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Chen LQ, Li X, Yao X, Li DZ, Barrett C, dePamphilis CW, Yu WB. Variations and reduction of plastome are associated with the evolution of parasitism in Convolvulaceae. PLANT MOLECULAR BIOLOGY 2024; 114:40. [PMID: 38622367 DOI: 10.1007/s11103-024-01440-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/09/2024] [Indexed: 04/17/2024]
Abstract
Parasitic lifestyle can often relax the constraint on the plastome, leading to gene pseudogenization and loss, and resulting in diverse genomic structures and rampant genome degradation. Although several plastomes of parasitic Cuscuta have been reported, the evolution of parasitism in the family Convolvulaceae which is linked to structural variations and reduction of plastome has not been well investigated. In this study, we assembled and collected 40 plastid genomes belonging to 23 species representing four subgenera of Cuscuta and ten species of autotrophic Convolvulaceae. Our findings revealed nine types of structural variations and six types of inverted repeat (IR) boundary variations in the plastome of Convolvulaceae spp. These structural variations were associated with the shift of parasitic lifestyle, and IR boundary shift, as well as the abundance of long repeats. Overall, the degradation of Cuscuta plastome proceeded gradually, with one clade exhibiting an accelerated degradation rate. We observed five stages of gene loss in Cuscuta, including NAD(P)H complex → PEP complex → Photosynthesis-related → Ribosomal protein subunits → ATP synthase complex. Based on our results, we speculated that the shift of parasitic lifestyle in early divergent time promoted relaxed selection on plastomes, leading to the accumulation of microvariations, which ultimately resulted in the plastome reduction. This study provides new evidence towards a better understanding of plastomic evolution, variation, and reduction in the genus Cuscuta.
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Affiliation(s)
- Li-Qiong Chen
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Xin Li
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Division of BiologicalScience, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Xin Yao
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Craig Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Claude W dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, State College, Pennsylvania, 16802, USA
| | - Wen-Bin Yu
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
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Füssy Z, Oborník M. Complex Endosymbioses I: From Primary to Complex Plastids, Serial Endosymbiotic Events. Methods Mol Biol 2024; 2776:21-41. [PMID: 38502496 DOI: 10.1007/978-1-0716-3726-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
A considerable part of the diversity of eukaryotic phototrophs consists of algae with plastids that evolved from endosymbioses between two eukaryotes. These complex plastids are characterized by a high number of envelope membranes (more than two) and some of them contain a residual nucleus of the endosymbiotic alga called a nucleomorph. Complex plastid-bearing algae are thus chimeric cell assemblies, eukaryotic symbionts living in a eukaryotic host. In contrast, the primary plastids of the Archaeplastida (plants, green algae, red algae, and glaucophytes) possibly evolved from a single endosymbiosis with a cyanobacterium and are surrounded by two membranes. Complex plastids have been acquired several times by unrelated groups of eukaryotic heterotrophic hosts, suggesting that complex plastids are somewhat easier to obtain than primary plastids. Evidence suggests that complex plastids arose twice independently in the green lineage (euglenophytes and chlorarachniophytes) through secondary endosymbiosis, and four times in the red lineage, first through secondary endosymbiosis in cryptophytes, then by higher-order events in stramenopiles, alveolates, and haptophytes. Engulfment of primary and complex plastid-containing algae by eukaryotic hosts (secondary, tertiary, and higher-order endosymbioses) is also responsible for numerous plastid replacements in dinoflagellates. Plastid endosymbiosis is accompanied by massive gene transfer from the endosymbiont to the host nucleus and cell adaptation of both endosymbiotic partners, which is related to the trophic switch to phototrophy and loss of autonomy of the endosymbiont. Such a process is essential for the metabolic integration and division control of the endosymbiont in the host. Although photosynthesis is the main advantage of acquiring plastids, loss of photosynthesis often occurs in algae with complex plastids. This chapter summarizes the essential knowledge of the acquisition, evolution, and function of complex plastids.
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Affiliation(s)
- Zoltán Füssy
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Miroslav Oborník
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
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Kharabian-Masouleh A, Furtado A, Alsubaie B, Al-Dossary O, Wu A, Al-Mssalem I, Henry R. Loss of plastid ndh genes in an autotrophic desert plant. Comput Struct Biotechnol J 2023; 21:5016-5027. [PMID: 37867970 PMCID: PMC10589726 DOI: 10.1016/j.csbj.2023.10.023] [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: 08/04/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/24/2023] Open
Abstract
Plant plastid genomes are highly conserved with most flowering plants having the same complement of essential plastid genes. Here, we report the loss of five of the eleven NADH dehydrogenase subunit genes (ndh) in the plastid of a desert plant jojoba (Simmondsia chinensis). The plastid genome of jojoba was 156,496 bp with one large single copy region (LSC), a very small single copy region (SSC) and two expanded inverted repeats (IRA + IRB). The NADH dehydrogenase (NDH) complex is comprised of several protein subunits, encoded by the ndh genes of the plastome and the nucleus. The ndh genes are critical to the proper functioning of the photosynthetic electron transport chain and protection of plants from oxidative stress. Most plants are known to contain all eleven ndh genes. Plants with missing or defective ndh genes are often heterotrophs either due to their complete or holo- or myco- parasitic nature. Plants with a defective NDH complex, caused by the deletion/pseudogenisation of some or all the ndh genes, survive in milder climates suggesting the likely extinction of plant lineages lacking these genes under harsh climates. Interestingly, some autotrophic plants do exist without ndh gene/s and can cope with high or low light. This implies that these plants are protected from oxidative stress by mechanisms excluding ndh genes. Jojoba has evolved mechanisms to cope with a non-functioning NDH complex and survives in extreme desert conditions with abundant sunlight and limited water.
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Affiliation(s)
- Ardashir Kharabian-Masouleh
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
| | - Bader Alsubaie
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
- College of Agriculture and Food Sciences, King Faisal University (KFU), Al Hofuf, 36362 Saudi Arabia
| | - Othman Al-Dossary
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
- College of Agriculture and Food Sciences, King Faisal University (KFU), Al Hofuf, 36362 Saudi Arabia
| | - Alex Wu
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
| | - Ibrahim Al-Mssalem
- College of Agriculture and Food Sciences, King Faisal University (KFU), Al Hofuf, 36362 Saudi Arabia
| | - Robert Henry
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
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Ni Y, Li J, Lu Q, Chen H. Characterizing the chloroplast genome of Mammillaria elongata DC. 1828 in the Cactaceae family and unveiling its phylogenetic affinities within the genus Mammillaria. Mitochondrial DNA B Resour 2023; 8:1071-1076. [PMID: 37842007 PMCID: PMC10569349 DOI: 10.1080/23802359.2023.2265100] [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: 09/04/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023] Open
Abstract
With its nearly 200 species, the Mammillaria genus is the most species-rich within the Cactaceae family, yet surprisingly, few of its chloroplast genomes have been studied. We focused on the species Mammillaria elongata DC. 1828, a petite cactus native to Mexico and favored by horticulturists, yet whose phylogenetic relationships remain uncertain due to a lack of genomic data. We extracted the DNA from a sample obtained in China, sequenced it using the NovaSeq 6000 platform, and assembled the chloroplast genome using GetOrganelle software. Our assembly resulted in a chloroplast genome of 110,981 base pairs with an overall GC content of 36.28%, which included 100 genes (95 unique). Notably, several protein-coding genes were absent. Phylogenetic analysis using 59 shared genes across nine Mammillaria species and one Obregonia species revealed that M. elongata and M. gracilis are closely related, suggesting a recent common ancestor and possible shared evolutionary pressures or ecological niches. This study provides crucial genomic data for M. elongata and hints at intriguing phylogenetic relationships within the Mammillaria genus.
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Affiliation(s)
- Yang Ni
- Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China
| | - Jingling Li
- Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, PR China
| | - Qianqi Lu
- Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China
| | - Haimei Chen
- Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China
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Chen Z, Zhou Z, Guo ZM, Van Do T, Sun H, Niu Y. Historical development of karst evergreen broadleaved forests in East Asia has shaped the evolution of a hemiparasitic genus Brandisia (Orobanchaceae). PLANT DIVERSITY 2023; 45:501-512. [PMID: 37936821 PMCID: PMC10625920 DOI: 10.1016/j.pld.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/14/2023] [Accepted: 03/17/2023] [Indexed: 11/09/2023]
Abstract
Brandisia is a shrubby genus of about eight species distributed basically in East Asian evergreen broadleaved forests (EBLFs), with distribution centers in the karst regions of Yunnan, Guizhou, and Guangxi in southwestern China. Based on the hemiparasitic and more or less liana habits of this genus, we hypothesized that its evolution and distribution were shaped by the development of EBLFs there. To test our hypothesis, the most comprehensive phylogenies of Brandisia hitherto were constructed based on plastome and nuclear loci (nrDNA, PHYA and PHYB); then divergence time and ancestral areas were inferred using the combined nuclear loci dataset. Phylogenetic analyses reconfirmed that Brandisia is a member of Orobanchaceae, with unstable placements caused by nuclear-plastid incongruences. Within Brandisia, three major clades were well supported, corresponding to the three subgenera based on morphology. Brandisia was inferred to have originated in the early Oligocene (32.69 Mya) in the Eastern Himalayas-SW China, followed by diversification in the early Miocene (19.45 Mya) in karst EBLFs. The differentiation dates of Brandisia were consistent with the origin of keystone species of EBLFs in this region (e.g., Fagaceae, Lauraceae, Theaceae, and Magnoliaceae) and the colonization of other characteristic groups (e.g., Gesneriaceae and Mahonia). These findings indicate that the distribution and evolution of Brandisia were facilitated by the rise of the karst EBLFs in East Asia. In addition, the woody and parasitic habits, and pollination characteristics of Brandisia may also be the important factors affecting its speciation and dispersal.
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Affiliation(s)
- Zhe Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
| | - Zhuo Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
| | - Ze-Min Guo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Truong Van Do
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay 10000, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay 10000, Hanoi, Vietnam
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
| | - Yang Niu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
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Yu J, Li J, Zuo Y, Qin Q, Zeng S, Rennenberg H, Deng H. Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae). BMC PLANT BIOLOGY 2023; 23:132. [PMID: 36882685 PMCID: PMC9993602 DOI: 10.1186/s12870-023-04148-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/01/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND The cactus family (Cactaceae) has been reported to have evolved a minimal photosynthetic plastome size, with the loss of inverted-repeat (IR) regions and NDH gene suites. However, there are very limited genomic data on the family, especially Cereoideae, the largest subfamily of cacti. RESULTS In the present study, we assembled and annotated 35 plastomes, 33 of which were representatives of Cereoideae, alongside 2 previously published plastomes. We analyzed the organelle genomes of 35 genera in the subfamily. These plastomes have variations rarely observed in those of other angiosperms, including size differences (with ~ 30 kb between the shortest and longest), dramatic dynamic changes in IR boundaries, frequent plastome inversions, and rearrangements. These results suggested that cacti have the most complex plastome evolution among angiosperms. CONCLUSION These results provide unique insight into the dynamic evolutionary history of Cereoideae plastomes and refine current knowledge of the relationships within the subfamily.
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Affiliation(s)
- Jie Yu
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
- No. 2 Tiansheng Road, Beibei District, Chongqing, 400716 China
| | - Jingling Li
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Youwei Zuo
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715 China
| | - Qiulin Qin
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Siyuan Zeng
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Heinz Rennenberg
- Center of Molecular Ecophysiology, College of Resources and Environment, Southwest University, Chongqing, 400715 China
| | - Hongping Deng
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715 China
- No. 2 Tiansheng Road, Beibei District, Chongqing, 400716 China
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Mathur V, Salomaki ED, Wakeman KC, Na I, Kwong WK, Kolisko M, Keeling PJ. Reconstruction of Plastid Proteomes of Apicomplexans and Close Relatives Reveals the Major Evolutionary Outcomes of Cryptic Plastids. Mol Biol Evol 2023; 40:6969433. [PMID: 36610734 PMCID: PMC9847631 DOI: 10.1093/molbev/msad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/18/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
Apicomplexans and related lineages comprise many obligate symbionts of animals; some of which cause notorious diseases such as malaria. They evolved from photosynthetic ancestors and transitioned into a symbiotic lifestyle several times, giving rise to species with diverse non-photosynthetic plastids. Here, we sought to reconstruct the evolution of the cryptic plastids in the apicomplexans, chrompodellids, and squirmids (ACS clade) by generating five new single-cell transcriptomes from understudied gregarine lineages, constructing a robust phylogenomic tree incorporating all ACS clade sequencing datasets available, and using these to examine in detail, the evolutionary distribution of all 162 proteins recently shown to be in the apicoplast by spatial proteomics in Toxoplasma. This expanded homology-based reconstruction of plastid proteins found in the ACS clade confirms earlier work showing convergence in the overall metabolic pathways retained once photosynthesis is lost, but also reveals differences in the degrees of plastid reduction in specific lineages. We show that the loss of the plastid genome is common and unexpectedly find many lineage- and species-specific plastid proteins, suggesting the presence of evolutionary innovations and neofunctionalizations that may confer new functional and metabolic capabilities that are yet to be discovered in these enigmatic organelles.
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Affiliation(s)
| | - Eric D Salomaki
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Kevin C Wakeman
- Institute for the Advancement of Higher Education, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan
| | - Ina Na
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada
| | - Waldan K Kwong
- Present address: Instituto Gulbenkian de Ciência (IGC) Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Martin Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada
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López-Barrera A, Santos-Ordóñez E, Pacheco-Coello R, Villao-Uzho L, Miranda M, Gutiérrez Y, Chóez-Guaranda I, Ruiz-Reyes SG. ITS1 Barcode and Phytochemical Analysis by Gas Chromatography-Mass Spectrometry of Corynaea crassa Hook. f (Balanophoraceae) from Ecuador and Peru. Genes (Basel) 2022; 14:genes14010088. [PMID: 36672828 PMCID: PMC9859250 DOI: 10.3390/genes14010088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/13/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
The use of medicinal plants is the basis of traditional healthcare. Recently, the use of herbal medicine has been increasing among consumers due to availability, economy, and less side effect. For instance, the hemiparasite plant Corynaea crassa has medicinal properties and could be found in some regions of America, from Costa Rica to Bolivia. Phytochemical and genetic characterization of medicinal plants is needed for proper identification of metabolites responsible for medicinal properties and for genotyping, respectively. Moreover, characterization of medicinal plants through the use of DNA barcodes is an important tool for phylogenetic analysis and identification of species; furthermore, complemented with phytochemical analysis, both are useful for identification of plant species and quality control of medicinal products. The objective of this study was to analyze the species of C. crassa collected in Ecuador and Peru from the phylogenetic and phytochemical point of view. Polymerase chain reaction (PCR) was performed for amplification of the internal transcribed spacer 1 (ITS1) region after DNA extraction of samples of C. crassa. Blast analysis was performed in the GenBank database with the ITS1 sequences obtained from two accessions of C. crassa from Ecuador (GenBank accession numbers OM471920 and OM471919 for isolates CIBE-17 and CIBE-18, respectively) and three from Peru (GenBank accession numbers OM471921, OM471922, and OM471923 for isolates CIBE-13, CIBE-14, and CIBE-15, respectively). The accessions available in the GenBank were used for phylogenetic analysis. For the phytochemical analysis, hydroalcoholic extracts were obtained by maceration using 80% ethanol as solvent, followed by a derivatization process and analysis by gas chromatography-mass spectrometry. Based on the phylogenetic analysis of the C. crassa samples, the ITS1 sequence could be used to differentiate C. crassa of different locations. The samples of C. crassa from Ecuador and Peru are more similar between them than with other clades including Helosis spp. The phytochemical study revealed differences in the presence and relative abundance of some metabolites; mainly eugenol, 1,4-lactone arabinonic acid, dimethoxyrabelomycin and azelaic acid, which are reported for the first time for the species under study and the genus Corynaea. These results are the first findings on the combined analysis using genetic and phytochemical analysis for C. crassa, which could be used as a useful tool for quality control of the C. crassa species in medicinal products.
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Affiliation(s)
- Alexandra López-Barrera
- Department of Pharmacy, Faculty of Chemical Sciences, Universidad de Guayaquil, Guayaquil 090514, Ecuador
| | - Efrén Santos-Ordóñez
- Facultad de Ciencias de la Vida, Campus Gustavo Galindo, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090902, Ecuador
- Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090902, Ecuador
- Correspondence:
| | - Ricardo Pacheco-Coello
- Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090902, Ecuador
| | - Liliana Villao-Uzho
- Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090902, Ecuador
| | - Migdalia Miranda
- Facultad de Ciencias Naturales y Matemáticas, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090902, Ecuador
| | - Yamilet Gutiérrez
- Department of Pharmacy, Institute of Pharmacy and Food, Universidad de La Habana, La Habana 10400, Cuba
| | - Iván Chóez-Guaranda
- Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090902, Ecuador
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Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmF C genes. BMC Genomics 2021; 22:816. [PMID: 34772334 PMCID: PMC8588681 DOI: 10.1186/s12864-021-08105-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/19/2021] [Indexed: 01/30/2023] Open
Abstract
Background The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus. Results The mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmFC gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT. Conclusions The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08105-z.
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Guo X, Zhang G, Fan L, Liu C, Ji Y. Highly degenerate plastomes in two hemiparasitic dwarf mistletoes: Arceuthobium chinense and A. pini (Viscaceae). PLANTA 2021; 253:125. [PMID: 34028602 DOI: 10.1007/s00425-021-03643-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/19/2021] [Indexed: 06/12/2023]
Abstract
The leafless and endophytic habitat may significantly relax the selection pressure on photosynthesis, and plastid transcription and translation, causing the loss/pseudogenization of several essential plastid-encoding genes in dwarf mistletoes. Dwarf mistletoes (Arceuthobium spp., Viscaceae) are the most destructive plant parasites to numerous conifer species worldwide. In this study, the plastid genomes (plastomes) of Arceuthobium chinense Lecomte and A. pini Hawksworth and Wiens were sequenced and characterized. Although dwarf mistletoes are hemiparasites capable of photosynthesis, their plastomes were highly degenerated, as indicated by the smallest plastome size, the lowest GC content, and relatively very few intact genes among the Santalales hemiparasites. Unexpectedly, several essential housekeeping genes (rpoA, rpoB, rpoC1, and rpoC2) and some core photosynthetic genes (psbZ and petL), as well as the rpl33 gene, that is indispensable for plants under stress conditions, were deleted or pseudogenized in the Arceuthobium plastomes. Our data suggest that the leafless and endophytic habit, which heavily relies on the coniferous hosts for nutrients and carbon requirement, may largely relax the selection pressure on photosynthesis, as well as plastid transcription and translation, thus resulting in the loss/pseudogenization of such essential plastid-encoding genes in dwarf mistletoes. Therefore, the higher level of plastome degradation in Arceuthobium species than other Santalales hemiparasites is likely correlated with the evolution of leafless and endophytic habit. A higher degree of plastome degradation in Arceuthobium. These findings provide new insights into the plastome degeneration associated with parasitism in Santalales and deepen our understanding of the biology of dwarf mistletoes.
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Affiliation(s)
- Xiaorong Guo
- Institute of Ecology and Geobotany, Yunnan University, Kunming, Yunnan, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Guangfei Zhang
- Institute of Ecology and Geobotany, Yunnan University, Kunming, Yunnan, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Linyuan Fan
- Yunnan General Administration of Forestry Seeds and Seedlings, 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
| | - 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.
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11
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Mathur V, Kwong WK, Husnik F, Irwin NAT, Kristmundsson Á, Gestal C, Freeman M, Keeling PJ. Phylogenomics Identifies a New Major Subgroup of Apicomplexans, Marosporida class nov., with Extreme Apicoplast Genome Reduction. Genome Biol Evol 2021; 13:evaa244. [PMID: 33566096 PMCID: PMC7875001 DOI: 10.1093/gbe/evaa244] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2020] [Indexed: 12/16/2022] Open
Abstract
The phylum Apicomplexa consists largely of obligate animal parasites that include the causative agents of human diseases such as malaria. Apicomplexans have also emerged as models to study the evolution of nonphotosynthetic plastids, as they contain a relict chloroplast known as the apicoplast. The apicoplast offers important clues into how apicomplexan parasites evolved from free-living ancestors and can provide insights into reductive organelle evolution. Here, we sequenced the transcriptomes and apicoplast genomes of three deep-branching apicomplexans, Margolisiella islandica, Aggregata octopiana, and Merocystis kathae. Phylogenomic analyses show that these taxa, together with Rhytidocystis, form a new lineage of apicomplexans that is sister to the Coccidia and Hematozoa (the lineages including most medically significant taxa). Members of this clade retain plastid genomes and the canonical apicomplexan plastid metabolism. However, the apicoplast genomes of Margolisiella and Rhytidocystis are the most reduced of any apicoplast, are extremely GC-poor, and have even lost genes for the canonical plastidial RNA polymerase. This new lineage of apicomplexans, for which we propose the class Marosporida class nov., occupies a key intermediate position in the apicomplexan phylogeny, and adds a new complexity to the models of stepwise reductive evolution of genome structure and organelle function in these parasites.
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Affiliation(s)
- Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Waldan K Kwong
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Filip Husnik
- Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Árni Kristmundsson
- Fish Disease Laboratory, Institute for Experimental Pathology, University of Iceland, Reykjavík, Iceland
| | - Camino Gestal
- Institute of Marine Research (IIM-CSIC), Vigo, Spain
| | - Mark Freeman
- Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis, West Indies
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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12
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Tanifuji G, Kamikawa R, Moore CE, Mills T, Onodera NT, Kashiyama Y, Archibald JM, Inagaki Y, Hashimoto T. Comparative Plastid Genomics of Cryptomonas Species Reveals Fine-Scale Genomic Responses to Loss of Photosynthesis. Genome Biol Evol 2020; 12:3926-3937. [PMID: 31922581 PMCID: PMC7058160 DOI: 10.1093/gbe/evaa001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2020] [Indexed: 01/20/2023] Open
Abstract
Loss of photosynthesis is a recurring theme in eukaryotic evolution. In organisms that have lost the ability to photosynthesize, nonphotosynthetic plastids are retained because they play essential roles in processes other than photosynthesis. The unicellular algal genus Cryptomonas contains both photosynthetic and nonphotosynthetic members, the latter having lost the ability to photosynthesize on at least three separate occasions. To elucidate the evolutionary processes underlying the loss of photosynthesis, we sequenced the plastid genomes of two nonphotosynthetic strains, Cryptomonas sp. CCAC1634B and SAG977-2f, as well as the genome of the phototroph Cryptomonas curvata CCAP979/52. These three genome sequences were compared with the previously sequenced plastid genome of the nonphotosynthetic species Cryptomonas paramecium CCAP977/2a as well as photosynthetic members of the Cryptomonadales, including C. curvata FBCC300012D. Intraspecies comparison between the two C. curvata strains showed that although their genome structures are stable, the substitution rates of their genes are relatively high. Although most photosynthesis-related genes, such as the psa and psb gene families, were found to have disappeared from the nonphotosynthetic strains, at least ten pseudogenes are retained in SAG977-2f. Although gene order is roughly shared among the plastid genomes of photosynthetic Cryptomonadales, genome rearrangements are seen more frequently in the smaller genomes of the nonphotosynthetic strains. Intriguingly, the light-independent protochlorophyllide reductase comprising chlB, L, and N is retained in nonphotosynthetic SAG977-2f and CCAC1634B. On the other hand, whereas CCAP977/2a retains ribulose-1,5-bisphosphate carboxylase/oxygenase-related genes, including rbcL, rbcS, and cbbX, the plastid genomes of the other two nonphotosynthetic strains have lost the ribulose-1,5-bisphosphate carboxylase/oxygenase protein-coding genes.
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Affiliation(s)
- Goro Tanifuji
- Department of Zoology, National Museum of Nature and Science, Ibaraki, Japan
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Christa E Moore
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Tyler Mills
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Naoko T Onodera
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Yuichiro Kashiyama
- Department of Applied Chemistry and Food Science, Fukui University of Technology, Fukui, Japan
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Yuji Inagaki
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
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13
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Chen S, Wang X, Wang Y, Zhang G, Song W, Dong X, Arnold ML, Wang W, Miao J, Chen W, Dong Y. Improved de novo Assembly of the Achlorophyllous Orchid Gastrodia elata. Front Genet 2020; 11:580568. [PMID: 33329718 PMCID: PMC7711107 DOI: 10.3389/fgene.2020.580568] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/19/2020] [Indexed: 12/01/2022] Open
Abstract
Achlorophyllous plants are full mycoheterotrophic plants with no chlorophyll and they obtain their nutrients from soil fungi. Gastrodia elata is a perennial, achlorophyllous orchid that displays distinctive evolutionary strategy of adaptation to the non-photosynthetic lifestyle. Here in this study, the genome of G. elata was assembled to 1.12 Gb with a contig N50 size of 110 kb and a scaffold N50 size of 1.64 Mb so that it helped unveil the genetic basics of those adaptive changes. Based on the genomic data, key genes related to photosynthesis, leaf development, and plastid division pathways were found to be lost or under relaxed selection during the course of evolution. Thus, the genome sequence of G. elata provides a good resource for future investigations of the evolution of orchids and other achlorophyllous plants.
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Affiliation(s)
- Shanshan Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
- BGI College, Zhengzhou University, Zhengzhou, China
| | - Xiao Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Jiaxing Synbiolab Biotechnology Co., Ltd., Jiaxing, China
| | - Yangzi Wang
- College of Biological Big Data, Yunnan Agricultural University, Kunming, China
| | - Guanghui Zhang
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Wanling Song
- College of Biological Big Data, Yunnan Agricultural University, Kunming, China
| | - Xiao Dong
- College of Biological Big Data, Yunnan Agricultural University, Kunming, China
| | - Michael L. Arnold
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Jianhua Miao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Wei Chen
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China
| | - Yang Dong
- College of Biological Big Data, Yunnan Agricultural University, Kunming, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China
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14
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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.
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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
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15
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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.
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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
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16
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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.
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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
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17
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Schwacke R, Ponce-Soto GY, Krause K, Bolger AM, Arsova B, Hallab A, Gruden K, Stitt M, Bolger ME, Usadel B. MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis. MOLECULAR PLANT 2019; 12:879-892. [PMID: 30639314 DOI: 10.1016/j.molp.2019.01.003] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/14/2018] [Accepted: 01/01/2019] [Indexed: 05/18/2023]
Abstract
Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. Furthermore, to keep pace with rapid production of genome sequences, this functional annotation process must be fully automated. Here we present a redesigned and significantly enhanced MapMan4 framework, together with a revised version of the associated online Mercator annotation tool. Compared with the original MapMan, the new ontology has been expanded almost threefold and enforces stricter assignment rules. This framework was then incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group, providing protein annotations for all embryophytes with a comparably high quality. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application.
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Affiliation(s)
- Rainer Schwacke
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Gabriel Y Ponce-Soto
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Kirsten Krause
- Department of Arctic and Marine Biology, The Arctic University of Norway, Biology Building, 9037 Tromsø, Norway
| | - Anthony M Bolger
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg, RWTH Aachen University, 52074 Aachen, Germany
| | - Borjana Arsova
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Asis Hallab
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Kristina Gruden
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
| | - Mark Stitt
- Max Planck Institute for Molecular Plant Physiology, Department of Systems Regulation, 14476 Potsdam-Golm, Germany
| | - Marie E Bolger
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany.
| | - Björn Usadel
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany; Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg, RWTH Aachen University, 52074 Aachen, Germany
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18
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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]
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19
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Williams AM, Friso G, van Wijk KJ, Sloan DB. Extreme variation in rates of evolution in the plastid Clp protease complex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:243-259. [PMID: 30570818 DOI: 10.1111/tpj.14208] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/29/2018] [Accepted: 12/10/2018] [Indexed: 05/08/2023]
Abstract
Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multi-subunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid-encoded gene (clpP1) and multiple nuclear genes. TheclpP1 gene is highly conserved across most green plants, but it is by far the fastest evolving plastid-encoded gene in some angiosperms. To better understand these extreme and mysterious patterns of divergence, we investigated the history ofclpP1 molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find thatclpP1 has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g. a loss of introns andRNA-editing sites) within seed plants. AlthoughclpP1 is often assumed to be a pseudogene in such cases, multiple lines of evidence suggest that this is rarely true. We applied comparative native gel electrophoresis of chloroplast protein complexes followed by protein mass spectrometry in two species within the angiosperm genusSilene, which has highly elevated and heterogeneous rates ofclpP1 evolution. We confirmed thatclpP1 is expressed as a stable protein and forms oligomeric complexes with the nuclear-encoded Clp subunits, even in one of the most divergentSilene species. Additionally, there is a tight correlation between amino acid substitution rates inclpP1 and the nuclear-encoded Clp subunits across a broad sampling of angiosperms, suggesting continuing selection on interactions within this complex.
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Affiliation(s)
- Alissa M Williams
- Department of Biology, Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Giulia Friso
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, 14853, USA
| | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, 14853, USA
| | - Daniel B Sloan
- Department of Biology, Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
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20
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Graupner N, Jensen M, Bock C, Marks S, Rahmann S, Beisser D, Boenigk J. Evolution of heterotrophy in chrysophytes as reflected by comparative transcriptomics. FEMS Microbiol Ecol 2019. [PMID: 29518196 PMCID: PMC6019013 DOI: 10.1093/femsec/fiy039] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Shifts in the nutritional mode between phototrophy, mixotrophy and heterotrophy are a widespread phenomenon in the evolution of eukaryotic diversity. The transition between nutritional modes is particularly pronounced in chrysophytes and occurred independently several times through parallel evolution. Thus, chrysophytes provide a unique opportunity for studying the molecular basis of nutritional diversification and of the accompanying pathway reduction and degradation of plastid structures. In order to analyze the succession in switching the nutritional mode from mixotrophy to heterotrophy, we compared the transcriptome of the mixotrophic Poterioochromonas malhamensis with the transcriptomes of three obligate heterotrophic species of Ochromonadales. We used the transcriptome of P. malhamensis as a reference for plastid reduction in the heterotrophic taxa. The analyzed heterotrophic taxa were in different stages of plastid reduction. We investigated the reduction of several photosynthesis related pathways e.g. the xanthophyll cycle, the mevalonate pathway, the shikimate pathway and the tryptophan biosynthesis as well as the reduction of plastid structures and postulate a presumable succession of pathway reduction and degradation of accompanying structures.
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Affiliation(s)
- Nadine Graupner
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, D-45141 Essen, Germany
| | - Manfred Jensen
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, D-45141 Essen, Germany
| | - Christina Bock
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, D-45141 Essen, Germany
| | - Sabina Marks
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, D-45141 Essen, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstr. 55, D-45147 Essen, Germany
| | - Daniela Beisser
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, D-45141 Essen, Germany
| | - Jens Boenigk
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, D-45141 Essen, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr. 2, D-45141 Essen, Germany
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21
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Robison TA, Wolf PG. ReFernment: An R package for annotating RNA editing in plastid genomes. APPLICATIONS IN PLANT SCIENCES 2019; 7:e01216. [PMID: 30828503 PMCID: PMC6384294 DOI: 10.1002/aps3.1216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 12/14/2018] [Indexed: 05/15/2023]
Abstract
PREMISE OF THE STUDY In the absence of cDNA, the annotation of RNA editing in plastomes must be done manually, representing a significant time cost to those studying the organellar genomes of ferns and hornworts. METHODS AND RESULTS We developed an R package to automatically annotate apparent nonsense mutations in plastid genomes. The software successfully annotates such sites and results in no false positives for data with no sequencing or assembly errors. CONCLUSIONS Compared to manual annotation, ReFernment offers greater speed and accuracy for annotating RNA editing sites. This software should be especially useful for researchers generating large numbers of plastome sequences for taxa with high levels of RNA editing.
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Affiliation(s)
| | - Paul G. Wolf
- Department of BiologyUtah State UniversityLoganUtahUSA
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22
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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.
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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
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23
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Ng SM, Lee XW, Mat-Isa MN, Aizat-Juhari MA, Adam JH, Mohamed R, Wan KL, Firdaus-Raih M. Comparative analysis of nucleus-encoded plastid-targeting proteins in Rafflesia cantleyi against photosynthetic and non-photosynthetic representatives reveals orthologous systems with potentially divergent functions. Sci Rep 2018; 8:17258. [PMID: 30467394 PMCID: PMC6250676 DOI: 10.1038/s41598-018-35173-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022] Open
Abstract
Parasitic plants are known to discard photosynthesis thus leading to the deletion or loss of the plastid genes. Despite plastid genome reduction in non-photosynthetic plants, some nucleus-encoded proteins are transported back to the plastid to carry out specific functions. In this work, we study such proteins in Rafflesia cantleyi, a member of the holoparasitic genus well-known for producing the largest single flower in the world. Our analyses of three transcriptome datasets, two holoparasites (R. cantleyi and Phelipanche aegyptiaca) and one photosynthetic plant (Arabidopsis thaliana), suggest that holoparasites, such as R. cantleyi, retain some common plastid associated processes such as biosynthesis of amino acids and lipids, but are missing photosynthesis components that can be extensions of these pathways. The reconstruction of two selected biosynthetic pathways involving plastids correlates the trend of plastid retention to pathway complexity - transcriptome evidence for R. cantleyi suggests alternate mechanisms in regulating the plastidial heme and terpenoid backbone biosynthesis pathways. The evolution to holoparasitism from autotrophy trends towards devolving the plastid genes to the nuclear genome despite the functional sites remaining in the plastid, or maintaining non-photosynthetic processes in the plastid, before the eventual loss of the plastid and any site dependent functions.
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Affiliation(s)
- Siuk-Mun Ng
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
- Codon Genomics SB, No 26, Jalan Dutamas 7, Taman Dutamas Balakong, 43200, Seri Kembangan, Selangor, Malaysia
| | - Xin-Wei Lee
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Mohd-Noor Mat-Isa
- Malaysia Genome Institute, Jalan Bangi, 43000, Kajang, Selangor, Malaysia
| | - Mohd Afiq Aizat-Juhari
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Jumaat Haji Adam
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Rahmah Mohamed
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
| | - Mohd Firdaus-Raih
- Centre for Frontier Sciences, Faculty of Science and Technology and Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
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Zhao J, Xu Y, Xi L, Yang J, Chen H, Zhang J. Characterization of the Chloroplast Genome Sequence of Acer miaotaiense: Comparative and Phylogenetic Analyses. Molecules 2018; 23:E1740. [PMID: 30018192 PMCID: PMC6099587 DOI: 10.3390/molecules23071740] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/03/2018] [Accepted: 07/13/2018] [Indexed: 11/17/2022] Open
Abstract
Acer miaotaiense is an endangered species within the Aceraceae family, and has only a few small natural distributions in China's Qingling Mountains and Bashan Mountains. Comparative analyses of the complete chloroplast genome could provide useful knowledge on the diversity and evolution of this species in different environments. In this study, we sequenced and compared the chloroplast genome of Acer miaotaiense from five ecological regions in the Qingling and Mashan Regions of China. The size of the chloroplast genome ranged from 156,260 bp to 156,204 bp, including two inverted repeat regions, a small single-copy region, and a large single-copy region. Across the whole chloroplast genome, there were 130 genes in total, and 92 of them were protein-coding genes. We observed four genes with non-synonymous mutations involving post-transcriptional modification (matK), photosynthesis (atpI), and self-replication (rps4 and rpl20). A total of 415 microsatellite loci were identified, and the dominant microsatellite types were composed of dinucleotide and trinucleotide motifs. The dominant repeat units were AT and AG, accounting for 37.92% and 31.16% of the total microsatellite loci, respectively. A phylogenetic analysis showed that samples with the same altitude (Xunyangba, Ningshan country, and Zhangliangmiao, Liuba country) had a strong bootstrap value (88%), while the remaining ones shared a similar longitude. These results provided clues about the importance of longitude/altitude for the genetic diversity of Acer miaotaiense. This information will be useful for the conservation and improved management of this endangered species.
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Affiliation(s)
- Jiantao Zhao
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Yao Xu
- College of Forestry, Northwest A&F University, Yangling 712100, China.
| | - Linjie Xi
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Junwei Yang
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Hongwu Chen
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Jing Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
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25
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Shin HW, Lee NS. Understanding plastome evolution in Hemiparasitic Santalales: Complete chloroplast genomes of three species, Dendrotrophe varians, Helixanthera parasitica, and Macrosolen cochinchinensis. PLoS One 2018; 13:e0200293. [PMID: 29975758 PMCID: PMC6033455 DOI: 10.1371/journal.pone.0200293] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 06/22/2018] [Indexed: 01/31/2023] Open
Abstract
Santalales is a large order, with over 2200 species, most of which are root or aerial (stem) hemiparasites. In this study, we report the newly assembled chloroplast genome of Dendrotrophe varians (140,666 bp) in the family Amphorogynaceae and the cp genomes of Helixanthera parasitica (124,881 bp) and Macrosolen cochinchinensis (122,986 bp), both in the family Loranthaceae. We compared the cp genomes of 11 Santalales including eight currently available cp genomes. Santalales cp genomes are slightly or not reduced in size (119-147 kb), similar to other hemiparasitic species, when compared with typical angiosperm cp genomes (120-170 kb). In a phylogeny examining gene content, the NADH dehydrogenase gene group is the only one among eight functional gene groups that lost complete functionally in all examined Santalales. This supports the idea that the functional loss of ndh genes is the initial stage in the evolution of the plastome of parasitic plants, but the loss has occurred independently multiple times in angiosperms, while they are not found in some parasites. This suggests that the functional loss of ndh genes is not essential for the transition from autotroph to parasite. We additionally examined the correlation between gene content and type of parasitism (obligate/facultative and stem/root parasites) of all hemiparasitic species in which cp genomes have been reported to date. Correlation was not found in any types of parasitism.
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Affiliation(s)
- Hye Woo Shin
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, Korea
| | - Nam Sook Lee
- Department of Life Science, Ewha Womans University, Seoul, Korea
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26
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Frailey DC, Chaluvadi SR, Vaughn JN, Coatney CG, Bennetzen JL. Gene loss and genome rearrangement in the plastids of five Hemiparasites in the family Orobanchaceae. BMC PLANT BIOLOGY 2018; 18:30. [PMID: 29409454 PMCID: PMC5801802 DOI: 10.1186/s12870-018-1249-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/30/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND The chloroplast genomes (plastome) of most plants are highly conserved in structure, gene content, and gene order. Parasitic plants, including those that are fully photosynthetic, often contain plastome rearrangements. These most notably include gene deletions that result in a smaller plastome size. The nature of gene loss and genome structural rearrangement has been investigated in several parasitic plants, but their timing and contributions to the adaptation of these parasites requires further investigation, especially among the under-studied hemi-parasites. RESULTS De novo sequencing, assembly and annotation of the chloroplast genomes of five photosynthetic parasites from the family Orobanchaceae were employed to investigate plastome dynamics. Four had major structural rearrangements, including gene duplications and gene losses, that differentiated the taxa. The facultative parasite Aureolaria virginica had the most similar genome content to its close non-parasitic relative, Lindenbergia philippensis, with similar genome size and organization, and no differences in gene content. In contrast, the facultative parasite Buchnera americana and three obligate parasites in the genus Striga all had enlargements of their plastomes, primarily caused by expansion within the large inverted repeats (IRs) that are a standard plastome feature. Some of these IR increases were shared by multiple investigated species, but others were unique to particular lineages. Gene deletions and pseudogenization were also both shared and lineage-specific, with particularly frequent and independent loss of the ndh genes involved in electron recycling. CONCLUSIONS Five new plastid genomes were fully assembled and compared. The results indicate that plastome instability is common in parasitic plants, even those that retain the need to perform essential plastid functions like photosynthesis. Gene losses were slow and not identical across taxa, suggesting that different lineages had different uses or needs for some of their plastome gene content, including genes involved in some aspects of photosynthesis. Recent repeat region extensions, some unique to terminal species branches, were observed after the divergence of the Buchnera/Striga clade, suggesting that this otherwise rare event has some special value in this lineage.
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Affiliation(s)
| | | | - Justin N. Vaughn
- Department of Genetics, University of Georgia, Athens, GA 30677 USA
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27
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Multiple losses of photosynthesis and convergent reductive genome evolution in the colourless green algae Prototheca. Sci Rep 2018; 8:940. [PMID: 29343788 PMCID: PMC5772498 DOI: 10.1038/s41598-017-18378-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/11/2017] [Indexed: 12/02/2022] Open
Abstract
Autotrophic eukaryotes have evolved by the endosymbiotic uptake of photosynthetic organisms. Interestingly, many algae and plants have secondarily lost the photosynthetic activity despite its great advantages. Prototheca and Helicosporidium are non-photosynthetic green algae possessing colourless plastids. The plastid genomes of Prototheca wickerhamii and Helicosporidium sp. are highly reduced owing to the elimination of genes related to photosynthesis. To gain further insight into the reductive genome evolution during the shift from a photosynthetic to a heterotrophic lifestyle, we sequenced the plastid and nuclear genomes of two Prototheca species, P. cutis JCM 15793 and P. stagnora JCM 9641, and performed comparative genome analyses among trebouxiophytes. Our phylogenetic analyses using plastid- and nucleus-encoded proteins strongly suggest that independent losses of photosynthesis have occurred at least three times in the clade of Prototheca and Helicosporidium. Conserved gene content among these non-photosynthetic lineages suggests that the plastid and nuclear genomes have convergently eliminated a similar set of photosynthesis-related genes. Other than the photosynthetic genes, significant gene loss and gain were not observed in Prototheca compared to its closest photosynthetic relative Auxenochlorella. Although it remains unclear why loss of photosynthesis occurred in Prototheca, the mixotrophic capability of trebouxiophytes likely made it possible to eliminate photosynthesis.
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28
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Füssy Z, Oborník M. Complex Endosymbioses I: From Primary to Complex Plastids, Multiple Independent Events. Methods Mol Biol 2018; 1829:17-35. [PMID: 29987712 DOI: 10.1007/978-1-4939-8654-5_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A substantial portion of eukaryote diversity consists of algae with complex plastids, i.e., plastids originating from eukaryote-to-eukaryote endosymbioses. These plastids are characteristic by a deviating number of envelope membranes (higher than two), and sometimes a remnant nucleus of the endosymbiont alga, termed the nucleomorph, is present. Complex plastid-bearing algae are therefore much like living matryoshka dolls, eukaryotes within eukaryotes. In comparison, primary plastids of Archaeplastida (plants, green algae, red algae, and glaucophytes) arose upon a single endosymbiosis event with a cyanobacterium and are surrounded by two membranes. Complex plastids were acquired several times by unrelated groups nested within eukaryotic heterotrophs, suggesting complex plastids are somewhat easier to obtain than primary plastids. This is consistent with the existence of higher-order and serial endosymbioses, i.e., engulfment of complex plastid-bearing algae by (tertiary) eukaryotic hosts and functional plastid replacements, respectively. Plastid endosymbiosis is typical by a massive transfer of genetic material from the endosymbiont to the host nucleus and metabolic rearrangements related to the trophic switch to phototrophy; this is necessary to establish metabolic integration of the plastid and control over its division. Although photosynthesis is the main advantage of plastid acquisition, algae that lost photosynthesis often maintain complex plastids, suggesting their roles beyond photosynthesis. This chapter summarizes basic knowledge on acquisition and functions of complex plastid.
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Affiliation(s)
- Zoltán Füssy
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Branišovská 31, České Budějovice, 37005, Czech Republic
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Miroslav Oborník
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Branišovská 31, České Budějovice, 37005, Czech Republic.
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005, České Budějovice, Czech Republic.
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Reductive evolution of chloroplasts in non-photosynthetic plants, algae and protists. Curr Genet 2017; 64:365-387. [DOI: 10.1007/s00294-017-0761-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/22/2017] [Accepted: 10/04/2017] [Indexed: 11/24/2022]
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30
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Wu CS, Chaw SM. Large-Scale Comparative Analysis Reveals the Mechanisms Driving Plastomic Compaction, Reduction, and Inversions in Conifers II (Cupressophytes). Genome Biol Evol 2017; 8:3740-3750. [PMID: 28039231 PMCID: PMC5491842 DOI: 10.1093/gbe/evw278] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 12/14/2022] Open
Abstract
Conifers II (cupressophytes), comprising about 400 tree species in five families, are the most diverse group of living gymnosperms. Their plastid genomes (plastomes) are highly variable in size and organization, but such variation has never been systematically studied. In this study, we assessed the potential mechanisms underlying the evolution of cupressophyte plastomes. We analyzed the plastomes of 24 representative genera in all of the five cupressophyte families, focusing on their variation in size, noncoding DNA content, and nucleotide substitution rates. Using a tree-based method, we further inferred the ancestral plastomic organizations of internal nodes and evaluated the inversions across the evolutionary history of cupressophytes. Our data showed that variation in plastome size is statistically associated with the dynamics of noncoding DNA content, which results in different degrees of plastomic compactness among the cupressophyte families. The degrees of plastomic inversions also vary among the families, with the number of inversions per genus ranging from 0 in Araucariaceae to 1.27 in Cupressaceae. In addition, we demonstrated that synonymous substitution rates are significantly correlated with plastome size as well as degree of inversions. These data suggest that in cupressophytes, mutation rates play a critical role in driving the evolution of plastomic size while plastomic inversions evolve in a neutral manner.
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Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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31
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Tonti-Filippini J, Nevill PG, Dixon K, Small I. What can we do with 1000 plastid genomes? THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:808-818. [PMID: 28112435 DOI: 10.1111/tpj.13491] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/17/2017] [Accepted: 01/17/2017] [Indexed: 05/21/2023]
Abstract
The plastid genome of plants is the smallest and most gene-rich of the three genomes in each cell and the one generally present in the highest copy number. As a result, obtaining plastid DNA sequence is a particularly cost-effective way of discovering genetic information about a plant. Until recently, the sequence information gathered in this way was generally limited to small portions of the genome amplified by polymerase chain reaction, but recent advances in sequencing technology have stimulated a substantial rate of increase in the sequencing of complete plastid genomes. Within the last year, the number of complete plastid genomes accessible in public sequence repositories has exceeded 1000. This sudden flood of data raises numerous challenges in data analysis and interpretation, but also offers the keys to potential insights across large swathes of plant biology. We examine what has been learnt so far, what more could be learnt if we look at the data in the right way, and what we might gain from the tens of thousands more genome sequences that will surely arrive in the next few years. The most exciting new discoveries are likely to be made at the interdisciplinary interfaces between molecular biology and ecology.
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Affiliation(s)
- Julian Tonti-Filippini
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Paul G Nevill
- Department of Environment and Agriculture, ARC Centre for Mine Site Restoration, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Kingsley Dixon
- Department of Environment and Agriculture, ARC Centre for Mine Site Restoration, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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32
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Yu J, Wang C, Gong X. Degeneration of photosynthetic capacity in mixotrophic plants, Chimaphila japonica and Pyrola decorata (Ericaceae). PLANT DIVERSITY 2017; 39:80-88. [PMID: 30159495 PMCID: PMC6112300 DOI: 10.1016/j.pld.2016.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 05/25/2023]
Abstract
The evolution of photosynthesis is an important feature of mixotrophic plants. Previous inferences proposed that mixotrophic taxa tend to retain most genes relating to photosynthetic functions but vary in plastid gene content. However, no sequence data are available to test this hypothesis in Ericaceae. To investigate changes in plastid genomes that may result from a transition from autotrophy to mixotrophy, the plastomes of two mixotrophic plants, Pyrola decorata and Chimaphila japonica, were sequenced at Illumina's Genome Analyzer and compared to the published plastome of the autotrophic plant Rhododendron simsii, which also belongs to Ericaceae. The greatest discrepancy between mixotrophic and autotrophic plants was that ndh genes for both P. decorata and C. japonica plastomes have nearly all become pseudogenes. P. decorata and C. japonica also retained all genes directly involved in photosynthesis under strong selection. The calculated rate of nonsynonymous nucleotide substitutions and synonymous substitutions of protein-coding genes (dN/dS) showed that substitution rates in shade plants were apparently higher than those in sunlight plants. The two mixotrophic plastomes were generally very similar to that of non-parasitic plants, although ndh genes were largely pseudogenized. Photosynthesis genes under strong selection were retained in the two mixotrophs, however, with greatly increased substitution rates. Further research is needed to gain a clearer understanding of the evolution of autotrophy and mixotrophy in Ericaceae.
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Affiliation(s)
- Jiaojun Yu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, PR China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Kunming, PR China
| | - Chaobo Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, PR China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Kunming, PR China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, PR China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Kunming, PR China
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Figueroa-Martinez F, Nedelcu AM, Reyes-Prieto A, Smith DR. The plastid genomes of nonphotosynthetic algae are not so small after all. Commun Integr Biol 2017; 10:e1283080. [PMID: 28377793 PMCID: PMC5363391 DOI: 10.1080/19420889.2017.1283080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 12/27/2022] Open
Abstract
The thing about plastid genomes in nonphotosynthetic plants and algae is that they are
usually very small and highly compact. This is not surprising: a heterotrophic existence
means that genes for photosynthesis can be easily discarded. But the loss of
photosynthesis cannot explain why the plastomes of heterotrophs are so often depauperate
in noncoding DNA. If plastid genomes from photosynthetic taxa can span the gamut of
compactness, why can't those of nonphotosynthetic species? Well, recently we showed
that they can. The free-living, heterotrophic green alga Polytoma uvella
has a plastid genome boasting more than 165 kilobases of noncoding DNA, making it the most
bloated plastome yet found in a heterotroph. In this addendum to the primary study, we
elaborate on why the P. uvella plastome is so inflated, discussing the
potential impact of a free-living vs. parasitic lifestyle on plastid genome expansion in
nonphotosynthetic lineages.
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Affiliation(s)
- Francisco Figueroa-Martinez
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada; CONACyT-Research Fellow, Universidad Autónoma Metropolitana, Iztapalapa, Vicentina, Mexico City, Mexico; Integrated Microbiology Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - Aurora M Nedelcu
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada; Integrated Microbiology Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada; Integrated Microbiology Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - David R Smith
- Integrated Microbiology Program, Canadian Institute for Advanced Research, Toronto, ON, Canada; Biology Department, University of Western Ontario, London, ON, Canada
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Häder DP, Iseki M. Photomovement in Euglena. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 979:207-235. [DOI: 10.1007/978-3-319-54910-1_11] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Sakamoto H, Suzuki S, Nagamune K, Kita K, Matsuzaki M. Investigation into the Physiological Significance of the Phytohormone Abscisic Acid in Perkinsus marinus, an Oyster Parasite Harboring a Nonphotosynthetic Plastid. J Eukaryot Microbiol 2016; 64:440-446. [PMID: 27813319 PMCID: PMC5573998 DOI: 10.1111/jeu.12379] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 09/30/2016] [Accepted: 10/17/2016] [Indexed: 12/03/2022]
Abstract
Some organisms have retained plastids even after they have lost the ability to photosynthesize. Several studies of nonphotosynthetic plastids in apicomplexan parasites have shown that the isopentenyl pyrophosphate biosynthesis pathway in the organelle is essential for their survival. A phytohormone, abscisic acid, one of several compounds biosynthesized from isopentenyl pyrophosphate, regulates the parasite cell cycle. Thus, it is possible that the phytohormone is universally crucial, even in nonphotosynthetic plastids. Here, we examined this possibility using the oyster parasite Perkinsus marinus, which is a plastid‐harboring cousin of apicomplexan parasites and has independently lost photosynthetic ability. Fluridone, an inhibitor of abscisic acid biosynthesis, blocked parasite growth and induced cell clustering. Nevertheless, abscisic acid and its intermediate carotenoids did not affect parasite growth or rescue the parasite from inhibition. Moreover, abscisic acid was not detected from the parasite using liquid chromatography mass spectrometry. Our findings show that abscisic acid does not play any significant roles in P. marinus.
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Affiliation(s)
- Hirokazu Sakamoto
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Shigeo Suzuki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kisaburo Nagamune
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.,Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Motomichi Matsuzaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
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36
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Roquet C, Coissac É, Cruaud C, Boleda M, Boyer F, Alberti A, Gielly L, Taberlet P, Thuiller W, Van Es J, Lavergne S. Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasite Cytinus hypocistis (Cytinaceae). ANNALS OF BOTANY 2016; 118:885-896. [PMID: 27443299 PMCID: PMC5055816 DOI: 10.1093/aob/mcw135] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/09/2016] [Accepted: 05/12/2016] [Indexed: 05/19/2023]
Abstract
Background and Aims Plant plastid genomes are highly conserved in size, gene content and structure; however, parasitic plants are a noticeable exception to this evolutionary stability. Although the evolution of parasites could help to better understand plastome evolution in general, complete plastomes of parasites have been sequenced only for some lineages so far. Here we contribute to filling this gap by providing and analysing the complete plastome sequence of Cytinus hypocistis, the first parasite sequenced for Malvales and a species suspected to have an extremely small genome. Methods We sequenced and assembled de novo the plastid genome of Cytinus hypocistis using a shotgun approach on genomic DNA. Phylogenomic analyses based on coding regions were performed on Malvidae. For each coding region present in Cytinus, we tested for relaxation or intensification of selective pressures in the Cytinus lineage compared with autotrophic Malvales. Key Results Cytinus hypocistis has an extremely divergent genome that is among the smallest sequenced to date (19·4 kb), with only 23 genes and no inverted repeat regions. Phylogenomic analysis confirmed the position of Cytinus within Malvales. All coding regions of Cytinus plastome presented very high substitution rates compared with non-parasitic Malvales. Conclusions Some regions were inferred to be under relaxed negative selection in Cytinus, suggesting that further plastome reduction is occurring due to relaxed purifying selection associated with the loss of photosynthetic activity. On the other hand, increased selection intensity and strong positive selection were detected for rpl22 in the Cytinus lineage, which might indicate an evolutionary role in the host-parasite arms race, a point that needs further research.
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Affiliation(s)
- Cristina Roquet
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
- *For correspondence. E-mail
| | - Éric Coissac
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Corinne Cruaud
- CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, FR-91057 Evry Cedex, France
| | - Martí Boleda
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Frédéric Boyer
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Adriana Alberti
- CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, FR-91057 Evry Cedex, France
| | - Ludovic Gielly
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Pierre Taberlet
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Wilfried Thuiller
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Jérémie Van Es
- Conservatoire Botanique National Alpin, Domaine de Charance, FR-05000 Gap, France
| | - Sébastien Lavergne
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
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Hadariová L, Vesteg M, Birčák E, Schwartzbach SD, Krajčovič J. An intact plastid genome is essential for the survival of colorless Euglena longa but not Euglena gracilis. Curr Genet 2016; 63:331-341. [PMID: 27553633 DOI: 10.1007/s00294-016-0641-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/02/2016] [Accepted: 08/13/2016] [Indexed: 12/18/2022]
Abstract
Euglena gracilis growth with antibacterial agents leads to bleaching, permanent plastid gene loss. Colorless Euglena (Astasia) longa resembles a bleached E. gracilis. To evaluate the role of bleaching in E. longa evolution, the effect of streptomycin, a plastid protein synthesis inhibitor, and ofloxacin, a plastid DNA gyrase inhibitor, on E. gracilis and E. longa growth and plastid DNA content were compared. E. gracilis growth was unaffected by streptomycin and ofloxacin. Quantitative PCR analyses revealed a time dependent loss of plastid genes in E. gracilis demonstrating that bleaching agents produce plastid gene deletions without affecting cell growth. Streptomycin and ofloxacin inhibited E. longa growth indicating that it requires plastid genes to survive. This suggests that evolutionary divergence of E. longa from E. gracilis was triggered by the loss of a cytoplasmic metabolic activity also occurring in the plastid. Plastid metabolism has become obligatory for E. longa cell growth. A process termed "intermittent bleaching", short term exposure to subsaturating concentrations of reversible bleaching agents followed by growth in the absence of a bleaching agent, is proposed as the molecular mechanism for E. longa plastid genome reduction. Various non-photosynthetic lineages could have independently arisen from their photosynthetic ancestors via a similar process.
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Affiliation(s)
- Lucia Hadariová
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina G-1, 842 15, Bratislava, Slovak Republic
| | - Matej Vesteg
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University, 974 01, Banská Bystrica, Slovakia
| | - Erik Birčák
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina G-1, 842 15, Bratislava, Slovak Republic
| | | | - Juraj Krajčovič
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina G-1, 842 15, Bratislava, Slovak Republic. .,Department of Biology, Faculty of Natural Sciences, University of ss. Cyril and Methodius, 917 01, Trnava, Slovakia.
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38
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Shapiro JA. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process. BIOLOGY 2016; 5:E27. [PMID: 27338490 PMCID: PMC4929541 DOI: 10.3390/biology5020027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/20/2016] [Accepted: 06/02/2016] [Indexed: 01/15/2023]
Abstract
The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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39
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Lim GS, Barrett CF, Pang CC, Davis JI. Drastic reduction of plastome size in the mycoheterotrophic Thismia tentaculata relative to that of its autotrophic relative Tacca chantrieri. AMERICAN JOURNAL OF BOTANY 2016; 103:1129-37. [PMID: 27335389 DOI: 10.3732/ajb.1600042] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/06/2016] [Indexed: 05/23/2023]
Abstract
PREMISE OF THE STUDY Heterotrophic angiosperms tend to have reduced plastome sizes relative to those of their autotrophic relatives because genes that code for proteins involved in photosynthesis are lost. However, some plastid-encoded proteins may have vital nonphotosynthetic functions, and the plastome therefore may be retained after the loss of photosynthesis. METHODS We sequenced the plastome of the mycoheterotrophic species Thismia tentaculata and a representative of its sister genus, Tacca chantrieri, using next-generation technology, and we compared sequences and structures of genes and genomes of these species. KEY RESULTS The plastome of Tacca chantrieri is similar to those of other autotrophic taxa of Dioscoreaceae, except in a few local rearrangements and one gene loss. The plastome of Thismia tentaculata is ca. 16 kbp long with a quadripartite structure and is among the smallest known plastomes. Synteny is minimal between the plastomes of Tacca chantrieri and Thismia tentaculata. The latter includes only 12 candidate genes, with all except accD involved in protein synthesis. Of the 12 genes, trnE, trnfM, and accD are frequently among the few that remain in depauperate plastomes. CONCLUSIONS The plastome of Thismia tentaculata, like those of most other heterotrophic plants, includes a small number of genes previously suggested to be essential to plastome survival.
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Affiliation(s)
- Gwynne S Lim
- The New York Botanical Garden, Pfizer Plant Research Laboratory, 2900 Southern Boulevard, Bronx, New York 10458 USA L. H. Bailey Hortorium, Section of Plant Biology, 412 Mann Library Building, Cornell University, Ithaca, New York 14853 USA
| | - Craig F Barrett
- Department of Biology, Life Sciences Building, PO Box 6057, Morgantown, West Virginia 26506 USA
| | - Chun-Chiu Pang
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jerrold I Davis
- L. H. Bailey Hortorium, Section of Plant Biology, 412 Mann Library Building, Cornell University, Ithaca, New York 14853 USA
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40
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Shefferson RP, Roy M, Püttsepp Ü, Selosse MA. Demographic shifts related to mycoheterotrophy and their fitness impacts in twoCephalantheraspecies. Ecology 2016; 97:1452-62. [DOI: 10.1890/15-1336.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Richard P. Shefferson
- Department of General Systems Sciences; University of Tokyo; 3-8-1 Komaba Tokyo 153-8902 Japan
| | - Mélanie Roy
- Laboratoire Evolution et Diversité Biologique; Université Paul Sabatier - CNRS; UMR5174; 118 route de Narbonne 31062 Toulouse Cedex France
| | - Ülle Püttsepp
- Institute of Agricultural and Environmental Sciences; Estonian University of Life Sciences; Street Kreutzwaldi 5 51014 Tartu Estonia
| | - Marc-André Selosse
- Institut de Systématique; Évolution, Biodiversité (ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE); Muséum national d'Histoire naturelle; Sorbonne Universités; 57 rue Cuvier CP50 75005 Paris France
- Department of Plant Taxonomy and Nature Conservation; University of Gdansk; Wita Stwosza 59 80-308 Gdansk Poland
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41
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O'Malley MA, Wideman JG, Ruiz-Trillo I. Losing Complexity: The Role of Simplification in Macroevolution. Trends Ecol Evol 2016; 31:608-621. [PMID: 27212432 DOI: 10.1016/j.tree.2016.04.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 10/21/2022]
Abstract
Macroevolutionary patterns can be produced by combinations of diverse and even oppositional dynamics. A growing body of data indicates that secondary simplifications of molecular and cellular structures are common. Some major diversifications in eukaryotes have occurred because of loss and minimalisation; numerous episodes in prokaryote evolution have likewise been driven by the reduction of structure. After examining a range of examples of secondary simplification and its consequences across the tree of life, we address how macroevolutionary explanations might incorporate simplification as well as complexification, and adaptive as well as nonadaptive dynamics.
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Affiliation(s)
- Maureen A O'Malley
- UMR5164, University of Bordeaux, 146 Rue Léo Saignat, Bordeaux 33076, France.
| | | | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain; Departament de Genètica, Universitat de Barcelona, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats, Pg Lluis Companys 23, 08010 Barcelona, Spain
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42
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Naumann J, Der JP, Wafula EK, Jones SS, Wagner ST, Honaas LA, Ralph PE, Bolin JF, Maass E, Neinhuis C, Wanke S, dePamphilis CW. Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic Plant Hydnora visseri (Hydnoraceae). Genome Biol Evol 2016; 8:345-63. [PMID: 26739167 PMCID: PMC4779604 DOI: 10.1093/gbe/evv256] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2015] [Indexed: 11/14/2022] Open
Abstract
Plastid genomes of photosynthetic flowering plants are usually highly conserved in both structure and gene content. However, the plastomes of parasitic and mycoheterotrophic plants may be released from selective constraint due to the reduction or loss of photosynthetic ability. Here we present the greatly reduced and highly divergent, yet functional, plastome of the nonphotosynthetic holoparasite Hydnora visseri (Hydnoraceae, Piperales). The plastome is 27 kb in length, with 24 genes encoding ribosomal proteins, ribosomal RNAs, tRNAs, and a few nonbioenergetic genes, but no genes related to photosynthesis. The inverted repeat and the small single copy region are only approximately 1.5 kb, and intergenic regions have been drastically reduced. Despite extreme reduction, gene order and orientation are highly similar to the plastome of Piper cenocladum, a related photosynthetic plant in Piperales. Gene sequences in Hydnora are highly divergent and several complementary approaches using the highest possible sensitivity were required for identification and annotation of this plastome. Active transcription is detected for all of the protein-coding genes in the plastid genome, and one of two introns is appropriately spliced out of rps12 transcripts. The whole-genome shotgun read depth is 1,400× coverage for the plastome, whereas the mitochondrial genome is covered at 40× and the nuclear genome at 2×. Despite the extreme reduction of the genome and high sequence divergence, the presence of syntenic, long transcriptionally active open-reading frames with distant similarity to other plastid genomes and a high plastome stoichiometry relative to the mitochondrial and nuclear genomes suggests that the plastome remains functional in H. visseri. A four-stage model of gene reduction, including the potential for complete plastome loss, is proposed to account for the range of plastid genomes in nonphotosynthetic plants.
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Affiliation(s)
- Julia Naumann
- Institut für Botanik, Technische Universität Dresden, Germany Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University
| | - Joshua P Der
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Department of Biological Science, California State University Fullerton
| | - Eric K Wafula
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University
| | - Samuel S Jones
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Intercollege Graduate Program in Plant Biology, The Pennsylvania State University
| | - Sarah T Wagner
- Institut für Botanik, Technische Universität Dresden, Germany
| | - Loren A Honaas
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University
| | - Paula E Ralph
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University
| | | | - Erika Maass
- Department of Biological Sciences, University of Namibia, Windhoek, Namibia
| | | | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Germany
| | - Claude W dePamphilis
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Intercollege Graduate Program in Plant Biology, The Pennsylvania State University
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43
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Ranade SS, García-Gil MR, Rosselló JA. Non-functional plastid ndh gene fragments are present in the nuclear genome of Norway spruce (Picea abies L. Karsch): insights from in silico analysis of nuclear and organellar genomes. Mol Genet Genomics 2016; 291:935-41. [PMID: 26732267 DOI: 10.1007/s00438-015-1159-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/09/2015] [Indexed: 12/24/2022]
Abstract
Many genes have been lost from the prokaryote plastidial genome during the early events of endosymbiosis in eukaryotes. Some of them were definitively lost, but others were relocated and functionally integrated to the host nuclear genomes through serial events of gene transfer during plant evolution. In gymnosperms, plastid genome sequencing has revealed the loss of ndh genes from several species of Gnetales and Pinaceae, including Norway spruce (Picea abies). This study aims to trace the ndh genes in the nuclear and organellar Norway spruce genomes. The plastid genomes of higher plants contain 11 ndh genes which are homologues of mitochondrial genes encoding subunits of the proton-pumping NADH-dehydrogenase (nicotinamide adenine dinucleotide dehydrogenase) or complex I (electron transport chain). Ndh genes encode 11 NDH polypeptides forming the Ndh complex (analogous to complex I) which seems to be primarily involved in chloro-respiration processes. We considered ndh genes from the plastidial genome of four gymnosperms (Cryptomeria japonica, Cycas revoluta, Ginkgo biloba, Podocarpus totara) and a single angiosperm species (Arabidopsis thaliana) to trace putative homologs in the nuclear and organellar Norway spruce genomes using tBLASTn to assess the evolutionary fate of ndh genes in Norway spruce and to address their genomic location(s), structure, integrity and functionality. The results obtained from tBLASTn were subsequently analyzed by performing homology search for finding ndh specific conserved domains using conserved domain search. We report the presence of non-functional plastid ndh gene fragments, excepting ndhE and ndhG genes, in the nuclear genome of Norway spruce. Regulatory transcriptional elements like promoters, TATA boxes and enhancers were detected in the upstream regions of some ndh fragments. We also found transposable elements in the flanking regions of few ndh fragments suggesting nuclear rearrangements in those regions. These evidences support the hypothesis that, at least in Picea, ndh translocations from the plastid to the nuclear genome have occurred, and that there might have been a functional machinery at some time during evolution to accommodate them within a nuclear-encoded environment, or attempts to form it.
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Affiliation(s)
- Sonali Sachin Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden.
| | - María Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Josep A Rosselló
- Jardí Botànic, Universidad de Valencia, c/Quart 80, 46008, Valencia, Spain
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Ross TG, Barrett CF, Soto Gomez M, Lam VK, Henriquez CL, Les DH, Davis JI, Cuenca A, Petersen G, Seberg O, Thadeo M, Givnish TJ, Conran J, Stevenson DW, Graham SW. Plastid phylogenomics and molecular evolution of Alismatales. Cladistics 2015; 32:160-178. [DOI: 10.1111/cla.12133] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2015] [Indexed: 11/27/2022] Open
Affiliation(s)
- T. Gregory Ross
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Craig F. Barrett
- Department of Biological Sciences 5151 State University Dr. California State University Los Angeles CA 90032‐8201 USA
| | - Marybel Soto Gomez
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Vivienne K.Y. Lam
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Claudia L. Henriquez
- Evolution, Ecology & Population Biology Division of Biology Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Donald H. Les
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT 06269‐3043 USA
| | - Jerrold I. Davis
- L. H. Bailey Hortorium and Section of Plant Biology Cornell University Ithaca NY 14853 USA
| | - Argelia Cuenca
- Natural History Museum of Denmark University of Copenhagen Sølvgade 83 Opg. S DK‐1307 Copenhagen Denmark
| | - Gitte Petersen
- Natural History Museum of Denmark University of Copenhagen Sølvgade 83 Opg. S DK‐1307 Copenhagen Denmark
| | - Ole Seberg
- Natural History Museum of Denmark University of Copenhagen Sølvgade 83 Opg. S DK‐1307 Copenhagen Denmark
| | | | | | - John Conran
- Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre School of Biological Sciences Benham Bldg DX 650 312 The University of Adelaide Adelaide SA 5005 Australia
| | | | - Sean W. Graham
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
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Zhan Y, Dhaliwal JS, Adjibade P, Uniacke J, Mazroui R, Zerges W. Localized control of oxidized RNA. J Cell Sci 2015; 128:4210-9. [PMID: 26449969 DOI: 10.1242/jcs.175232] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 09/23/2015] [Indexed: 12/23/2022] Open
Abstract
The oxidation of biological molecules by reactive oxygen species (ROS) can render them inactive or toxic. This includes the oxidation of RNA, which appears to underlie the detrimental effects of oxidative stress, aging and certain neurodegenerative diseases. Here, we investigate the management of oxidized RNA in the chloroplast of the green alga Chlamydomonas reinhardtii. Our immunofluorescence microscopy results reveal that oxidized RNA (with 8-hydroxyguanine) is localized in the pyrenoid, a chloroplast microcompartment where CO2 is assimilated by the Calvin cycle enzyme Rubisco. Results of genetic analyses support a requirement for the Rubisco large subunit (RBCL), but not Rubisco, in the management of oxidized RNA. An RBCL pool that can carry out such a 'moonlighting' function is revealed by results of biochemical fractionation experiments. We also show that human (HeLa) cells localize oxidized RNA to cytoplasmic foci that are distinct from stress granules, processing bodies and mitochondria. Our results suggest that the compartmentalization of oxidized RNA management is a general phenomenon and therefore has some fundamental significance.
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Affiliation(s)
- Yu Zhan
- Biology Department & Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke W, Montreal, Quebec, Canada H4B 1R6
| | - James S Dhaliwal
- Biology Department & Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke W, Montreal, Quebec, Canada H4B 1R6
| | - Pauline Adjibade
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University, Centre de Recherche le CHU de Quebec, Quebec, Canada G1V 4G2
| | - James Uniacke
- Biology Department & Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke W, Montreal, Quebec, Canada H4B 1R6
| | - Rachid Mazroui
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University, Centre de Recherche le CHU de Quebec, Quebec, Canada G1V 4G2
| | - William Zerges
- Biology Department & Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke W, Montreal, Quebec, Canada H4B 1R6
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Behdarvandi B, Guinel FC, Costea M. Differential effects of ephemeral colonization by arbuscular mycorrhizal fungi in two Cuscuta species with different ecology. MYCORRHIZA 2015; 25:573-585. [PMID: 25720736 DOI: 10.1007/s00572-015-0632-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 02/06/2015] [Indexed: 06/04/2023]
Abstract
Seedlings of parasitic Cuscuta species are autotrophic but can survive only a short period of time, during which they must locate and attach to a suitable host. They have an ephemeral root-like organ considered not a "true" root by most studies. In the present study, two species with contrasting ecology were examined: Cuscuta gronovii, a North American riparian species, and Cuscuta campestris, an invasive dodder that thrives in disturbed habitats. The morphology, structure, and absorptive capability of their root-like organ were compared, their potential for colonization by two species of arbuscular mycorrhizal fungi (AMF) was assessed, and the effect of the AMF on seedling growth and survival was determined. The root of both species absorbed water and interacted with AMF, but the two species exhibited dissimilar growth and survival patterns depending on the colonization level of their seedlings. The extensively colonized seedlings of C. gronovii grew more and survived longer than non-colonized seedlings. In contrast, the scarce colonization of C. campestris seedlings did not increase their growth or longevity. The differential growth responses of the AMF-colonized and non-colonized Cuscuta species suggest a mycorrhizal relationship and reflect their ecology. While C. gronovii roots have retained a higher ability to interact with AMF and are likely to take advantage of fungal communities in riparian habitats, the invasive C. campestris has largely lost this ability possibly as an adaptation to disturbed ecosystems. These results indicate that dodders have a true root, even if much reduced and ephemeral, that can interact with AMF.
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Affiliation(s)
- Behrang Behdarvandi
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada
| | - Frédérique C Guinel
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada
| | - Mihai Costea
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada.
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Auxenochlorella protothecoides and Prototheca wickerhamii plastid genome sequences give insight into the origins of non-photosynthetic algae. Sci Rep 2015; 5:14465. [PMID: 26403826 PMCID: PMC4585924 DOI: 10.1038/srep14465] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 08/28/2015] [Indexed: 01/16/2023] Open
Abstract
The forfeiting of photosynthetic capabilities has occurred independently many times throughout eukaryotic evolution. But almost all non-photosynthetic plants and algae still retain a colorless plastid and an associated genome, which performs fundamental processes apart from photosynthesis. Unfortunately, little is known about the forces leading to photosynthetic loss; this is largely because there is a lack of data from transitional species. Here, we compare the plastid genomes of two “transitional” green algae: the photosynthetic, mixotrophic Auxenochlorella protothecoides and the non-photosynthetic, obligate heterotroph Prototheca wickerhamii. Remarkably, the plastid genome of A. protothecoides is only slightly larger than that of P. wickerhamii, making it among the smallest plastid genomes yet observed from photosynthetic green algae. Even more surprising, both algae have almost identical plastid genomic architectures and gene compositions (with the exception of genes involved in photosynthesis), implying that they are closely related. This close relationship was further supported by phylogenetic and substitution rate analyses, which suggest that the lineages giving rise to A. protothecoides and P. wickerhamii diverged from one another around six million years ago.
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48
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Lam VKY, Soto Gomez M, Graham SW. The Highly Reduced Plastome of Mycoheterotrophic Sciaphila (Triuridaceae) Is Colinear with Its Green Relatives and Is under Strong Purifying Selection. Genome Biol Evol 2015; 7:2220-36. [PMID: 26170229 PMCID: PMC4558852 DOI: 10.1093/gbe/evv134] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2015] [Indexed: 11/14/2022] Open
Abstract
The enigmatic monocot family Triuridaceae provides a potentially useful model system for studying the effects of an ancient loss of photosynthesis on the plant plastid genome, as all of its members are mycoheterotrophic and achlorophyllous. However, few studies have placed the family in a comparative context, and its phylogenetic placement is only partly resolved. It was also unclear whether any taxa in this family have retained a plastid genome. Here, we used genome survey sequencing to retrieve plastid genome data for Sciaphila densiflora (Triuridaceae) and ten autotrophic relatives in the orders Dioscoreales and Pandanales. We recovered a highly reduced plastome for Sciaphila that is nearly colinear with Carludovica palmata, a photosynthetic relative that belongs to its sister group in Pandanales, Cyclanthaceae-Pandanaceae. This phylogenetic placement is well supported and robust to a broad range of analytical assumptions in maximum-likelihood inference, and is congruent with recent findings based on nuclear and mitochondrial evidence. The 28 genes retained in the S. densiflora plastid genome are involved in translation and other nonphotosynthetic functions, and we demonstrate that nearly all of the 18 protein-coding genes are under strong purifying selection. Our study confirms the utility of whole plastid genome data in phylogenetic studies of highly modified heterotrophic plants, even when they have substantially elevated rates of substitution.
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Affiliation(s)
- Vivienne 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
| | - Marybel Soto Gomez
- 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
| | - Sean 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
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Kamikawa R, Tanifuji G, Ishikawa SA, Ishii KI, Matsuno Y, Onodera NT, Ishida KI, Hashimoto T, Miyashita H, Mayama S, Inagaki Y. Proposal of a Twin Aarginine Translocator System-Mediated Constraint against Loss of ATP Synthase Genes from Nonphotosynthetic Plastid Genomes. Mol Biol Evol 2015; 32:2598-604. [DOI: 10.1093/molbev/msv134] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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50
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Barrett CF, Freudenstein JV, Li J, Mayfield-Jones DR, Perez L, Pires JC, Santos C. Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms. Mol Biol Evol 2014; 31:3095-112. [PMID: 25172958 DOI: 10.1093/molbev/msu252] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Parasitic organisms exemplify morphological and genomic reduction. Some heterotrophic, parasitic plants harbor drastically reduced and degraded plastid genomes resulting from relaxed selective pressure on photosynthetic function. However, few studies have addressed the initial stages of plastome degradation in groups containing both photosynthetic and nonphotosynthetic species. Corallorhiza is a genus of leafless, heterotrophic orchids that contains both green, photosynthetic species and nongreen, putatively nonphotosynthetic species, and represents an ideal system in which to assess the beginning of the transition to a "minimal plastome." Complete plastomes were generated for nine taxa of Corallorhiza using Illumina paired-end sequencing of genomic DNA to assess the degree of degradation among taxa, and for comparison with a general model of degradation among angiosperms. Quantification of total chlorophyll suggests that nongreen Corallorhiza still produce chlorophyll, but at 10-fold lower concentrations than green congeners. Complete plastomes and partial nuclear rDNA cistrons yielded a fully resolved tree for Corallorhiza, with at least two independent losses of photosynthesis, evidenced by gene deletions and pseudogenes in Co. striata and nongreen Co. maculata. All Corallorhiza show some evidence of degradation in genes of the NAD(P)H dehydrogenase complex. Among genes with open reading frames, photosynthesis-related genes displayed evidence of neutral evolution in nongreen Corallorhiza, whereas genes of the ATP synthase complex displayed some evidence of positive selection in these same groups, though for reasons unknown. Corallorhiza spans the early stages of a general model of plastome degradation and has added critical insight for understanding the process of plastome evolution in heterotrophic angiosperms.
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Affiliation(s)
- Craig F Barrett
- Department of Biological Sciences, California State University, Los Angeles
| | - John V Freudenstein
- Department of Evolution, Ecology, and Organismal Biology and the Museum of Biological Diversity, Ohio State University
| | - Jeff Li
- Department of Biological Sciences, California State University, Los Angeles
| | | | - Leticia Perez
- Department of Biological Sciences, California State University, Los Angeles
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri
| | - Cristian Santos
- Department of Biological Sciences, California State University, Los Angeles
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