynthetic parasite, which is unable to photosynthesize with its own plastid due to the total loss of all photosynthesis genes, raises intriguing questions on parasite-host organelle genome capabilities and interactions.
Collapse
Affiliation(s)
- Maren Preuss
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Giuseppe C Zuccarello
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| |
Collapse
|
33
|
Chen X, Fang D, Wu C, Liu B, Liu Y, Sahu SK, Song B, Yang S, Yang T, Wei J, Wang X, Zhang W, Xu Q, Wang H, Yuan L, Liao X, Chen L, Chen Z, Yuan F, Chang Y, Lu L, Yang H, Wang J, Xu X, Liu X, Wicke S, Liu H. Comparative Plastome Analysis of Root- and Stem-Feeding Parasites of Santalales Untangle the Footprints of Feeding Mode and Lifestyle Transitions. Genome Biol Evol 2020; 12:3663-3676. [PMID: 31845987 PMCID: PMC6953812 DOI: 10.1093/gbe/evz271] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2019] [Indexed: 12/17/2022] Open
Abstract
In plants, parasitism triggers the reductive evolution of plastid genomes (plastomes). To disentangle the molecular evolutionary associations between feeding on other plants below- or aboveground and general transitions from facultative to obligate parasitism, we analyzed 34 complete plastomes of autotrophic, root- and stem-feeding hemiparasitic, and holoparasitic Santalales. We observed inexplicable losses of housekeeping genes and tRNAs in hemiparasites and dramatic genomic reconfiguration in holoparasitic Balanophoraceae, whose plastomes have exceptionally low GC contents. Genomic changes are related primarily to the evolution of hemi- or holoparasitism, whereas the transition from a root- to a stem-feeding mode plays no major role. In contrast, the rate of molecular evolution accelerates in a stepwise manner from autotrophs to root- and then stem-feeding parasites. Already the ancestral transition to root-parasitism coincides with a relaxation of selection in plastomes. Another significant selectional shift in plastid genes occurs as stem-feeders evolve, suggesting that this derived form coincides with trophic specialization despite the retention of photosynthetic capacity. Parasitic Santalales fill a gap in our understanding of parasitism-associated plastome degeneration. We reveal that lifestyle-genome associations unfold interdependently over trophic specialization and feeding mode transitions, where holoparasitic Balanophoraceae provide a system for exploring the functional realms of plastomes.
Collapse
Affiliation(s)
- Xiaoli Chen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Dongming Fang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Chenyu Wu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- BGI-Shenzhen, Shenzhen, China.,Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Sunil Kumar Sahu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Bo Song
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shuai Yang
- BGI-Shenzhen, Shenzhen, China.,School of Basic Medical, Qingdao University, China
| | - Tuo Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jinpu Wei
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xuebing Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Wen Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Qiwu Xu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Huafeng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Langxing Yuan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Xuezhu Liao
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lipeng Chen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ziqiang Chen
- College of Chinese Medicine Materials, Jilin Agricultural University, China
| | - Fu Yuan
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yue Chang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lihua Lu
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Germany†These authors contributed equally to this work
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| |
Collapse
|
34
|
Guo X, Liu C, Zhang G, Su W, Landis JB, Zhang X, Wang H, Ji Y. The Complete Plastomes of Five Hemiparasitic Plants ( Osyris wightiana, Pyrularia edulis, Santalum album, Viscum liquidambaricolum, and V. ovalifolium): Comparative and Evolutionary Analyses Within Santalales. Front Genet 2020; 11:597. [PMID: 32612639 PMCID: PMC7308561 DOI: 10.3389/fgene.2020.00597] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 05/18/2020] [Indexed: 11/27/2022] Open
Abstract
Most species of Santalales (the sandalwood order) are hemiparasites, including both facultative and obligate hemiparasites. Despite its rich diversity, only a small fraction of the species in the sandalwood order have sequenced plastomes. The evolution of parasitism-associated plastome reduction in Santalales remains under-studied. Here, we report the complete plastomes of three facultative hemiparasites (Pyrularia edulis, Cervantesiaceae; Osyris wightiana, and Santalum album, Santalaceae), and two obligate hemiparasites (Viscum liquidambaricolum and Viscum ovalifolium, Viscaceae). Coupled with publicly available data, we investigated the dynamics of plastome degradation in Santalales hemiparasites. Our results indicate that these hemiparasites can be characterized by various degrees of plastome downsizing, structural rearrangement, and gene loss. The loss or pseudogenization of ndh genes was commonly observed in Santalales hemiparasites, which may be correlated to the lifestyle shift from photoautotroph to hemiparasitism. However, the obligate hemiparasites did not exhibit a consistently higher level of gene loss or pseudogenization compared to facultative hemiparasites, which suggests that the degree of plastome reduction is not correlated with the trophic level facultative or obligate hemiparasitism. Instead, closely related taxa tend to possess highly similar plastome size, structure, and gene content. This implies the parasitism-associated plastome degradation in Santalales may evolve in a lineage-specific manner.
Collapse
Affiliation(s)
- Xiaorong Guo
- Institute of Ecology and Geobotany, Yunnan University, Kunming, China
| | - Changkun Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Guangfei Zhang
- Institute of Ecology and Geobotany, Yunnan University, Kunming, China
| | - Wenhua Su
- Institute of Ecology and Geobotany, Yunnan University, Kunming, China
| | - Jacob B. Landis
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
35
|
Li Z, Ma X, Wen Y, Chen S, Jiang Y, Jin X. Plastome of the mycoheterotrophic eudicot Exacum paucisquama (Gentianaceae) exhibits extensive gene loss and a highly expanded inverted repeat region. PeerJ 2020; 8:e9157. [PMID: 32551191 PMCID: PMC7292021 DOI: 10.7717/peerj.9157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 04/18/2020] [Indexed: 11/20/2022] Open
Abstract
Mycoheterotrophic plants are highly specialized species able to acquire organic carbon from symbiotic fungi, with relaxed dependence on photosynthesis for carbon fixation. The relaxation of the functional constraint of photosynthesis and thereby the relaxed selective pressure on functional photosynthetic genes usually lead to substantial gene loss and a highly degraded plastid genome in heterotrophs. In this study, we sequenced and analyzed the plastome of the eudicot Exacum paucisquama, providing the first plastid genome of a mycoheterotroph in the family Gentianaceae to date. The E. paucisquama plastome was 44,028 bp in length, which is much smaller than the plastomes of autotrophic eudicots. Although the E. paucisquama plastome had a quadripartite structure, a distinct boundary shift was observed in comparison with the plastomes of other eudicots. We detected extensive gene loss and only 21 putative functional genes (15 protein-coding genes, four rRNA genes and two tRNA genes). Our results provide valuable information for comparative evolutionary analyses of plastomes of heterotrophic species belonging to different phylogenetic groups.
Collapse
Affiliation(s)
- Zhanghai Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao Ma
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yi Wen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sisi Chen
- Nanchang University, Nanchang, China
| | - Yan Jiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences (CAS-SEABRI), Xishuangbanna, China
| |
Collapse
|
36
|
Chen J, Yu R, Dai J, Liu Y, Zhou R. The loss of photosynthesis pathway and genomic locations of the lost plastid genes in a holoparasitic plant Aeginetia indica. BMC PLANT BIOLOGY 2020; 20:199. [PMID: 32384868 PMCID: PMC7206726 DOI: 10.1186/s12870-020-02415-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 04/29/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND With three origins of holoparasitism, Orobanchaceae provides an ideal system to study the evolution of holoparasitic lifestyle in plants. The evolution of holoparasitism can be revealed by plastid genome degradation and coordinated changes in the nuclear genome, since holoparasitic plants lost the capability of photosynthesis. Among the three clades with holoparasitic plants in Orobanchaceae, only Clade VI has no available plastid genome sequences for holoparasitic plants. In this study, we sequenced the plastome and transcriptome of Aeginetia indica, a holoparasitic plant in Clade VI of Orobanchaceae, to study its plastome evolution and the corresponding changes in the nuclear genome as a response of the loss of photosynthetic function. RESULTS The plastome of A. indica is reduced to 86,212 bp in size, and almost all photosynthesis-related genes were lost. Massive fragments of the lost plastid genes were transferred into the mitochondrial and/or nuclear genomes. These fragments could not be detected in its transcriptomes, suggesting that they were non-functional. Most protein coding genes in the plastome showed the signal of relaxation of purifying selection. Plastome and transcriptome analyses indicated that the photosynthesis pathway is completely lost, and that the porphyrin and chlorophyll metabolism pathway is partially retained, although chlorophyll synthesis is not possible. CONCLUSIONS Our study suggests the loss of photosynthesis-related functions in A. indica in both the nuclear and plastid genomes. The lost plastid genes are transferred into its nuclear and/or mitochondrial genomes, and exist in very small fragments with no expression and are thus non-functional. The Aeginetia indica plastome also provides a resource for comparative studies on the repeated evolution of holoparasitism in Orobanchaceae.
Collapse
Affiliation(s)
- Jingfang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, 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, 510275, China
| | - Jinhong Dai
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, 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, 510275, 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, 510275, China.
| |
Collapse
|
37
|
Oyebanji O, Zhang R, Chen SY, Yi TS. New Insights Into the Plastome Evolution of the Millettioid/Phaseoloid Clade (Papilionoideae, Leguminosae). FRONTIERS IN PLANT SCIENCE 2020; 11:151. [PMID: 32210983 PMCID: PMC7076112 DOI: 10.3389/fpls.2020.00151] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/31/2020] [Indexed: 05/21/2023]
Abstract
The Millettioid/Phaseoloid (MP) clade from the subfamily Papilionoideae (Leguminosae) consists of six tribes and ca. 3,000 species. Previous studies have revealed some plastome structural variations (PSVs) within this clade. However, many deep evolutionary relationships within the clade remain unresolved. Due to limited taxon sampling and few genetic markers in previous studies, our understanding of the evolutionary history of this clade is limited. To address this issue, we sampled 43 plastomes (35 newly sequenced) representing all the six tribes of the MP clade to examine genomic structural variations and phylogenetic relationships. Plastomes of the species from the MP clade were typically quadripartite (size ranged from 140,029 to 160,040 bp) and contained 109-111 unique genes. We revealed four independent gene losses (ndhF, psbI, rps16, and trnS-GCU), multiple IR-SC boundary shifts, and six inversions in the tribes Desmodieae, Millettieae, and Phaseoleae. Plastomes of the species from the MP clade have experienced significant variations which provide valuable information on the evolution of the clade. Plastid phylogenomic analyses using Maximum Likelihood and Bayesian methods yielded a well-resolved phylogeny at the tribal and generic levels within the MP clade. This result indicates that plastome data is useful and reliable data for resolving the evolutionary relationships of the MP clade. This study provides new insights into the phylogenetic relationships and PSVs within this clade.
Collapse
Affiliation(s)
- Oyetola Oyebanji
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Si-Yun Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
38
|
The First Plastid Genome of the Holoparasitic Genus Prosopanche (Hydnoraceae). PLANTS 2020; 9:plants9030306. [PMID: 32121567 PMCID: PMC7154897 DOI: 10.3390/plants9030306] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 02/07/2023]
Abstract
Plastomes of parasitic and mycoheterotrophic plants show different degrees of reduction depending on the plants’ level of heterotrophy and host dependence in comparison to photoautotrophic sister species, and the amount of time since heterotrophic dependence was established. In all but the most recent heterotrophic lineages, this reduction involves substantial decrease in genome size and gene content and sometimes alterations of genome structure. Here, we present the first plastid genome of the holoparasitic genus Prosopanche, which shows clear signs of functionality. The plastome of Prosopanche americana has a length of 28,191 bp and contains only 24 unique genes, i.e., 14 ribosomal protein genes, four ribosomal RNA genes, five genes coding for tRNAs and three genes with other or unknown function (accD, ycf1, ycf2). The inverted repeat has been lost. Despite the split of Prosopanche and Hydnora about 54 MYA ago, the level of genome reduction is strikingly congruent between the two holoparasites although highly dissimilar nucleotide sequences are observed. Our results lead to two possible evolutionary scenarios that will be tested in the future with a larger sampling: 1) a Hydnoraceae plastome, similar to those of Hydnora and Prosopanche today, existed already in the most recent common ancestor and has not changed much with respect to gene content and structure, or 2) the genome similarities we observe today are the result of two independent evolutionary trajectories leading to almost the same endpoint. The first hypothesis would be most parsimonious whereas the second would point to taxon dependent essential gene sets for plants released from photosynthetic constraints.
Collapse
|
39
|
Liu X, Fu W, Tang Y, Zhang W, Song Z, Li L, Yang J, Ma H, Yang J, Zhou C, Davis CC, Wang Y. Diverse trajectories of plastome degradation in holoparasitic Cistanche and genomic location of the lost plastid genes. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:877-892. [PMID: 31639183 DOI: 10.1093/jxb/erz456] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
The plastid genomes (plastomes) of non-photosynthetic plants generally undergo gene loss and pseudogenization. Despite massive plastomes reported in different parasitism types of the broomrape family (Orobanchaceae), more plastomes representing different degradation patterns in a single genus are expected to be explored. Here, we sequence and assemble the complete plastomes of three holoparasitic Cistanche species (C. salsa, C. mongolica, and C. sinensis) and compare them with the available plastomes of Orobanchaceae. We identified that the diverse degradation trajectories under purifying selection existed among three Cistanche clades, showing obvious size differences in the entire plastome, long single copy region, and non-coding region, and different patterns of the retention/loss of functional genes. With few exceptions of putatively functional genes, massive plastid fragments, which have been lost and transferred into the mitochondrial or nuclear genomes, are non-functional. In contrast to the equivalents of the Orobanche species, some plastid-derived genes with diverse genomic locations are found in Cistanche. The early and initially diverged clades in different genera such as Cistanche and Aphyllon possess obvious patterns of plastome degradation, suggesting that such key lineages should be considered prior to comparative analysis of plastome evolution, especially in the same genus.
Collapse
Affiliation(s)
- Xiaoqing Liu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Weirui Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Yiwei Tang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Wenju Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhiping Song
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Plant Biology, Center for Evolutionary Biology, Fudan University, Shanghai, China
- Department of Biology, Institute of Molecular Evolutionary Genetics, and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Jianhua Yang
- College of Pharmacy, The First Affiliated Hospital, Xinjiang Medical University, Urumqi, China
| | - Chan Zhou
- Department of Population and Quantitative Health Sciences, Massachusetts General Hospital, 55 Lake Ave, North Worcester, MA, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA, USA
| | - Yuguo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| |
Collapse
|
40
|
Petersen G, Darby H, Lam VKY, Pedersen HÆ, Merckx VSFT, Zervas A, Seberg O, Graham SW. Mycoheterotrophic Epirixanthes (Polygalaceae) has a typical angiosperm mitogenome but unorthodox plastid genomes. ANNALS OF BOTANY 2019; 124:791-807. [PMID: 31346602 PMCID: PMC6868387 DOI: 10.1093/aob/mcz114] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 07/24/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Fully mycoheterotrophic plants derive carbon and other nutrients from root-associated fungi and have lost the ability to photosynthesize. While mycoheterotroph plastomes are often degraded compared with green plants, the effect of this unusual symbiosis on mitochondrial genome evolution is unknown. By providing the first complete organelle genome data from Polygalaceae, one of only three eudicot families that developed mycoheterotrophy, we explore how both organellar genomes evolved after loss of photosynthesis. METHODS We sequenced and assembled four complete plastid genomes and a mitochondrial genome from species of Polygalaceae, focusing on non-photosynthetic Epirixanthes. We compared these genomes with those of other mycoheterotroph and parasitic plant lineages, and assessed whether organelle genes in Epirixanthes experienced relaxed or intensified selection compared with autotrophic relatives. KEY RESULTS Plastomes of two species of Epirixanthes have become substantially degraded compared with that of autotrophic Polygala. Although the lack of photosynthesis is presumably homologous in the genus, the surveyed Epirixanthes species have marked differences in terms of plastome size, structural rearrangements, gene content and substitution rates. Remarkably, both apparently replaced a canonical plastid inverted repeat with large directly repeated sequences. The mitogenome of E. elongata incorporated a considerable number of fossilized plastid genes, by intracellular transfer from an ancestor with a less degraded plastome. Both plastid and mitochondrial genes in E. elongata have increased substitution rates, but the plastid genes of E. pallida do not. Despite this, both species have similar selection patterns operating on plastid housekeeping genes. CONCLUSIONS Plastome evolution largely fits with patterns of gene degradation seen in other heterotrophic plants, but includes highly unusual directly duplicated regions. The causes of rate elevation in the sequenced Epirixanthes mitogenome and of rate differences in plastomes of related mycoheterotrophic species are not currently understood.
Collapse
Affiliation(s)
- G Petersen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- For correspondence. E-mail:
| | - H Darby
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - V K Y Lam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - H Æ Pedersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - A Zervas
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Department of Environmental Science, Aarhus University, Denmark
| | - O Seberg
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - S W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
41
|
Li X, Qian X, Yao G, Zhao Z, Zhang D. Plastome of mycoheterotrophic Burmannia itoana Mak. (Burmanniaceae) exhibits extensive degradation and distinct rearrangements. PeerJ 2019; 7:e7787. [PMID: 31608171 PMCID: PMC6788436 DOI: 10.7717/peerj.7787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/29/2019] [Indexed: 02/03/2023] Open
Abstract
Plastomes of heterotrophs went through varying degrees of degradation along with the transition from autotrophic to heterotrophic lifestyle. Here, we identified the plastome of mycoheterotrophic species Burmannia itoana and compared it with those of its reported relatives including three autotrophs and one heterotroph (Thismia tentaculata) in Dioscoreales. B. itoana yields a rampantly degraded plastome reduced in size and gene numbers at the advanced stages of degradation. Its length is 44,463 bp with a quadripartite structure. B. itoana plastome contains 33 tentatively functional genes and six tentative pseudogenes, including several unusually retained genes. These unusual retention suggest that the inverted repeats (IRs) regions and possibility of being compensated may prolong retention of genes in plastome at the advanced stage of degradation. Otherwise, six rearrangements including four inversions (Inv1/Inv2/Inv3/Inv4) and two translocations (Trans1/Trans2) were detected in B. itoana plastome vs. its autotrophic relative B. disticha. We speculate that Inv1 may be mediated by recombination of distinct tRNA genes, while Inv2 is likely consequence of extreme gene losses due to the shift to heterotrophic lifestyle. The other four rearrangements involved in IRs and small single copy region may attribute to multiple waves of IRs and overlapping inversions. Our study fills the gap of knowledge about plastomes of heterotroph in Burmannia and provides a new evidence for the convergent degradation patterns of plastomes en route to heterotrophic lifestyle.
Collapse
Affiliation(s)
- Xiaojuan Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin Qian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Yao
- South China Limestone Plants Research Center, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Zhongtao Zhao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
42
|
Qu XJ, Fan SJ, Wicke S, Yi TS. Plastome Reduction in the Only Parasitic Gymnosperm Parasitaxus Is Due to Losses of Photosynthesis but Not Housekeeping Genes and Apparently Involves the Secondary Gain of a Large Inverted Repeat. Genome Biol Evol 2019; 11:2789-2796. [PMID: 31504501 PMCID: PMC6786476 DOI: 10.1093/gbe/evz187] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2019] [Indexed: 02/06/2023] Open
Abstract
Plastid genomes (plastomes) of parasitic plants undergo dramatic reductions as the need for photosynthesis relaxes. Here, we report the plastome of the only known heterotrophic gymnosperm Parasitaxus usta (Podocarpaceae). With 68 unique genes, of which 33 encode proteins, 31 tRNAs, and four rRNAs in a plastome of 85.3-kb length, Parasitaxus has both the smallest and the functionally least capable plastid genome of gymnosperms. Although the heterotroph retains chlorophyll, all genes for photosynthesis are physically or functionally lost, making photosynthetic energy gain impossible. The pseudogenization of the three plastome-encoded light-independent chlorophyll biosynthesis genes chlB, chlL, and chlN implies that Parasitaxus relies on either only the light-dependent chlorophyll biosynthesis pathway or another regulation system. Nesting within a group of gymnosperms known for the absence of the large inverted repeat regions (IRs), another unusual feature of the Parasitaxus plastome is the existence of a 9,256-bp long IR. Its short length and a gene composition that completely differs from those of IR-containing gymnosperms together suggest a regain of this critical, plastome structure-stabilizing feature. In sum, our findings highlight the particular path of lifestyle-associated reductive plastome evolution, where structural features might provide additional cues of a continued selection for plastome maintenance.
Collapse
Affiliation(s)
- Xiao-Jian Qu
- Key Lab of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Shou-Jin Fan
- Key Lab of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, China
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Germany
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| |
Collapse
|
43
|
Schelkunov MI, Nuraliev MS, Logacheva MD. Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known. PeerJ 2019; 7:e7500. [PMID: 31565552 PMCID: PMC6745192 DOI: 10.7717/peerj.7500] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 07/16/2019] [Indexed: 11/20/2022] Open
Abstract
Although most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their plastid genomes markedly differ from the plastid genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing other plants. The genome is highly reduced (18,622 base pairs vs. approximately 150 kbp in autotrophic plants) and possesses an extraordinarily high AT content, 86.8%, which is inferior only to AT contents of plastid genomes of Balanophora, a genus from the same family. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologs from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.
Collapse
Affiliation(s)
- Mikhail I. Schelkunov
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute for Information Transmission Problems, Moscow, Russia
| | - Maxim S. Nuraliev
- Faculty of Biology, Moscow State University, Moscow, Russia
- Joint Russian–Vietnamese Tropical Scientific and Technological Center, Cau Giay, Hanoi, Vietnam
| | - Maria D. Logacheva
- Skolkovo Institute of Science and Technology, Moscow, Russia
- A.N. Belozersky Research Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| |
Collapse
|
44
|
Barrett CF, Sinn BT, Kennedy AH. Unprecedented Parallel Photosynthetic Losses in a Heterotrophic Orchid Genus. Mol Biol Evol 2019; 36:1884-1901. [PMID: 31058965 PMCID: PMC6736286 DOI: 10.1093/molbev/msz111] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Heterotrophic plants are evolutionary experiments in genomic, morphological, and physiological change. Yet, genomic sampling gaps exist among independently derived heterotrophic lineages, leaving unanswered questions about the process of genome modification. Here, we have sequenced complete plastid genomes for all species of the leafless orchid genus Hexalectris, including multiple individuals for most, and leafy relatives Basiphyllaea and Bletia. Our objectives are to determine the number of independent losses of photosynthesis and to test hypotheses on the process of genome degradation as a result of relaxed selection. We demonstrate four to five independent losses of photosynthesis in Hexalectris based on degradation of the photosynthetic apparatus, with all but two species displaying evidence of losses, and variation in gene loss extending below the species level. Degradation in the atp complex is advanced in Hexalectris warnockii, whereas only minimal degradation (i.e., physical loss) has occurred among some "housekeeping" genes. We find genomic rearrangements, shifts in Inverted Repeat boundaries including complete loss in one accession of H. arizonica, and correlations among substitutional and genomic attributes. Our unprecedented finding of multiple, independent transitions to a fully mycoheterotrophic lifestyle in a single genus reveals that the number of such transitions among land plants is likely underestimated. This study underscores the importance of dense taxon sampling, which is highly informative for advancing models of genome evolution in heterotrophs. Mycoheterotrophs such as Hexalectris provide forward-genetic opportunities to study the consequences of radical genome evolution beyond what is possible with mutational studies in model organisms alone.
Collapse
Affiliation(s)
- Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, WV
| | - Brandon T Sinn
- Department of Biology, West Virginia University, Morgantown, WV
| | - Aaron H Kennedy
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA-APHIS, Beltsville, MD
| |
Collapse
|
45
|
Banerjee A, Stefanović S. Caught in action: fine-scale plastome evolution in the parasitic plants of Cuscuta section Ceratophorae (Convolvulaceae). PLANT MOLECULAR BIOLOGY 2019; 100:621-634. [PMID: 31140020 DOI: 10.1007/s11103-019-00884-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/18/2019] [Indexed: 05/02/2023]
Abstract
An exhaustive analysis of a group of closely related parasitic plants shows a predominantly gradual reduction in plastid genome composition and provides the most reduced plastomes in the genus Cuscuta. Parasitic plants have a diminished to completely absent reliance on photosynthesis, and are characterized by sweeping morphological, physiological, and genomic changes. The plastid genome (plastome) is highly conserved in autotrophic plants but is often reduced in parasites, and provides a useful system for documenting the genomic effects of a loss of photosynthesis. Previous studies have shown a substantial degree of heterogeneity in plastome length and composition across the species of the genus Cuscuta. Specifically, species in Cuscuta sect. Ceratophorae were suspected to exhibit even more dynamic plastome evolution than the rest of the genus. This complex of eight closely related species was exhaustively sampled here, and one accession per species was sequenced via a high-throughput approach. Complete plastid genomes were assembled and annotated for each of these species and were found to be 61-87 kbp in length, representing a 45-60% reduction relative to autotrophic Convolvulaceae. The most reduced plastomes on this spectrum have lost the bulk of their photosynthetic genes and are the first fully holoparasitic plastomes described for Cuscuta. The fine-scale nature of the system introduced here allowed us to phylogenetically triangulate the locations of gene loss and pseudogenization events precisely, and to construct a step-by-step model of plastome evolution in these plants. This model reveals an intense burst of gene loss along the branch leading to the most reduced plastomes, and a few idiosyncratic changes elsewhere, allowing us to conclude that the tempo of plastid evolution in sect. Ceratophorae is a blend of gradual and punctuated mode.
Collapse
Affiliation(s)
- 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
| |
Collapse
|
46
|
Arias-Agudelo LM, González F, Isaza JP, Alzate JF, Pabón-Mora N. Plastome reduction and gene content in New World Pilostyles (Apodanthaceae) unveils high similarities to African and Australian congeners. Mol Phylogenet Evol 2019; 135:193-202. [DOI: 10.1016/j.ympev.2019.03.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/22/2019] [Accepted: 03/22/2019] [Indexed: 02/06/2023]
|
47
|
Zervas A, Petersen G, Seberg O. Mitochondrial genome evolution in parasitic plants. BMC Evol Biol 2019; 19:87. [PMID: 30961535 PMCID: PMC6454704 DOI: 10.1186/s12862-019-1401-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/22/2019] [Indexed: 11/10/2022] Open
Abstract
Background Parasitic plants rely on their host to cover their nutritional requirements either for their entire life or a smaller part of it. Depending on the level of parasitism, a proportional reduction on the plastid genome has been found. However, knowledge on gene loss and evolution of the mitogenome of parasitic plants is only available for four hemiparasitic Viscum species (Viscaceae), which lack many of the mitochondrial genes, while the remaining genes exhibit very fast molecular evolution rates. In this study, we include another genus, Phoradendron, from the Viscaceae, as well as 10 other hemiparasitic or holoparasitic taxa from across the phylogeny of the angiosperms to investigate how fast molecular evolution works on their mitogenomes, and the extent of gene loss. Results Our observations from Viscum were replicated in Phoradendron liga, whereas the remaining parasitic plants in the study have a complete set of the core mitochondrial genes and exhibit moderate or only slightly raised substitution rates compared to most autotrophic taxa, without any statistically significant difference between the different groups (autotrophs, hemiparasites and holoparasites). Additionally, further evidence is provided for the placement of Balanophoraceae within the order Santalales, while the exact placement of Cynomoriaceae still remains elusive. Conclusions We examine the mitochondrial gene content of 11 hemiparasitic and holoparasitic plants and confirm previous observations in Viscaceae. We show that the remaining parasitic plants do not have significantly higher substitution rates than autotrophic plants in their mitochondrial genes. We provide further evidence for the placement of Balanophoraceae in the Santalales. Electronic supplementary material The online version of this article (10.1186/s12862-019-1401-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Athanasios Zervas
- The Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Sølvgade 83, opg. S, DK-1307, Copenhagen K, Denmark.
| | - Gitte Petersen
- The Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Sølvgade 83, opg. S, DK-1307, Copenhagen K, Denmark
| | - Ole Seberg
- The Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Sølvgade 83, opg. S, DK-1307, Copenhagen K, Denmark
| |
Collapse
|
48
|
Su HJ, Barkman TJ, Hao W, Jones SS, Naumann J, Skippington E, Wafula EK, Hu JM, Palmer JD, dePamphilis CW. Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora. Proc Natl Acad Sci U S A 2019; 116:934-943. [PMID: 30598433 PMCID: PMC6338844 DOI: 10.1073/pnas.1816822116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plastid genomes (plastomes) vary enormously in size and gene content among the many lineages of nonphotosynthetic plants, but key lineages remain unexplored. We therefore investigated plastome sequence and expression in the holoparasitic and morphologically bizarre Balanophoraceae. The two Balanophora plastomes examined are remarkable, exhibiting features rarely if ever seen before in plastomes or in any other genomes. At 15.5 kb in size and with only 19 genes, they are among the most reduced plastomes known. They have no tRNA genes for protein synthesis, a trait found in only three other plastid lineages, and thus Balanophora plastids must import all tRNAs needed for translation. Balanophora plastomes are exceptionally compact, with numerous overlapping genes, highly reduced spacers, loss of all cis-spliced introns, and shrunken protein genes. With A+T contents of 87.8% and 88.4%, the Balanophora genomes are the most AT-rich genomes known save for a single mitochondrial genome that is merely bloated with AT-rich spacer DNA. Most plastid protein genes in Balanophora consist of ≥90% AT, with several between 95% and 98% AT, resulting in the most biased codon usage in any genome described to date. A potential consequence of its radical compositional evolution is the novel genetic code used by Balanophora plastids, in which TAG has been reassigned from stop to tryptophan. Despite its many exceptional properties, the Balanophora plastome must be functional because all examined genes are transcribed, its only intron is correctly trans-spliced, and its protein genes, although highly divergent, are evolving under various degrees of selective constraint.
Collapse
Affiliation(s)
- Huei-Jiun Su
- Department of Earth and Life Sciences, University of Taipei, 100 Taipei, Taiwan
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
| | - Todd J Barkman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202
| | - Samuel S Jones
- Graduate Program in Plant Biology, Pennsylvania State University, University Park, PA 16802
| | - Julia Naumann
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
| | | | - Eric K Wafula
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
| | - Jer-Ming Hu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, 106 Taipei, Taiwan
| | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, IN 47405;
| | - Claude W dePamphilis
- Department of Biology, Pennsylvania State University, University Park, PA 16802;
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
- Graduate Program in Plant Biology, Pennsylvania State University, University Park, PA 16802
| |
Collapse
|
49
|
Barrett CF, Kennedy AH. Plastid Genome Degradation in the Endangered, Mycoheterotrophic, North American Orchid Hexalectris warnockii. Genome Biol Evol 2018; 10:1657-1662. [PMID: 29850794 PMCID: PMC7206652 DOI: 10.1093/gbe/evy107] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2018] [Indexed: 01/02/2023] Open
Abstract
Heterotrophic plants provide evolutionarily independent, natural experiments in the genomic consequences of radically altered nutritional regimes. Here, we have sequenced and annotated the plastid genome of the endangered mycoheterotrophic orchid Hexalectris warnockii. This orchid bears a plastid genome that is ∼80% the total length of the leafy, photosynthetic Phalaenopsis, and contains just over half the number of putatively functional genes of the latter. The plastid genome of H. warnockii bears pseudogenes and has experienced losses of genes encoding proteins directly (e.g., psa/psb, rbcL) and indirectly involved in photosynthesis (atp genes), suggesting it has progressed beyond the initial stages of plastome degradation, based on previous models of plastid genome evolution. Several dispersed and tandem repeats were detected, that are potentially useful as conservation genetic markers. In addition, a 29-kb inversion and a significant contraction of the inverted repeat boundaries are observed in this plastome. The Hexalectris warnockii plastid genome adds to a growing body of data useful in refining evolutionary models in parasites, and provides a resource for conservation studies in these endangered orchids.
Collapse
Affiliation(s)
| | - Aaron H Kennedy
- Department of Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA-APHIS, Beltsville, Maryland
| |
Collapse
|
50
|
Petersen G, Zervas A, Pedersen HÆ, Seberg O. Genome Reports: Contracted Genes and Dwarfed Plastome in Mycoheterotrophic Sciaphila thaidanica (Triuridaceae, Pandanales). Genome Biol Evol 2018; 10:976-981. [PMID: 29608731 PMCID: PMC5952968 DOI: 10.1093/gbe/evy064] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2018] [Indexed: 12/30/2022] Open
Abstract
With a reduced need for photosynthesis, the plastome of parasitic and mycoheterotrophic plants degrades. In the tiny, fully mycoheterotrophic plant Sciaphila thaidanica, we find one of the smallest plastomes yet encountered. Its size is just 12,780 bp and it contains only 20 potentially functional housekeeping genes. Thus S. thaidanica fits the proposed model of gene loss in achlorophyllous plants. The most astonishing feature of the plastome is its extremely compact nature, with more than half of the genes having overlapping reading frames. Additionally, intergenic sequences have been reduced to a bare minimum, and the retained genes have been reduced in length both compared with the orthologous genes in another mycoheterotrophic species of Sciaphila and in the autotrophic relative Carludovica.
Collapse
Affiliation(s)
- Gitte Petersen
- Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Athanasios Zervas
- Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Henrik Æ Pedersen
- Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Ole Seberg
- Natural History Museum of Denmark, University of Copenhagen, Denmark
| |
Collapse
|