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Sanchez-Puerta MV, Ceriotti LF, Gatica-Soria LM, Roulet ME, Garcia LE, Sato HA. Invited Review Beyond parasitic convergence: unravelling the evolution of the organellar genomes in holoparasites. ANNALS OF BOTANY 2023; 132:909-928. [PMID: 37503831 PMCID: PMC10808021 DOI: 10.1093/aob/mcad108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/27/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND The molecular evolution of organellar genomes in angiosperms has been studied extensively, with some lineages, such as parasitic ones, displaying unique characteristics. Parasitism has emerged 12 times independently in angiosperm evolution. Holoparasitism is the most severe form of parasitism, and is found in ~10 % of parasitic angiosperms. Although a few holoparasitic species have been examined at the molecular level, most reports involve plastomes instead of mitogenomes. Parasitic plants establish vascular connections with their hosts through haustoria to obtain water and nutrients, which facilitates the exchange of genetic information, making them more susceptible to horizontal gene transfer (HGT). HGT is more prevalent in the mitochondria than in the chloroplast or nuclear compartments. SCOPE This review summarizes current knowledge on the plastid and mitochondrial genomes of holoparasitic angiosperms, compares the genomic features across the different lineages, and discusses their convergent evolutionary trajectories and distinctive features. We focused on Balanophoraceae (Santalales), which exhibits extraordinary traits in both their organelles. CONCLUSIONS Apart from morphological similarities, plastid genomes of holoparasitic plants also display other convergent features, such as rampant gene loss, biased nucleotide composition and accelerated evolutionary rates. In addition, the plastomes of Balanophoraceae have extremely low GC and gene content, and two unexpected changes in the genetic code. Limited data on the mitochondrial genomes of holoparasitic plants preclude thorough comparisons. Nonetheless, no obvious genomic features distinguish them from the mitochondria of free-living angiosperms, except for a higher incidence of HGT. HGT appears to be predominant in holoparasitic angiosperms with a long-lasting endophytic stage. Among the Balanophoraceae, mitochondrial genomes exhibit disparate evolutionary paths with notable levels of heteroplasmy in Rhopalocnemis and unprecedented levels of HGT in Lophophytum. Despite their differences, these Balanophoraceae share a multichromosomal mitogenome, a feature also found in a few free-living angiosperms.
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Affiliation(s)
- M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - Luis F Ceriotti
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - Leonardo M Gatica-Soria
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - M Emilia Roulet
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
| | - Laura E Garcia
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - Hector A Sato
- Facultad de Ciencias Agrarias, Cátedra de Botánica General–Herbario JUA, Alberdi 47, Universidad Nacional de Jujuy, 4600 Jujuy, Argentina
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Pan H, Zagorchev L, Chen L, Tao Y, Cai C, Jiang M, Sun Z, Li J. Complete chloroplast genomes of five Cuscuta species and their evolutionary significance in the Cuscuta genus. BMC Genomics 2023; 24:310. [PMID: 37291497 DOI: 10.1186/s12864-023-09427-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/03/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND Cuscuta, a parasitic plant species in the Convolvulaceae family, grows in many countries and regions. However, the relationship between some species is still unclear. Therefore, more studies are needed to assess the variation of the chloroplast (cp) genome in Cuscuta species and their relationship with subgenera or sections, thus, providing important information on the evolution of Cuscuta species. RESULTS In the present study, we identified the whole cp genomes of C. epithymum, C. europaea, C. gronovii, C. chinensis and C. japonica, and then constructed a phylogenetic tree of 23 Cuscuta species based on the complete genome sequences and protein-coding genes. The complete cp genome sequences of C. epithymum and C. europaea were 96,292 and 97,661 bp long, respectively, and lacked an inverted repeat region. Most cp genomes of Cuscuta spp. have tetragonal and circular structures except for C. epithymum, C. europaea, C. pedicellata and C. approximata. Based on the number of genes and the structure of cp genome and the patterns of gene reduction, we found that C. epithymum and C. europaea belonged to subgenus Cuscuta. Most of the cp genomes of the 23 Cuscuta species had single nucleotide repeats of A and T. The inverted repeat region boundaries among species were similar in the same subgenera. Several cp genes were lost. In addition, the numbers and types of the lost genes in the same subgenus were similar. Most of the lost genes were related to photosynthesis (ndh, rpo, psa, psb, pet, and rbcL), which could have gradually caused the plants to lose the ability to photosynthesize. CONCLUSION Our results enrich the data on cp. genomes of genus Cuscuta. This study provides new insights into understanding the phylogenetic relationships and variations in the cp genome of Cuscuta species.
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Affiliation(s)
- Hangkai Pan
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Lyuben Zagorchev
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- Department of Biochemistry, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tsankov Blvd., Sofia, 1164, Bulgaria
| | - Luxi Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
| | - Yutian Tao
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Electronics and Information Engineering, Taizhou University, Taizhou, 318000, China
| | - Chaonan Cai
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Advanced Study, Taizhou University, Taizhou, 318000, China
| | - Ming Jiang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
| | - Zhongshuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Advanced Study, Taizhou University, Taizhou, 318000, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China.
- School of Advanced Study, Taizhou University, Taizhou, 318000, China.
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Timilsena PR, Barrett CF, Piñeyro-Nelson A, Wafula EK, Ayyampalayam S, McNeal JR, Yukawa T, Givnish TJ, Graham SW, Pires JC, Davis JI, Ané C, Stevenson DW, Leebens-Mack J, Martínez-Salas E, Álvarez-Buylla ER, dePamphilis CW. Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages. Genome Biol Evol 2023; 15:evac183. [PMID: 36582124 PMCID: PMC9887272 DOI: 10.1093/gbe/evac183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/13/2022] [Accepted: 12/18/2022] [Indexed: 12/31/2022] Open
Abstract
Mycoheterotrophy is an alternative nutritional strategy whereby plants obtain sugars and other nutrients from soil fungi. Mycoheterotrophy and associated loss of photosynthesis have evolved repeatedly in plants, particularly in monocots. Although reductive evolution of plastomes in mycoheterotrophs is well documented, the dynamics of nuclear genome evolution remains largely unknown. Transcriptome datasets were generated from four mycoheterotrophs in three families (Orchidaceae, Burmanniaceae, Triuridaceae) and related green plants and used for phylogenomic analyses to resolve relationships among the mycoheterotrophs, their relatives, and representatives across the monocots. Phylogenetic trees based on 602 genes were mostly congruent with plastome phylogenies, except for an Asparagales + Liliales clade inferred in the nuclear trees. Reduction and loss of chlorophyll synthesis and photosynthetic gene expression and relaxation of purifying selection on retained genes were progressive, with greater loss in older nonphotosynthetic lineages. One hundred seventy-four of 1375 plant benchmark universally conserved orthologous genes were undetected in any mycoheterotroph transcriptome or the genome of the mycoheterotrophic orchid Gastrodia but were expressed in green relatives, providing evidence for massively convergent gene loss in nonphotosynthetic lineages. We designate this set of deleted or undetected genes Missing in Mycoheterotrophs (MIM). MIM genes encode not only mainly photosynthetic or plastid membrane proteins but also a diverse set of plastid processes, genes of unknown function, mitochondrial, and cellular processes. Transcription of a photosystem II gene (psb29) in all lineages implies a nonphotosynthetic function for this and other genes retained in mycoheterotrophs. Nonphotosynthetic plants enable novel insights into gene function as well as gene expression shifts, gene loss, and convergence in nuclear genomes.
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Affiliation(s)
- Prakash Raj Timilsena
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania
| | - Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia
| | - Alma Piñeyro-Nelson
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania
| | | | - Joel R McNeal
- Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, Georgia
| | - Tomohisa Yukawa
- Tsukuba Botanical Garden, National Museum of Nature and Science, 1-1, Amakubo 4, Tsukuba, 305-0005, Japan
| | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4Canada
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri–Columbia, Columbia, Missouri
| | - Jerrold I Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 1485
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Statistics, University of Wisconsin–Madison, Madison, Wisconsin
| | | | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia, 3060
| | - Esteban Martínez-Salas
- Departmento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, México
| | - Elena R Álvarez-Buylla
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Claude W dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania
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Guo X, Liu C, Wang H, Zhang G, Yan H, Jin L, Su W, Ji Y. The complete plastomes of two flowering epiparasites (Phacellaria glomerata and P. compressa): Gene content, organization, and plastome degradation. Genomics 2020; 113:447-455. [PMID: 33370586 DOI: 10.1016/j.ygeno.2020.12.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 03/10/2020] [Accepted: 12/22/2020] [Indexed: 11/28/2022]
Abstract
A plant parasite obligately parasitizing another plant parasite is referred to as epiparasite, which is extremely rare in angiosperms, and their complete plastome sequences have not been characterized to date. In this study, the complete plastomes of two flowering epiparasites: Phacellaria compressa and P. glomerata (Amphorogynaceae, Santalales) were sequenced. The plastomes of both species are of similar size, structure, gene content, and arrangement of genes to other hemiparasites in Santalales. Their plastomes were characterized by the functional loss of plastid-encoded NAD(P)H-dehydrogenase and infA genes, which strongly coincides with the general pattern of plastome degradation observed in Santalales hemiparasites. Our study demonstrates that the relatively higher level of nutritional reliance on the host plants and the reduced vegetative bodies of P. compressa and P. glomerata do not appear to cause any unique plastome degradation compared with their closely related hemiparasites.
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Affiliation(s)
- Xiaorong Guo
- Institute of Ecology and Geobotany, Yunnan University, Kunming, Yunnan, China
| | - Changkun Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Guangfei Zhang
- Institute of Ecology and Geobotany, Yunnan University, Kunming, Yunnan, China
| | - Hanjing Yan
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Lei Jin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China; School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Wenhua Su
- Institute of Ecology and Geobotany, Yunnan University, Kunming, Yunnan, China
| | - Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China; Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
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5
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Schneider AC, Braukmann T, Banerjee A, Stefanovic S. Convergent Plastome Evolution and Gene Loss in Holoparasitic Lennoaceae. Genome Biol Evol 2018; 10:2663-2670. [PMID: 30169817 PMCID: PMC6178340 DOI: 10.1093/gbe/evy190] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2018] [Indexed: 11/15/2022] Open
Abstract
The Lennoaceae, a small monophyletic plant family of root parasites endemic to the Americas, are one of the last remaining independently evolved lineages of parasitic angiosperms lacking a published plastome. In this study, we present the assembled and annotated plastomes of two species spanning the crown node of Lennoaceae, Lennoa madreporoides and Pholisma arenarium, as well as their close autotrophic relative from the sister family Ehretiaceae, Tiquilia plicata. We find that the plastomes of L. madreporoides and P. arenarium are similar in size and gene content, and substantially reduced compared to T. plicata, consistent with trends seen in other holoparasitic lineages. In particular, most plastid genes involved in photosynthesis function have been lost, whereas housekeeping genes (ribosomal protein-coding genes, rRNAs, and tRNAs) are retained. One notable exception is the persistence of a rbcL open reading frame in P. arenarium but not L. madreporoides suggesting a nonphotosynthetic function for this gene. Of the retained coding genes, dN/dS ratios indicate that some remain under purifying selection, whereas others show relaxed selection. Overall, this study supports the mounting evidence for convergent plastome evolution in flowering plants following the shift to heterotrophy.
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Affiliation(s)
- Adam C Schneider
- Department of Biology, University of Toronto Mississauga, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.,Department of Biology, Hendrix College, Conway, AR
| | - Thomas Braukmann
- Centre for Biodiversity Genomics, University of Guelph, Ontario, Canada
| | - Arjan Banerjee
- Department of Biology, University of Toronto Mississauga, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Saša Stefanovic
- Department of Biology, University of Toronto Mississauga, Ontario, Canada
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6
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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: 51] [Impact Index Per Article: 8.5] [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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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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Bellot S, Cusimano N, Luo S, Sun G, Zarre S, Gröger A, Temsch E, Renner SS. Assembled Plastid and Mitochondrial Genomes, as well as Nuclear Genes, Place the Parasite Family Cynomoriaceae in the Saxifragales. Genome Biol Evol 2016; 8:2214-30. [PMID: 27358425 PMCID: PMC4987112 DOI: 10.1093/gbe/evw147] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cynomoriaceae, one of the last unplaced families of flowering plants, comprise one or two species or subspecies of root parasites that occur from the Mediterranean to the Gobi Desert. Using Illumina sequencing, we assembled the mitochondrial and plastid genomes as well as some nuclear genes of a
Cynomorium
specimen from Italy. Selected genes were also obtained by Sanger sequencing from individuals collected in China and Iran, resulting in matrices of 33 mitochondrial, 6 nuclear, and 14 plastid genes and rDNAs enlarged to include a representative angiosperm taxon sampling based on data available in GenBank. We also compiled a new geographic map to discern possible discontinuities in the parasites’ occurrence.
Cynomorium
has large genomes of 13.70–13.61 (Italy) to 13.95–13.76 pg (China). Its mitochondrial genome consists of up to 49 circular subgenomes and has an overall gene content similar to that of photosynthetic angiosperms, while its plastome retains only 27 of the normally 116 genes. Nuclear, plastid and mitochondrial phylogenies place Cynomoriaceae in Saxifragales, and we found evidence for several horizontal gene transfers from different hosts, as well as intracellular gene transfers.
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Affiliation(s)
- Sidonie Bellot
- Department of Plant Sciences, Plant Biodiversity Research, Technical University of Munich (TUM), Freising, Germany
| | - Natalie Cusimano
- Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Germany
| | - Shixiao Luo
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Guangzhou, China
| | - Guiling Sun
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, China
| | - Shahin Zarre
- Department of Plant Sciences, University of Tehran, Iran
| | | | - Eva Temsch
- Department of Systematic and Evolutionary Botany, University of Vienna, Austria
| | - Susanne S Renner
- Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Germany
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Logacheva MD, Schelkunov MI, Shtratnikova VY, Matveeva MV, Penin AA. Comparative analysis of plastid genomes of non-photosynthetic Ericaceae and their photosynthetic relatives. Sci Rep 2016; 6:30042. [PMID: 27452401 PMCID: PMC4958920 DOI: 10.1038/srep30042] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/27/2016] [Indexed: 12/24/2022] Open
Abstract
Although plastid genomes of flowering plants are typically highly conserved regarding their size, gene content and order, there are some exceptions. Ericaceae, a large and diverse family of flowering plants, warrants special attention within the context of plastid genome evolution because it includes both non-photosynthetic and photosynthetic species with rearranged plastomes and putative losses of "essential" genes. We characterized plastid genomes of three species of Ericaceae, non-photosynthetic Monotropa uniflora and Hypopitys monotropa and photosynthetic Pyrola rotundifolia, using high-throughput sequencing. As expected for non-photosynthetic plants, M. uniflora and H. monotropa have small plastid genomes (46 kb and 35 kb, respectively) lacking genes related to photosynthesis, whereas P. rotundifolia has a larger genome (169 kb) with a gene set similar to other photosynthetic plants. The examined genomes contain an unusually high number of repeats and translocations. Comparative analysis of the expanded set of Ericaceae plastomes suggests that the genes clpP and accD that are present in the plastid genomes of almost all plants have not been lost in this family (as was previously thought) but rather persist in these genomes in unusual forms. Also we found a new gene in P. rotundifolia that emerged as a result of duplication of rps4 gene.
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Affiliation(s)
- Maria D. Logacheva
- Lomonosov Moscow State University, A.N Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Kazan Federal University, Institute of Fundamental Biology and Medicine, Kazan, Russia
| | - Mikhail I. Schelkunov
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Victoria Y. Shtratnikova
- Lomonosov Moscow State University, Department of Bioengineering and Bioinformatics, Moscow, Russia
| | - Maria V. Matveeva
- Kazan Federal University, Institute of Fundamental Biology and Medicine, Kazan, Russia
| | - Aleksey A. Penin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Lomonosov Moscow State University, Department of Genetics, Moscow, Russia
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10
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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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11
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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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12
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Smith DR, Asmail SR. Next-generation sequencing data suggest that certain nonphotosynthetic green plants have lost their plastid genomes. THE NEW PHYTOLOGIST 2014; 204:7-11. [PMID: 24962290 DOI: 10.1111/nph.12919] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Sara Raad Asmail
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
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13
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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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14
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Molina J, Hazzouri KM, Nickrent D, Geisler M, Meyer RS, Pentony MM, Flowers JM, Pelser P, Barcelona J, Inovejas SA, Uy I, Yuan W, Wilkins O, Michel CI, LockLear S, Concepcion GP, Purugganan MD. Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae). Mol Biol Evol 2014; 31:793-803. [PMID: 24458431 PMCID: PMC3969568 DOI: 10.1093/molbev/msu051] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Rafflesia is a genus of holoparasitic plants endemic to Southeast Asia that has lost the ability to undertake photosynthesis. With short-read sequencing technology, we assembled a draft sequence of the mitochondrial genome of Rafflesia lagascae Blanco, a species endemic to the Philippine island of Luzon, with ∼350× sequencing depth coverage. Using multiple approaches, however, we were only able to identify small fragments of plastid sequences at low coverage depth (<2×) and could not recover any substantial portion of a chloroplast genome. The gene fragments we identified included photosynthesis and energy production genes (atp, ndh, pet, psa, psb, rbcL), ribosomal RNA genes (rrn16, rrn23), ribosomal protein genes (rps7, rps11, rps16), transfer RNA genes, as well as matK, accD, ycf2, and multiple nongenic regions from the inverted repeats. None of the identified plastid gene sequences had intact reading frames. Phylogenetic analysis suggests that ∼33% of these remnant plastid genes may have been horizontally transferred from the host plant genus Tetrastigma with the rest having ambiguous phylogenetic positions (<50% bootstrap support), except for psaB that was strongly allied with the plastid homolog in Nicotiana. Our inability to identify substantial plastid genome sequences from R. lagascae using multiple approaches—despite success in identifying and developing a draft assembly of the much larger mitochondrial genome—suggests that the parasitic plant genus Rafflesia may be the first plant group for which there is no recognizable plastid genome, or if present is found in cryptic form at very low levels.
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Affiliation(s)
- Jeanmaire Molina
- Department of Biology, Long Island University, Brooklyn
- Center for Genomics and Systems Biology, New York University
- *Corresponding author: E-mail: ;
| | - Khaled M. Hazzouri
- Center for Genomics and Systems Biology, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Daniel Nickrent
- Department of Plant Biology, Southern Illinois University, Carbondale
| | - Matthew Geisler
- Department of Plant Biology, Southern Illinois University, Carbondale
| | - Rachel S. Meyer
- Center for Genomics and Systems Biology, New York University
| | - Melissa M. Pentony
- Computational Genomics Core, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Jonathan M. Flowers
- Center for Genomics and Systems Biology, New York University
- Center for Genomics and Systems Biology, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Pieter Pelser
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Julie Barcelona
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Samuel Alan Inovejas
- Electron Microscope Facility, St. Luke’s Medical Center, Quezon City, Philippines
| | - Iris Uy
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City, Philippines
| | - Wei Yuan
- Center for Genomics and Systems Biology, New York University
| | - Olivia Wilkins
- Center for Genomics and Systems Biology, New York University
| | | | | | - Gisela P. Concepcion
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City, Philippines
| | - Michael D. Purugganan
- Center for Genomics and Systems Biology, New York University
- Center for Genomics and Systems Biology, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
- *Corresponding author: E-mail: ;
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15
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Wicke S, Schäferhoff B, dePamphilis CW, Müller KF. Disproportional plastome-wide increase of substitution rates and relaxed purifying selection in genes of carnivorous Lentibulariaceae. Mol Biol Evol 2013; 31:529-45. [PMID: 24344209 DOI: 10.1093/molbev/mst261] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Carnivorous Lentibulariaceae exhibit the most sophisticated implementation of the carnivorous syndrome in plants. Their unusual lifestyle coincides with distinct genomic peculiarities such as the smallest angiosperm nuclear genomes and extremely high nucleotide substitution rates across all genomic compartments. Here, we report the complete plastid genomes from each of the three genera Pinguicula, Utricularia, and Genlisea, and investigate plastome-wide changes in their molecular evolution as the carnivorous syndrome unfolds. We observe a size reduction by up to 9% mostly due to the independent loss of genes for the plastid NAD(P)H dehydrogenase and altered proportions of plastid repeat DNA, as well as a significant plastome-wide increase of substitution rates and microstructural changes. Protein-coding genes across all gene classes show a disproportional elevation of nonsynonymous substitutions, particularly in Utricularia and Genlisea. Significant relaxation of purifying selection relative to noncarnivores occurs in the plastid-encoded fraction of the photosynthesis ATP synthase complex, the photosystem I, and in several other photosynthesis and metabolic genes. Shifts in selective regimes also affect housekeeping genes including the plastid-encoded polymerase, for which evidence for relaxed purifying selection was found once during the transition to carnivory, and a second time during the diversification of the family. Lentibulariaceae significantly exhibit enhanced rates of nucleotide substitution in most of the 130 noncoding regions. Various factors may underlie the observed patterns of relaxation of purifying selection and substitution rate increases, such as reduced net photosynthesis rates, alternative paths of nutrient uptake (including organic carbon), and impaired DNA repair mechanisms.
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Affiliation(s)
- Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
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16
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Naumann J, Salomo K, Der JP, Wafula EK, Bolin JF, Maass E, Frenzke L, Samain MS, Neinhuis C, dePamphilis CW, Wanke S. Single-copy nuclear genes place haustorial Hydnoraceae within piperales and reveal a cretaceous origin of multiple parasitic angiosperm lineages. PLoS One 2013; 8:e79204. [PMID: 24265760 PMCID: PMC3827129 DOI: 10.1371/journal.pone.0079204] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 09/20/2013] [Indexed: 11/19/2022] Open
Abstract
Extreme haustorial parasites have long captured the interest of naturalists and scientists with their greatly reduced and highly specialized morphology. Along with the reduction or loss of photosynthesis, the plastid genome often decays as photosynthetic genes are released from selective constraint. This makes it challenging to use traditional plastid genes for parasitic plant phylogenetics, and has driven the search for alternative phylogenetic and molecular evolutionary markers. Thus, evolutionary studies, such as molecular clock-based age estimates, are not yet available for all parasitic lineages. In the present study, we extracted 14 nuclear single copy genes (nSCG) from Illumina transcriptome data from one of the “strangest plants in the world”, Hydnora visseri (Hydnoraceae). A ∼15,000 character molecular dataset, based on all three genomic compartments, shows the utility of nSCG for reconstructing phylogenetic relationships in parasitic lineages. A relaxed molecular clock approach with the same multi-locus dataset, revealed an ancient age of ∼91 MYA for Hydnoraceae. We then estimated the stem ages of all independently originated parasitic angiosperm lineages using a published dataset, which also revealed a Cretaceous origin for Balanophoraceae, Cynomoriaceae and Apodanthaceae. With the exception of Santalales, older parasite lineages tend to be more specialized with respect to trophic level and have lower species diversity. We thus propose the “temporal specialization hypothesis” (TSH) implementing multiple independent specialization processes over time during parasitic angiosperm evolution.
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Affiliation(s)
- Julia Naumann
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- * E-mail: (JN); (SW)
| | - Karsten Salomo
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Joshua P. Der
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Eric K. Wafula
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jay F. Bolin
- Department of Biology, Catawba College, Salisbury, North Carolina, United States of America
| | - Erika Maass
- Department of Biological Sciences, University of Namibia, Windhoek, Namibia
| | - Lena Frenzke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | | | | | - Claude W. dePamphilis
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- * E-mail: (JN); (SW)
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17
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Xi Z, Wang Y, Bradley RK, Sugumaran M, Marx CJ, Rest JS, Davis CC. Massive mitochondrial gene transfer in a parasitic flowering plant clade. PLoS Genet 2013; 9:e1003265. [PMID: 23459037 PMCID: PMC3573108 DOI: 10.1371/journal.pgen.1003265] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 12/07/2012] [Indexed: 11/18/2022] Open
Abstract
Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Parasitic plants have provided the strongest evidence of HGT, which appears to be facilitated by the intimate physical association between the parasites and their hosts. A recent phylogenomic study demonstrated that in the holoparasite Rafflesia cantleyi (Rafflesiaceae), whose close relatives possess the world's largest flowers, about 2.1% of nuclear gene transcripts were likely acquired from its obligate host. Here, we used next-generation sequencing to obtain the 38 protein-coding and ribosomal RNA genes common to the mitochondrial genomes of angiosperms from R. cantleyi and five additional species, including two of its closest relatives and two host species. Strikingly, our phylogenetic analyses conservatively indicate that 24%–41% of these gene sequences show evidence of HGT in Rafflesiaceae, depending on the species. Most of these transgenic sequences possess intact reading frames and are actively transcribed, indicating that they are potentially functional. Additionally, some of these transgenes maintain synteny with their donor and recipient lineages, suggesting that native genes have likely been displaced via homologous recombination. Our study is the first to comprehensively assess the magnitude of HGT in plants involving a genome (i.e., mitochondria) and a species interaction (i.e., parasitism) where it has been hypothesized to be potentially rampant. Our results establish for the first time that, although the magnitude of HGT involving nuclear genes is appreciable in these parasitic plants, HGT involving mitochondrial genes is substantially higher. This may represent a more general pattern for other parasitic plant clades and perhaps more broadly for angiosperms. Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Here, using phylogenomic approaches, we demonstrate that as much as ∼40% of the mitochondrial genes in the parasitic plant species Rafflesiaceae are acquired from their hosts via HGT. These transgenes are likely functional in their recipient species and in some cases appear to have displaced native copies in the same genomic location. These results establish for the first time that, although the magnitude of HGT involving nuclear genes is appreciable in parasitic plants, HGT involving mitochondrial genes is substantially higher.
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Affiliation(s)
- Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Yuguo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
- Department of Ecology and Evolutionary Biology, School of Life Science, Fudan University, Shanghai, China
| | - Robert K. Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - M. Sugumaran
- Rimba Ilmu Botanic Garden, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Christopher J. Marx
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Joshua S. Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Charles C. Davis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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18
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Braukmann T, Kuzmina M, Stefanovic S. Plastid genome evolution across the genus Cuscuta (Convolvulaceae): two clades within subgenus Grammica exhibit extensive gene loss. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:977-89. [PMID: 23349139 PMCID: PMC3580819 DOI: 10.1093/jxb/ers391] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The genus Cuscuta (Convolvulaceae, the morning glory family) is one of the most intensely studied lineages of parasitic plants. Whole plastome sequencing of four Cuscuta species has demonstrated changes to both plastid gene content and structure. The presence of photosynthetic genes under purifying selection indicates that Cuscuta is cryptically photosynthetic. However, the tempo and mode of plastid genome evolution across the diversity of this group (~200 species) remain largely unknown. A comparative investigation of plastid genome content, grounded within a phylogenetic framework, was conducted using a slot-blot Southern hybridization approach. Cuscuta was extensively sampled (~56% of species), including groups previously suggested to possess more altered plastomes compared with other members of this genus. A total of 56 probes derived from all categories of protein-coding genes, typically found within the plastomes of flowering plants, were used. The results indicate that two clades within subgenus Grammica (clades 'O' and 'K') exhibit substantially more plastid gene loss relative to other members of Cuscuta. All surveyed members of the 'O' clade show extensive losses of plastid genes from every category of genes typically found in the plastome, including otherwise highly conserved small and large ribosomal subunits. The extent of plastid gene losses within this clade is similar in magnitude to that observed previously in some non-asterid holoparasites, in which the very presence of a plastome has been questioned. The 'K' clade also exhibits considerable loss of plastid genes. Unlike in the 'O' clade, in which all species seem to be affected, the losses in clade 'K' progress phylogenetically, following a pattern consistent with the Evolutionary Transition Series hypothesis. This clade presents an ideal opportunity to study the reduction of the plastome of parasites 'in action'. The widespread plastid gene loss in these two clades is hypothesized to be a consequence of the complete loss of photosynthesis. Additionally, taxa that would be the best candidates for entire plastome sequencing are identified in order to investigate further the loss of photosynthesis and reduction of the plastome within Cuscuta.
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Affiliation(s)
- Thomas Braukmann
- Department of Biology, University of Toronto-Mississauga, 3359 Mississauga Rd. N, Mississauga, Ontario, Canada.
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19
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Barrett CF, Davis JI. The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation. AMERICAN JOURNAL OF BOTANY 2012; 99:1513-23. [PMID: 22935364 DOI: 10.3732/ajb.1200256] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY Plastid genomes of nonphotosynthetic, mycoheterotrophic plants represent apt systems in which to study effects of relaxed evolutionary constraints. The few mycoheterotrophic angiosperm plastomes sequenced to date display drastic patterns of degradation/reduction relative to those of photosynthetic relatives. The goal of this study was to focus on a mycoheterotrophic orchid hypothesized to be in the "early" stages of plastome degradation, to provide perspective on this process. METHODS Short-read sequencing was used to generate a complete plastome sequence for Corallorhiza striata var. vreelandii, a mycoheterotrophic orchid, to investigate the extent of plastome degradation. Patterns of nonsynonymous/synonymous mutations were also assessed, and comparisons were made between Corallorhiza and other heterotrophic plant lineages. KEY RESULTS Corallorhiza yielded a plastome of 137505 bp, with several photosynthesis-related genes either lost or pseudogenized. Members of all major photosynthesis complexes, except ATP-synthase genes, were affected. "Housekeeping" genes were intact, despite the loss of a single tRNA. Intact photosynthesis genes (excluding atp genes) together displayed elevated nonsynonymous changes, while housekeeping genes did not. CONCLUSIONS The Corallorhiza plastome is not drastically reduced in overall size (∼6% reduction relative to that of photosynthetic Oncidium), but displays a pattern congruent with a loss of photosynthetic function. Comparing Corallorhiza with other heterotrophs allows some emergent evolutionary patterns to be inferred, but these remain as hypotheses to be tested, especially at lower taxonomic levels, and in lineages illustrating transitions from autotrophy to heterotrophy. The independent, unique processes of plastome modification among mycoheterotrophic lineages illustrate the urgency of their conservation.
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Affiliation(s)
- Craig F Barrett
- Department of Plant Biology and L.H. Bailey Hortorium, 412 Mann Library, Cornell University, Ithaca, New York 14853, USA.
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Su HJ, Murata J, Hu JM. Morphology and phylogenetics of two holoparasitic plants, Balanophora japonica and Balanophora yakushimensis (Balanophoraceae), and their hosts in Taiwan and Japan. JOURNAL OF PLANT RESEARCH 2012; 125:317-326. [PMID: 21894574 DOI: 10.1007/s10265-011-0447-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 08/02/2011] [Indexed: 05/31/2023]
Abstract
Balanophora japonica and B. yakushimensis are two putatively agamospermic taxa previously reported from southern Japan. Their inflorescences superficially represent those of B. laxiflora and B. fungosa. In this study we confirmed their presence in Taiwan by morphological and phylogenetic analysis using nuclear 18S rDNA and nrITS sequences with related taxa. B. japonica, B. yakushimensis, and B. laxiflora formed a well-supported clade that is distinct from other Balanophora. All three taxa also show considerable differences on morphological and nucleotide sequence differences, therefore the name of B. yakushimensis is retained. The results provide new insights on the intrageneric classification of Balanophora and suggest the positioning of female flowers should be down-weighted. We also successfully identify the hosts of B. japonica and B. yakushimensis by amplifying chloroplast matK sequences from the connected root tissues. The results showed that B. japonica parasitizes on Symplocos species, and that B. yakushimensis parasitizes on Distylium racemosum in Japan and Schima superba in Taiwan's population.
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Affiliation(s)
- Huei-Jiun Su
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Rm 1227, Life Science Building, 1 Sec. 4, Roosevelt Road, Taipei 106, Taiwan
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Keeling PJ. The endosymbiotic origin, diversification and fate of plastids. Philos Trans R Soc Lond B Biol Sci 2010; 365:729-48. [PMID: 20124341 DOI: 10.1098/rstb.2009.0103] [Citation(s) in RCA: 378] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Plastids and mitochondria each arose from a single endosymbiotic event and share many similarities in how they were reduced and integrated with their host. However, the subsequent evolution of the two organelles could hardly be more different: mitochondria are a stable fixture of eukaryotic cells that are neither lost nor shuffled between lineages, whereas plastid evolution has been a complex mix of movement, loss and replacement. Molecular data from the past decade have substantially untangled this complex history, and we now know that plastids are derived from a single endosymbiotic event in the ancestor of glaucophytes, red algae and green algae (including plants). The plastids of both red algae and green algae were subsequently transferred to other lineages by secondary endosymbiosis. Green algal plastids were taken up by euglenids and chlorarachniophytes, as well as one small group of dinoflagellates. Red algae appear to have been taken up only once, giving rise to a diverse group called chromalveolates. Additional layers of complexity come from plastid loss, which has happened at least once and probably many times, and replacement. Plastid loss is difficult to prove, and cryptic, non-photosynthetic plastids are being found in many non-photosynthetic lineages. In other cases, photosynthetic lineages are now understood to have evolved from ancestors with a plastid of different origin, so an ancestral plastid has been replaced with a new one. Such replacement has taken place in several dinoflagellates (by tertiary endosymbiosis with other chromalveolates or serial secondary endosymbiosis with a green alga), and apparently also in two rhizarian lineages: chlorarachniophytes and Paulinella (which appear to have evolved from chromalveolate ancestors). The many twists and turns of plastid evolution each represent major evolutionary transitions, and each offers a glimpse into how genomes evolve and how cells integrate through gene transfers and protein trafficking.
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Affiliation(s)
- Patrick J Keeling
- Botany Department, Canadian Institute for Advanced Research, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4.
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Wurdack KJ, Davis CC. Malpighiales phylogenetics: Gaining ground on one of the most recalcitrant clades in the angiosperm tree of life. AMERICAN JOURNAL OF BOTANY 2009; 96:1551-1570. [PMID: 21628300 DOI: 10.3732/ajb.0800207] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The eudicot order Malpighiales contains ∼16000 species and is the most poorly resolved large rosid clade. To clarify phylogenetic relationships in the order, we used maximum likelihood, Bayesian, and parsimony analyses of DNA sequence data from 13 gene regions, totaling 15604 bp, and representing all three genomic compartments (i.e., plastid: atpB, matK, ndhF, and rbcL; mitochondrial: ccmB, cob, matR, nad1B-C, nad6, and rps3; and nuclear: 18S rDNA, PHYC, and newly developed low-copy EMB2765). Our sampling of 190 taxa includes representatives from all families of Malpighiales. These data provide greatly increased support for the recent additions of Aneulophus, Bhesa, Centroplacus, Ploiarium, and Rafflesiaceae to Malpighiales; sister relations of Phyllanthaceae + Picrodendraceae, monophyly of Hypericaceae, and polyphyly of Clusiaceae. Oxalidales + Huaceae, followed by Celastrales are successive sisters to Malpighiales. Parasitic Rafflesiaceae, which produce the world's largest flowers, are confirmed as embedded within a paraphyletic Euphorbiaceae. Novel findings show a well-supported placement of Ctenolophonaceae with Erythroxylaceae + Rhizophoraceae, sister-group relationships of Bhesa + Centroplacus, and the exclusion of Medusandra from Malpighiales. New taxonomic circumscriptions include the addition of Bhesa to Centroplacaceae, Medusandra to Peridiscaceae (Saxifragales), Calophyllaceae applied to Clusiaceae subfamily Kielmeyeroideae, Peraceae applied to Euphorbiaceae subfamily Peroideae, and Huaceae included in Oxalidales.
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Affiliation(s)
- Kenneth J Wurdack
- Department of Botany, Smithsonian Institution, P.O. Box 37012 NMNH MRC-166, Washington, District of Columbia 20013-7012 USA
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Nickrent DL, García MA. On the brink of holoparasitism: plastome evolution in dwarf mistletoes (Arceuthobium, Viscaceae). J Mol Evol 2009; 68:603-15. [PMID: 19479176 DOI: 10.1007/s00239-009-9224-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Revised: 03/03/2009] [Accepted: 03/05/2009] [Indexed: 11/30/2022]
Abstract
Chloroplast sequences spanning rps7 to 23S rDNA in Arceuthobium campylopodum and A. pendens were generated and compared to Arabidopsis and seven other parasitic plants. Pseudogenes for trnV, trnI (GAU), and trnA (UGC) were seen in both Arceuthobium species, paralleling the situation in the holoparasite Epifagus (Orobanchaceae). These tRNA genes were intact, however, in two other members of Santalales (Ximenia and Phoradendron). The 16S-23S rDNA intergenic spacer was sequenced for 13 additional species of Arceuthobium representing both Old and New World taxa. All species examined had pseudogenes for trnI and trnA, however, deletions in these tRNAs have occurred in different regions among various lineages of the genus. The aligned 16S-23S rDNA intergenic spacer was analyzed using maximum parsimony and compared with nuclear ITS rDNA using a similar suite of species. Overall species relationships were generally congruent, although two cases of potential lineage sorting or chloroplast capture were detected. Arceuthobium is a valuable genetic model to contrast with holoparasites because, despite significant alteration and truncation of its plastome, it still maintains photosynthetic function.
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Affiliation(s)
- Daniel L Nickrent
- Department of Plant Biology, Southern Illinois University, Carbondale, IL 62901-6509, USA.
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Davis CC. Floral Evolution: Dramatic Size Change Was Recent and Rapid in the World's Largest Flowers. Curr Biol 2008; 18:R1102-4. [DOI: 10.1016/j.cub.2008.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Distribution and Evolution of Pseudogenes, Gene Losses, and a Gene Rearrangement in the Plastid Genome of the Nonphotosynthetic Liverwort, Aneura mirabilis (Metzgeriales, Jungermanniopsida). J Mol Evol 2008; 67:111-22. [DOI: 10.1007/s00239-008-9133-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 05/28/2008] [Accepted: 06/09/2008] [Indexed: 10/21/2022]
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Barkman TJ, McNeal JR, Lim SH, Coat G, Croom HB, Young ND, Depamphilis CW. Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants. BMC Evol Biol 2007; 7:248. [PMID: 18154671 PMCID: PMC2234419 DOI: 10.1186/1471-2148-7-248] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Accepted: 12/21/2007] [Indexed: 11/16/2022] Open
Abstract
Background Some of the most difficult phylogenetic questions in evolutionary biology involve identification of the free-living relatives of parasitic organisms, particularly those of parasitic flowering plants. Consequently, the number of origins of parasitism and the phylogenetic distribution of the heterotrophic lifestyle among angiosperm lineages is unclear. Results Here we report the results of a phylogenetic analysis of 102 species of seed plants designed to infer the position of all haustorial parasitic angiosperm lineages using three mitochondrial genes: atp1, coxI, and matR. Overall, the mtDNA phylogeny agrees with independent studies in terms of non-parasitic plant relationships and reveals at least 11 independent origins of parasitism in angiosperms, eight of which consist entirely of holoparasitic species that lack photosynthetic ability. From these results, it can be inferred that modern-day parasites have disproportionately evolved in certain lineages and that the endoparasitic habit has arisen by convergence in four clades. In addition, reduced taxon, single gene analyses revealed multiple horizontal transfers of atp1 from host to parasite lineage, suggesting that parasites may be important vectors of horizontal gene transfer in angiosperms. Furthermore, in Pilostyles we show evidence for a recent host-to-parasite atp1 transfer based on a chimeric gene sequence that indicates multiple historical xenologous gene acquisitions have occurred in this endoparasite. Finally, the phylogenetic relationships inferred for parasites indicate that the origins of parasitism in angiosperms are strongly correlated with horizontal acquisitions of the invasive coxI group I intron. Conclusion Collectively, these results indicate that the parasitic lifestyle has arisen repeatedly in angiosperm evolutionary history and results in increasing parasite genomic chimerism over time.
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Affiliation(s)
- Todd J Barkman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, 49008, USA.
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McNeal JR, Arumugunathan K, Kuehl JV, Boore JL, Depamphilis CW. Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae). BMC Biol 2007; 5:55. [PMID: 18078516 PMCID: PMC2242782 DOI: 10.1186/1741-7007-5-55] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 12/13/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Cuscuta L. (Convolvulaceae), commonly known as dodders, are epiphytic vines that invade the stems of their host with haustorial feeding structures at the points of contact. Although they lack expanded leaves, some species are noticeably chlorophyllous, especially as seedlings and in maturing fruits. Some species are reported as crop pests of worldwide distribution, whereas others are extremely rare and have local distributions and apparent niche specificity. A strong phylogenetic framework for this large genus is essential to understand the interesting ecological, morphological and molecular phenomena that occur within these parasites in an evolutionary context. RESULTS Here we present a well-supported phylogeny of Cuscuta using sequences of the nuclear ribosomal internal transcribed spacer and plastid rps2, rbcL and matK from representatives across most of the taxonomic diversity of the genus. We use the phylogeny to interpret morphological and plastid genome evolution within the genus. At least three currently recognized taxonomic sections are not monophyletic and subgenus Cuscuta is unequivocally paraphyletic. Plastid genes are extremely variable with regards to evolutionary constraint, with rbcL exhibiting even higher levels of purifying selection in Cuscuta than photosynthetic relatives. Nuclear genome size is highly variable within Cuscuta, particularly within subgenus Grammica, and in some cases may indicate the existence of cryptic species in this large clade of morphologically similar species. CONCLUSION Some morphological characters traditionally used to define major taxonomic splits within Cuscuta are homoplastic and are of limited use in defining true evolutionary groups. Chloroplast genome evolution seems to have evolved in a punctuated fashion, with episodes of loss involving suites of genes or tRNAs followed by stabilization of gene content in major clades. Nearly all species of Cuscuta retain some photosynthetic ability, most likely for nutrient apportionment to their seeds, while complete loss of photosynthesis and possible loss of the entire chloroplast genome is limited to a single small clade of outcrossing species found primarily in western South America.
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Affiliation(s)
- Joel R McNeal
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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Abstract
Species of Rafflesiaceae possess the world's largest flowers (up to 1 meter in diameter), yet their precise evolutionary relationships have been elusive, hindering our understanding of the evolution of their extraordinary reproductive morphology. We present results of phylogenetic analyses of mitochondrial, nuclear, and plastid data showing that Rafflesiaceae are derived from within Euphorbiaceae, the spurge family. Most euphorbs produce minute flowers, suggesting that the enormous flowers of Rafflesiaceae evolved from ancestors with tiny flowers. Given the inferred phylogeny, we estimate that there was a circa 79-fold increase in flower diameter on the stem lineage of Rafflesiaceae, making this one of the most dramatic cases of size evolution reported for eukaryotes.
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Affiliation(s)
- Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA.
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Barbrook AC, Howe CJ, Purton S. Why are plastid genomes retained in non-photosynthetic organisms? TRENDS IN PLANT SCIENCE 2006; 11:101-8. [PMID: 16406301 DOI: 10.1016/j.tplants.2005.12.004] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Revised: 12/05/2005] [Accepted: 12/20/2005] [Indexed: 05/06/2023]
Abstract
The evolution of the plastid from a photosynthetic bacterial endosymbiont involved a dramatic reduction in the complexity of the plastid genome, with many genes either discarded or transferred to the nucleus of the eukaryotic host. However, this evolutionary process has not gone to completion and a subset of genes remains in all plastids examined to date. The various hypotheses put forward to explain the retention of the plastid genome have tended to focus on the need for photosynthetic organisms to retain a genetic system in the chloroplast, and they fail to explain why heterotrophic plants and algae, and the apicomplexan parasites all retain a genome in their non-photosynthetic plastids. Here we consider two additional explanations: the 'essential tRNAs' hypothesis and the 'transfer-window' hypothesis.
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Affiliation(s)
- Adrian C Barbrook
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
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Randle CP, Wolfe AD. The evolution and expression of RBCL in holoparasitic sister-genera Harveya and Hyobanche (Orobanchaceae). AMERICAN JOURNAL OF BOTANY 2005; 92:1575-1585. [PMID: 21646175 DOI: 10.3732/ajb.92.9.1575] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The evolution of holoparasitism decreases the adaptive value of genes maintaining the photosynthetic apparatus. These may become pseudogenes through insertion or deletion events resulting in frameshift mutations, or by the evolution of premature stop codons. The holoparasitic sister genera Harveya and Hyobanche have undergone alternate pathways of evolution and expression at the plastid locus rbcL. An open reading frame in all but a single species of Harveya is maintained by purifying selection and is expressed. However, the function of Rubisco in this putative holoparasite is unknown. Conversely, Hyobanche has undergone rbcL pseudogene formation, and comparison of synonymous and nonsynonymous rates of evolution indicates that selection has not played a role in its evolution. This is complicated by the following findings: multiple pseudogene copies of rbcL exist in tissues of Hyobanche, rbcL transcripts also encode pseudogenes, and the large subunit is present in some tissues of Hyobanche. We hypothesize that the rbcL operon is in a state of degradation as may be expected in a holoparasite and is not endogenously expressed. Rather, the large subunit may be taken up from the host plants, and accumulate in tissues as a result of transpiration.
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Affiliation(s)
- Christopher P Randle
- Department of Ecology and Evolutionary Biology and the Natural History Museum, University of Kansas, 1200 Sunnyside Ave., Lawrence, Kansas 66045 USA
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García MA, Nicholson EH, Nickrent DL. Extensive intraindividual variation in plastid rDNA sequences from the holoparasite Cynomorium coccineum (Cynomoriaceae). J Mol Evol 2004; 58:322-32. [PMID: 15045487 DOI: 10.1007/s00239-003-2554-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2003] [Accepted: 10/06/2003] [Indexed: 10/26/2022]
Abstract
Ribosomal genes are considered to have a high degree of sequence conservation between species and also at higher taxonomic levels. In this paper we document a case where a single individual of Cynomorium coccineum (Cynomoriaceae), a nonphotosynthetic holoparasitic plant, contains highly divergent plastid ribosomal genes. PCR amplification a nearly complete ribosomal DNA cistron was performed using genomic DNA, the products cloned, and the 23S rDNA genes were sequenced from 19 colonies. Of these, five distinct types were identified. Fifteen of the sequences were nearly identical (11 or fewer differences) and these were designated Type I. The remaining types (II-V) were each represented by a single clone and differed from Type I by 93 to 255 changes. Compared with green vascular plants, we found that there are more substitutional differences in the 23S rDNA sequences within a single individual of Cynomorium than among all sequenced photosynthetic vascular plants. Several trends of molecular evolution observed in 16S rDNA from other holoparasitic angiosperms and heterotrophic green algae have been also observed in Cynomorium 23S rDNA. Higher-order structures were constructed for representatives of the five clone types, and in all cases these possessed complete complements of the major structural elements present in functional plastid 23S rRNAs. These data indicate that such molecules may be subject to purifying selection, thus providing indirect evidence that they have retained some degree of functionality. This intraindividual polymorphism is probably a case of plastid heteroplasmy but translocation of ribosomal cistrons to the nucleus or mitochondria has not been tested and therefore cannot be ruled out.
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Affiliation(s)
- Miguel A García
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014-Madrid, Spain
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Nickrent DL, Blarer A, Qiu YL, Vidal-Russell R, Anderson FE. Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer. BMC Evol Biol 2004; 4:40. [PMID: 15496229 PMCID: PMC528834 DOI: 10.1186/1471-2148-4-40] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2004] [Accepted: 10/20/2004] [Indexed: 11/16/2022] Open
Abstract
Background The phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial matR gene placed Rafflesia, Rhizanthes and Sapria (Rafflesiaceae s. str.) in the angiosperm order Malpighiales and Mitrastema (Mitrastemonaceae) in Ericales. These phylogenetic studies did not, however, sample two additional groups traditionally classified within Rafflesiales (Apodantheaceae and Cytinaceae). Here we provide molecular phylogenetic evidence using DNA sequence data from mitochondrial and nuclear genes for representatives of all genera in Rafflesiales. Results Our analyses indicate that the phylogenetic affinities of the large-flowered clade and Mitrastema, ascertained using mitochondrial matR, are congruent with results from nuclear SSU rDNA when these data are analyzed using maximum likelihood and Bayesian methods. The relationship of Cytinaceae to Malvales was recovered in all analyses. Relationships between Apodanthaceae and photosynthetic angiosperms varied depending upon the data partition: Malvales (3-gene), Cucurbitales (matR) or Fabales (atp1). The latter incongruencies suggest that horizontal gene transfer (HGT) may be affecting the mitochondrial gene topologies. The lack of association between Mitrastema and Ericales using atp1 is suggestive of HGT, but greater sampling within eudicots is needed to test this hypothesis further. Conclusions Rafflesiales are not monophyletic but composed of three or four independent lineages (families): Rafflesiaceae, Mitrastemonaceae, Apodanthaceae and Cytinaceae. Long-branch attraction appears to be misleading parsimony analyses of nuclear small-subunit rDNA data, but model-based methods (maximum likelihood and Bayesian analyses) recover a topology that is congruent with the mitochondrial matR gene tree, thus providing compelling evidence for organismal relationships. Horizontal gene transfer appears to be influencing only some taxa and some mitochondrial genes, thus indicating that the process is acting at the single gene (not whole genome) level.
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Affiliation(s)
- Daniel L Nickrent
- Department of Plant Biology, Southern Illinois University, Carbondale, IL 62901-6509, USA
| | - Albert Blarer
- Institute of Systematic Botany, University of Zurich, 8008 Zurich, Switzerland
| | - Yin-Long Qiu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Romina Vidal-Russell
- Department of Plant Biology, Southern Illinois University, Carbondale, IL 62901-6509, USA
| | - Frank E Anderson
- Department of Zoology, Southern Illinois University, Carbondale IL, 62901-6501, USA
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Barkman TJ, Lim SH, Salleh KM, Nais J. Mitochondrial DNA sequences reveal the photosynthetic relatives of Rafflesia, the world's largest flower. Proc Natl Acad Sci U S A 2004; 101:787-92. [PMID: 14715901 PMCID: PMC321759 DOI: 10.1073/pnas.0305562101] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2003] [Indexed: 11/18/2022] Open
Abstract
All parasites are thought to have evolved from free-living ancestors. However, the ancestral conditions facilitating the shift to parasitism are unclear, particularly in plants because the phylogenetic position of many parasites is unknown. This is especially true for Rafflesia, an endophytic holoparasite that produces the largest flowers in the world and has defied confident phylogenetic placement since its discovery >180 years ago. Here we present results of a phylogenetic analysis of 95 species of seed plants designed to infer the position of Rafflesia in an evolutionary context using the mitochondrial gene matR (1,806 aligned base pairs). Overall, the estimated phylogenetic tree is highly congruent with independent analyses and provides a strongly supported placement of Rafflesia with the order Malpighiales, which includes poinsettias, violets, and passionflowers. Furthermore, the phylogenetic placement of Mitrastema, another enigmatic, holoparasitic angiosperm with the order Ericales (which includes blueberries and persimmons), was obtained with these data. Although traditionally classified together, Rafflesia and Mitrastema are only distantly related, implying that their endoparasitic habits result from convergent evolution. Our results indicate that the previous significant difficulties associated with phylogenetic placement of holoparasitic plants may be overcome by using mitochondrial DNA so that a broader understanding of the origins and evolution of parasitism may emerge.
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Affiliation(s)
- Todd J Barkman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, USA.
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Abstract
The plastid genome of the nonphotosynthetic parasitic plant Epifagus virginiana contains only 17 of the 30 tRNA genes normally found in angiosperm plastid DNA. Although this is insufficient for translation, the genome is functional, so import of cytosolic tRNAs into plastids has been suggested. This raises the question of whether the tRNA genes that remain in E. virginiana plastid DNA are active or have just fortuitously escaped deletion. We report the sequences of 20 plastid tRNA loci from Orobanche minor, which shares a nonphotosynthetic ancestor with E. virginiana. The two species have 9 intact tRNA genes in common, the others being defunct in one or both species. The intron-containing trnLUAA gene is absent from E. virginiana, but it is intact, transcribed, and spliced in O. minor. The shared intact genes are better conserved than intergenic sequences, which indicates that these genes are being maintained by natural selection and, therefore, must be functional. For the most part, the tRNA species conserved in nonphotosynthetic plastids are also those that have never been found to be imported in plant mitochondria, which suggests that the same rules may govern tRNA import in the two organelles. A small photosynthesis gene, psbI, is still intact in O. minor, and computer simulations show that some small nonessential genes have an appreciable chance of escaping deletion.
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Affiliation(s)
- A J Lohan
- Department of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
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