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Wu CS, Wang RJ, Chaw SM. Integration of large and diverse angiosperm DNA fragments into Asian Gnetum mitogenomes. BMC Biol 2024; 22:140. [PMID: 38915079 PMCID: PMC11197197 DOI: 10.1186/s12915-024-01924-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 05/21/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus. RESULTS We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots-mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT. CONCLUSIONS Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages.
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Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Rui-Jiang Wang
- South China Botanical Garden, Chinese Academy of Science, Guangzhou, China
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
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2
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Keeling PJ. Horizontal gene transfer in eukaryotes: aligning theory with data. Nat Rev Genet 2024; 25:416-430. [PMID: 38263430 DOI: 10.1038/s41576-023-00688-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 01/25/2024]
Abstract
Horizontal gene transfer (HGT), or lateral gene transfer, is the non-sexual movement of genetic information between genomes. It has played a pronounced part in bacterial and archaeal evolution, but its role in eukaryotes is less clear. Behaviours unique to eukaryotic cells - phagocytosis and endosymbiosis - have been proposed to increase the frequency of HGT, but nuclear genomes encode fewer HGTs than bacteria and archaea. Here, I review the existing theory in the context of the growing body of data on HGT in eukaryotes, which suggests that any increased chance of acquiring new genes through phagocytosis and endosymbiosis is offset by a reduced need for these genes in eukaryotes, because selection in most eukaryotes operates on variation not readily generated by HGT.
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Affiliation(s)
- Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
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3
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Li G, Zhang H, Lin Z, Li H, Xu G, Xu Y, Ji R, Luo W, Qiu Y, Qiu S, Tang H. Comparative analysis of chloroplast and mitochondrial genomes of sweet potato provides evidence of gene transfer. Sci Rep 2024; 14:4547. [PMID: 38402284 PMCID: PMC10894244 DOI: 10.1038/s41598-024-55150-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/20/2024] [Indexed: 02/26/2024] Open
Abstract
The increasing number of plant mitochondrial DNA genomes (mtDNA) sequenced reveals the extent of transfer from both chloroplast DNA genomes (cpDNA) and nuclear DNA genomes (nDNA). This study created a library and assembled the chloroplast and mitochondrial genomes of the leafy sweet potato better to understand the extent of mitochondrial and chloroplast gene transfer. The full-length chloroplast genome of the leafy sweet potato (OM808940) is 161,387 bp, with 132 genes annotated, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The mitochondrial genome (OM808941) was 269,578 bp in length and contained 69 functional genes, including 39 protein-coding genes, 6 rRNA genes, and 24 tRNA genes. 68 SSR loci were found in the leafy sweet potato organelle genome, including 54 in the chloroplast genome and 14 in the mitochondria genome. In the sweet potato mitochondrial genome, most genes have RNA editing sites, and the conversion ratio from hydrophilic amino acids to hydrophobic amino acids is the highest, reaching 47.12%. Horizontal transfer occurs in the sweet potato organelle genome and nuclear genome. 40 mitochondrial genome segments share high homology with 14 chloroplast genome segments, 33 of which may be derived from chloroplast genome horizontal transfer. 171 mitochondrial genome sequences come from the horizontal transfer of nuclear genome. The phylogenetic analysis of organelle genes revealed that the leafy sweet potato was closely related to the tetraploid wild species Ipomoea tabascana and the wild diploid species Ipomoea trifida.
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Affiliation(s)
- GuoLiang Li
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Hong Zhang
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Zhaomiao Lin
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Huawei Li
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Guochun Xu
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Yongqing Xu
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Rongchang Ji
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Wenbin Luo
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Yongxiang Qiu
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Sixin Qiu
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China.
| | - Hao Tang
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
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4
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Zumkeller S, Polsakiewicz M, Knoop V. Rickettsial DNA and a trans-splicing rRNA group I intron in the unorthodox mitogenome of the fern Haplopteris ensiformis. Commun Biol 2023; 6:296. [PMID: 36941328 PMCID: PMC10027690 DOI: 10.1038/s42003-023-04659-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/03/2023] [Indexed: 03/23/2023] Open
Abstract
Plant mitochondrial genomes can be complex owing to highly recombinant structures, lack of gene syntenies, heavy RNA editing and invasion of chloroplast, nuclear or even foreign DNA by horizontal gene transfer (HGT). Leptosporangiate ferns remained the last major plant clade without an assembled mitogenome, likely owing to a demanding combination of the above. We here present both organelle genomes now for Haplopteris ensiformis. More than 1,400 events of C-to-U RNA editing and over 500 events of reverse U-to-C edits affect its organelle transcriptomes. The Haplopteris mtDNA is gene-rich, lacking only the ccm gene suite present in ancestral land plant mitogenomes, but is highly unorthodox, indicating extraordinary recombinogenic activity. Although eleven group II introns known in disrupted trans-splicing states in seed plants exist in conventional cis-arrangements, a particularly complex structure is found for the mitochondrial rrnL gene, which is split into two parts needing reassembly on RNA level by a trans-splicing group I intron. Aside from ca. 80 chloroplast DNA inserts that complicated the mitogenome assembly, the Haplopteris mtDNA features as an idiosyncrasy 30 variably degenerated protein coding regions from Rickettiales bacteria indicative of heavy bacterial HGT on top of tRNA genes of chlamydial origin.
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Affiliation(s)
- Simon Zumkeller
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Monika Polsakiewicz
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany.
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5
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SUKSANGA A, SIRIPONGVUTIKORN S, YUPANQUI CT, LEELAWATTANA R. The potential antidiabetic properties of Liang (Gnetum gnemon var.tenerum) leaves. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.64522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmF C genes. BMC Genomics 2021; 22:816. [PMID: 34772334 PMCID: PMC8588681 DOI: 10.1186/s12864-021-08105-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/19/2021] [Indexed: 01/30/2023] Open
Abstract
Background The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus. Results The mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmFC gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT. Conclusions The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08105-z.
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7
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Aubin E, El Baidouri M, Panaud O. Horizontal Gene Transfers in Plants. Life (Basel) 2021; 11:life11080857. [PMID: 34440601 PMCID: PMC8401529 DOI: 10.3390/life11080857] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022] Open
Abstract
In plants, as in all eukaryotes, the vertical transmission of genetic information through reproduction ensures the maintenance of the integrity of species. However, many reports over the past few years have clearly shown that horizontal gene transfers, referred to as HGTs (the interspecific transmission of genetic information across reproductive barriers) are very common in nature and concern all living organisms including plants. The advent of next-generation sequencing technologies (NGS) has opened new perspectives for the study of HGTs through comparative genomic approaches. In this review, we provide an up-to-date view of our current knowledge of HGTs in plants.
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8
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Filip E, Skuza L. Horizontal Gene Transfer Involving Chloroplasts. Int J Mol Sci 2021; 22:ijms22094484. [PMID: 33923118 PMCID: PMC8123421 DOI: 10.3390/ijms22094484] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 02/04/2023] Open
Abstract
Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.
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Affiliation(s)
- Ewa Filip
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland;
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
- Correspondence:
| | - Lidia Skuza
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland;
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
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9
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Garcia LE, Edera AA, Palmer JD, Sato H, Sanchez-Puerta MV. Horizontal gene transfers dominate the functional mitochondrial gene space of a holoparasitic plant. THE NEW PHYTOLOGIST 2021; 229:1701-1714. [PMID: 32929737 DOI: 10.1111/nph.16926] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
Although horizontal gene transfer (HGT) is common in angiosperm mitochondrial DNAs (mtDNAs), few cases of functional foreign genes have been identified. The one outstanding candidate for large-scale functional HGT is the holoparasite Lophophytum mirabile, whose mtDNA has lost most native genes but contains intact foreign homologs acquired from legume host plants. To investigate the extent to which this situation results from functional replacement of native by foreign genes, functional mitochondrial gene transfer to the nucleus, and/or loss of mitochondrial biochemical function in the context of extreme parasitism, we examined the Lophophytum mitochondrial and nuclear transcriptomes by deep paired-end RNA sequencing. Most foreign mitochondrial genes in Lophophytum are highly transcribed, accurately spliced, and efficiently RNA edited. By contrast, we found no evidence for functional gene transfer to the nucleus or loss of mitochondrial functions in Lophophytum. Many functional replacements occurred via the physical replacement of native genes by foreign genes. Some of these events probably occurred as the final act of HGT itself. Lophophytum mtDNA has experienced an unprecedented level of functional replacement of native genes by foreign copies. This raises important questions concerning population-genetic and molecular regimes that underlie such a high level of foreign gene takeover.
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Affiliation(s)
- Laura E Garcia
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, Mendoza, M5502JMA, Argentina
| | - Alejandro A Edera
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Argentina
| | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Hector Sato
- Facultad de Ciencias Agrarias (UNJu), Cátedra de Botánica General-Herbario JUA, Alberdi 47, Jujuy, CP 4600, Argentina
| | - M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, Mendoza, M5502JMA, Argentina
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10
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Chen R, Huangfu L, Lu Y, Fang H, Xu Y, Li P, Zhou Y, Xu C, Huang J, Yang Z. Adaptive innovation of green plants by horizontal gene transfer. Biotechnol Adv 2020; 46:107671. [PMID: 33242576 DOI: 10.1016/j.biotechadv.2020.107671] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022]
Abstract
Horizontal gene transfer (HGT) refers to the movement of genetic material between distinct species by means other than sexual reproduction. HGT has contributed tremendously to the genome plasticity and adaptive evolution of prokaryotes and certain unicellular eukaryotes. The evolution of green plants from chlorophyte algae to angiosperms and from water to land represents a process of adaptation to diverse environments, which has been facilitated by acquisition of genetic material from other organisms. In this article, we review the occurrence of HGT in major lineages of green plants, including chlorophyte and charophyte green algae, bryophytes, lycophytes, ferns, and seed plants. In addition, we discuss the significance of horizontally acquired genes in the adaptive innovations of green plants and their potential applications to crop breeding and improvement.
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Affiliation(s)
- Rujia Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Liexiang Huangfu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yue Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Huimin Fang
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yang Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Pengcheng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC 28590, USA; State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
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11
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Jin WY, Liu B, Zhang SZ, Wan T, Hou C, Yang Y. Gnetum chinense, a new species of Gnetaceae from southwestern China. PHYTOKEYS 2020; 148:105-117. [PMID: 32523394 PMCID: PMC7266837 DOI: 10.3897/phytokeys.148.48510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/31/2020] [Indexed: 06/11/2023]
Abstract
Gnetum chinense sp. nov., a new lianoid species of Gnetaceae, is described from southwestern China. The new species is morphologically similar to G. montanum Markgr. in its oblong elliptic leaves and the ovoid to ellipsoid chlamydosperm, but differs from the latter by its shorter male spikes having fewer involucral collars (7-10 vs. 13-18 in G. montanum). We also did a new molecular analysis using one nuclear marker (i.e. nrITS) and four chloroplast markers (i.e. matK gene, rpoC1 intron, psbB-rps12 IGS, and trnF-trnV IGS). The result suggests that this specific clade is sister to a large clade consisting of all other known Chinese lianoid species of Gnetum except G. parvifolium (Warb.) W.C. Cheng.
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Affiliation(s)
- Wei-Yin Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, ChinaInstitute of Botany, Chinese Academy of SciencesBeijingChina
- Tonghua Normal University, 950 Yucai Road, Dongchang District, Tonghua City, Jilin Province 134000, ChinaGuangdong Academy of ForestryGuangzhouChina
| | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, ChinaInstitute of Botany, Chinese Academy of SciencesBeijingChina
| | - Shou-Zhou Zhang
- Shenzhen Fairy Lake Botanical Garden, Shenzhen, ChinaTonghua Normal UniversityTonghuaChina
| | - Tao Wan
- Shenzhen Fairy Lake Botanical Garden, Shenzhen, ChinaTonghua Normal UniversityTonghuaChina
| | - Chen Hou
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
- Guangdong Academy of Forestry, Guangzhou, 510520, ChinaShenzhen Fairy Lake Botanical GardenShenzhenChina
| | - Yong Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, ChinaInstitute of Botany, Chinese Academy of SciencesBeijingChina
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12
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Petersen G, Anderson B, Braun HP, Meyer EH, Møller IM. Mitochondria in parasitic plants. Mitochondrion 2020; 52:173-182. [DOI: 10.1016/j.mito.2020.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/05/2020] [Accepted: 03/23/2020] [Indexed: 02/06/2023]
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13
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Hou C, Saunders RMK, Deng N, Wan T, Su Y. Pollination Drop Proteome and Reproductive Organ Transcriptome Comparison in Gnetum Reveals Entomophilous Adaptation. Genes (Basel) 2019; 10:E800. [PMID: 31614866 PMCID: PMC6826882 DOI: 10.3390/genes10100800] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/30/2019] [Accepted: 10/11/2019] [Indexed: 11/16/2022] Open
Abstract
Gnetum possesses morphologically bisexual but functionally unisexual reproductive structures that exude sugary pollination drops to attract insects. Previous studies have revealed that the arborescent species (G. gnemon L.) and the lianoid species (G. luofuense C.Y.Cheng) possess different pollination syndromes. This study compared the proteome in the pollination drops of these two species using label-free quantitative techniques. The transcriptomes of fertile reproductive units (FRUs) and sterile reproductive units (SRUs) for each species were furthermore compared using Illumina Hiseq sequencing, and integrated proteomic and transcriptomic analyses were subsequently performed. Our results show that the differentially expressed proteins between FRUs and SRUs were involved in carbohydrate metabolism, the biosynthesis of amino acids and ovule defense. In addition, the differentially expressed genes between the FRUs and SRUs (e.g., MADS-box genes) were engaged in reproductive development and the formation of pollination drops. The integrated protein-transcript analyses revealed that FRUs and their exudates were relatively conservative while the SRUs and their exudates were more diverse, probably functioning as pollinator attractants. The evolution of reproductive organs appears to be synchronized with changes in the pollination drop proteome of Gnetum, suggesting that insect-pollinated adaptations are not restricted to angiosperms but also occur in gymnosperms.
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Affiliation(s)
- Chen Hou
- School of Life Sciences, Sun Yat-Sen University, Xingangxi Road No. 135, Guangzhou 510275, China.
| | - Richard M K Saunders
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
| | - Nan Deng
- Institute of Ecology, Hunan Academy of Forestry, Shaoshannan Road, No. 6581, Changsha 410004, China.
- Hunan Cili Forest Ecosystem State Research Station, Cili 427200, China.
| | - Tao Wan
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Liantangxianhu Road, No. 160, Shenzhen 518004, China.
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Moshan, Wuhan 430074, China.
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-Sen University, Xingangxi Road No. 135, Guangzhou 510275, China.
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14
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Forgione I, Bonavita S, Regina TMR. Mitochondria of Cedrus atlantica and allied species: A new chapter in the horizontal gene transfer history. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:93-101. [PMID: 30824066 DOI: 10.1016/j.plantsci.2019.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 12/30/2018] [Accepted: 01/15/2019] [Indexed: 06/09/2023]
Abstract
The extraordinary incidence of Horizontal Gene Transfer (HGT) mostly in mitochondrial genomes of flowering plants is well known. Here, we report another episode of HGT affecting a large mitochondrial gene region in the evergreen conifer Atlas cedar (Cedrus atlantica). Mitochondria of this Pinaceae species possess an rps3 gene that harbours two introns and shares the same genomic context with a downstream overlapping rpl16 gene, like in the major groups of gymnosperms and angiosperms analyzed so far. Interestingly, C. atlantica contains additional copies of the rps3 and rpl16 sequences that are more closely related to angiosperm counterparts than to those from gymnosperms, as also confirmed by phylogenetic analyses. This suggests that a lateral transfer from a flowering plant donor is the most likely mechanism for the origin of the Atlas cedar extra sequences. Quantitative PCR and reverse-transcription (RT)-PCR analyses demonstrate, respectively, mitochondrial location and lack of expression for the rps3 and rpl16 additional sequences in C. atlantica. Furthermore, our study provides evidence that a similar HGT event takes place in two other Cedrus species, which occurr in Cyprus and North Africa. Only the West Himalayan C. deodara lacks the transferred genes. The potential donor and the molecular mechanism underlying this lateral DNA transfer remain still unclear.
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Affiliation(s)
- Ivano Forgione
- Dipartimento di Biologia, Ecologia e Scienze della Terra (DiBEST), Università della Calabria, via Ponte P. Bucci, 87036, Arcavacata di Rende, Cosenza, Italy
| | - Savino Bonavita
- Dipartimento di Biologia, Ecologia e Scienze della Terra (DiBEST), Università della Calabria, via Ponte P. Bucci, 87036, Arcavacata di Rende, Cosenza, Italy
| | - Teresa Maria Rosaria Regina
- Dipartimento di Biologia, Ecologia e Scienze della Terra (DiBEST), Università della Calabria, via Ponte P. Bucci, 87036, Arcavacata di Rende, Cosenza, Italy.
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15
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Abstract
A fundamental tenet of multicellular eukaryotic evolution is that vertical inheritance is paramount, with natural selection acting on genetic variants transferred from parents to offspring. This lineal process means that an organism's adaptive potential can be restricted by its evolutionary history, the amount of standing genetic variation, and its mutation rate. Lateral gene transfer (LGT) theoretically provides a mechanism to bypass many of these limitations, but the evolutionary importance and frequency of this process in multicellular eukaryotes, such as plants, remains debated. We address this issue by assembling a chromosome-level genome for the grass Alloteropsis semialata, a species surmised to exhibit two LGTs, and screen it for other grass-to-grass LGTs using genomic data from 146 other grass species. Through stringent phylogenomic analyses, we discovered 57 additional LGTs in the A. semialata nuclear genome, involving at least nine different donor species. The LGTs are clustered in 23 laterally acquired genomic fragments that are up to 170 kb long and have accumulated during the diversification of Alloteropsis. The majority of the 59 LGTs in A. semialata are expressed, and we show that they have added functions to the recipient genome. Functional LGTs were further detected in the genomes of five other grass species, demonstrating that this process is likely widespread in this globally important group of plants. LGT therefore appears to represent a potent evolutionary force capable of spreading functional genes among distantly related grass species.
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16
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Kim HT, Kim KJ. Evolution of six novel ORFs in the plastome of Mankyua chejuense and phylogeny of eusporangiate ferns. Sci Rep 2018; 8:16466. [PMID: 30405200 PMCID: PMC6220310 DOI: 10.1038/s41598-018-34825-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/26/2018] [Indexed: 11/17/2022] Open
Abstract
In this paper, three plastomes of Mankyua chejuense, Helminthostachys zeylanica, and Botrychium ternatum in Ophioglossaceae were completely sequenced in order to investigate the plastome evolution and phylogeny of eusporangiate ferns. They were similar to each other in terms of length and the gene orders; however, six unknown open reading frames (ORFs) were found between rps4 and trnL-UAA genes in M. chejuense. Similar sequence regions of six ORFs of M. chejuense were found at the plastomes of Ophioglossum californicum and H. zeylanica, as well as the mitochondrial genome (mitogenome) of H. zeylanica, but not in B. ternatum. Interestingly, the translated amino acid sequences of three ORFs were more similar to the proteins of distantly related taxa such as algae and bacteria than they were to proteins in land plants. It is likely that the six ORFs region arose from endosymbiotic gene transfer (EGT) or horizontal gene transfer (HGT), but further study is needed to verify this. Phylogenetic analyses suggested that Mankyua was resolved as the earliest diverging lineage and that Ophioglossum was subsequently diverged in Ophioglossaceae. This result supports why the plastome of M. chejuense have contained the most ancestral six ORFs in the family.
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Affiliation(s)
- Hyoung Tae Kim
- Division of Life Sciences, School of Life Sciences, Korea University, Seoul, 02841, Korea
- Institute of Agricultural Science and Technology, Chungbuk National University, Chengju, 41566, Korea
| | - Ki-Joong Kim
- Division of Life Sciences, School of Life Sciences, Korea University, Seoul, 02841, Korea.
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17
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Guo X, Thomas DC, Saunders RM. Gene tree discordance and coalescent methods support ancient intergeneric hybridisation between Dasymaschalon and Friesodielsia (Annonaceae). Mol Phylogenet Evol 2018; 127:14-29. [DOI: 10.1016/j.ympev.2018.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 03/23/2018] [Accepted: 04/09/2018] [Indexed: 01/10/2023]
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18
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Dong S, Zhao C, Chen F, Liu Y, Zhang S, Wu H, Zhang L, Liu Y. The complete mitochondrial genome of the early flowering plant Nymphaea colorata is highly repetitive with low recombination. BMC Genomics 2018; 19:614. [PMID: 30107780 PMCID: PMC6092842 DOI: 10.1186/s12864-018-4991-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 08/02/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Mitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. The mitogenome of the earliest angiosperm Amborella is remarkable in carrying rampant foreign DNAs, in contrast to Liriodendron, the other only known early angiosperm mitogenome that is described as 'fossilized'. The distinctive features observed in the two early flowering plant mitogenomes add to the current confusions of what early flowering plants look like. Expanded sampling would provide more details in understanding the mitogenomic evolution of early angiosperms. Here we report the complete mitochondrial genome of water lily Nymphaea colorata from Nymphaeales, one of the three orders of the earliest angiosperms. RESULTS Assembly of data from Pac-Bio long-read sequencing yielded a circular mitochondria chromosome of 617,195 bp with an average depth of 601×. The genome encoded 41 protein coding genes, 20 tRNA and three rRNA genes with 25 group II introns disrupting 10 protein coding genes. Nearly half of the genome is composed of repeated sequences, which contributed substantially to the intron size expansion, making the gross intron length of the Nymphaea mitochondrial genome one of the longest among angiosperms, including an 11.4-Kb intron in cox2, which is the longest organellar intron reported to date in plants. Nevertheless, repeat mediated homologous recombination is unexpectedly low in Nymphaea evidenced by 74 recombined reads detected from ten recombinationally active repeat pairs among 886,982 repeat pairs examined. Extensive gene order changes were detected in the three early angiosperm mitogenomes, i.e. 38 or 44 events of inversions and translocations are needed to reconcile the mitogenome of Nymphaea with Amborella or Liriodendron, respectively. In contrast to Amborella with six genome equivalents of foreign mitochondrial DNA, not a single horizontal gene transfer event was observed in the Nymphaea mitogenome. CONCLUSIONS The Nymphaea mitogenome resembles the other available early angiosperm mitogenomes by a similarly rich 64-coding gene set, and many conserved gene clusters, whereas stands out by its highly repetitive nature and resultant remarkable intron expansions. The low recombination level in Nymphaea provides evidence for the predominant master conformation in vivo with a highly substoichiometric set of rearranged molecules.
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Affiliation(s)
- Shanshan Dong
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chaoxian Zhao
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- Department of Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Fei Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanhui Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shouzhou Zhang
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Hong Wu
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Liangsheng Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yang Liu
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, 518083 China
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Szlachetko DL, Kolanowska M, Naczk A, Górniak M, Dudek M, Rutkowski P, Chiron G. Taxonomy of Cyrtochilum-alliance (Orchidaceae) in the light of molecular and morphological data. BOTANICAL STUDIES 2017; 58:8. [PMID: 28510191 PMCID: PMC5430592 DOI: 10.1186/s40529-017-0164-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 01/08/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The generic separateness and specific composition of the orchid genus Cyrtochilum was discussed for almost two centuries. Over the years several smaller taxa were segregated from this taxon, but their separateness was recently questioned based on molecular studies outcomes. The aim of our study was to revise concepts of morphological-based generic delimitation in Cyrtochilum-alliance and to compare it with the results of genetic analysis. We used phylogenetic framework in combination with phenetical analysis to provide proposal of the generic delimitation within Cyrtochilum-alliance. Two molecular markers, ITS and matK were used to construct phylogenetic tree. A total of over 5000 herbarium specimens were included in the morphological examination and the phenetical analysis included 29 generative and vegetative characters. RESULTS Comparative morphology of the previously recognized genera: Buesiella, Dasyglossum, Neodryas, Rusbyella, Siederella and Trigonochilum is presented. A new species within the the latter genus is described. Fourteen new combinations are proposed. The key to the identification of the genera of the Cyrtochilum-alliance and morphological characteristics of each genus are provided. CONCLUSIONS A total of six separated genera are recognized within Cyrtochilum-alliance. The reasons of the incompatibility between morphological differences observed within studied taxa and phylogenetic tree are argued and the taxonomic implications of such inconsistency, resulting in fragmentation or lumping of taxonomic units, are discussed.
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Affiliation(s)
- Dariusz L. Szlachetko
- Department of Plant Taxonomy and Nature Conservation, The University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Marta Kolanowska
- Department of Plant Taxonomy and Nature Conservation, The University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
- Department of Biodiversity Research, Global Change Research Institute AS CR, Bělidla 4a., 603 00 Brno, Czech Republic
| | - Aleksandra Naczk
- Department of Molecular Evolution, The University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Marcin Górniak
- Department of Molecular Evolution, The University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Magdalena Dudek
- Department of Plant Taxonomy and Nature Conservation, The University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Piotr Rutkowski
- Department of Plant Taxonomy and Nature Conservation, The University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Guy Chiron
- Herbiers, Université de Lyon I, 69622 Villeurbanne Cedex, France
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Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
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Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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21
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Yin H, Wu X, Shi D, Chen Y, Qi K, Ma Z, Zhang S. TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species. Mob DNA 2017; 8:14. [PMID: 29093758 PMCID: PMC5659011 DOI: 10.1186/s13100-017-0098-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/18/2017] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Long terminal repeat retrotransposons (LTR-RTs) are major components of plant genomes. Common LTR-RTs contain the palindromic dinucleotide 5'-'TG'-'CA'-3' motif at the ends. Thus, further analyses of non-canonical LTR-RTs with non-palindromic motifs will enhance our understanding of their structures and evolutionary history. RESULTS Here, we report two new LTR-RT subfamilies (TGTT and AACA) with atypical dinucleotide ends of 5'-'TG'-'TT'-3', and 5'-'AA'-'CA'-3' in pear, apple, peach and mei. In total, 91 intact LTR-RTs were identified and classified into four TGTT and four AACA families. A structural annotation analysis showed that the four TGTT families, together with AACA1 and AACA2, belong to the Copia-like superfamily, whereas AACA3 and AACA4 appeared to be TRIM elements. The average amplification time frames for the eight families ranged from 0.05 to 2.32 million years. Phylogenetics coupled with sequence analyses revealed that the TGTT1 elements of peach were horizontally transferred from apple. In addition, 32 elements from two TGTT and three AACA families had detectable transcriptional activation, and a qRT-PCR analysis indicated that their expression levels varied dramatically in different species, organs and stress treatments. CONCLUSIONS Two novel LTR-RT subfamilies that terminated with non-palindromic dinucleotides at the ends of their LTRs were identified in four Rosaceae species, and a deep analysis showed their recent activity, horizontal transfer and varied transcriptional levels in different species, organs and stress treatments. This work enhances our understanding of the structural variation and evolutionary history of LTR-RTs in plants and also provides a valuable resource for future investigations of LTR-RTs having specific structures in other species.
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Affiliation(s)
- Hao Yin
- Center of Pear Engineering Technology Research, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xiao Wu
- Center of Pear Engineering Technology Research, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Dongqing Shi
- Center of Pear Engineering Technology Research, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yangyang Chen
- Center of Pear Engineering Technology Research, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Kaijie Qi
- Center of Pear Engineering Technology Research, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Zhengqiang Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shaoling Zhang
- Center of Pear Engineering Technology Research, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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22
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Bock R. Witnessing Genome Evolution: Experimental Reconstruction of Endosymbiotic and Horizontal Gene Transfer. Annu Rev Genet 2017; 51:1-22. [PMID: 28846455 DOI: 10.1146/annurev-genet-120215-035329] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Present day mitochondria and plastids (chloroplasts) evolved from formerly free-living bacteria that were acquired through endosymbiosis more than a billion years ago. Conversion of the bacterial endosymbionts into cell organelles involved the massive translocation of genetic material from the organellar genomes to the nucleus. The development of transformation technologies for organellar genomes has made it possible to reconstruct this endosymbiotic gene transfer in laboratory experiments and study the mechanisms involved. Recently, the horizontal transfer of genetic information between organisms has also become amenable to experimental investigation. It led to the discovery of horizontal genome transfer as an asexual process generating new species and new combinations of nuclear and organellar genomes. This review describes experimental approaches towards studying endosymbiotic and horizontal gene transfer processes, discusses the new knowledge gained from these approaches about both the evolutionary significance of gene transfer and the underlying molecular mechanisms, and highlights exciting possibilities to exploit gene and genome transfer in biotechnology and synthetic biology.
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Affiliation(s)
- Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany;
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23
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Mahelka V, Krak K, Kopecký D, Fehrer J, Šafář J, Bartoš J, Hobza R, Blavet N, Blattner FR. Multiple horizontal transfers of nuclear ribosomal genes between phylogenetically distinct grass lineages. Proc Natl Acad Sci U S A 2017; 114:1726-1731. [PMID: 28137844 PMCID: PMC5320982 DOI: 10.1073/pnas.1613375114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The movement of nuclear DNA from one vascular plant species to another in the absence of fertilization is thought to be rare. Here, nonnative rRNA gene [ribosomal DNA (rDNA)] copies were identified in a set of 16 diploid barley (Hordeum) species; their origin was traceable via their internal transcribed spacer (ITS) sequence to five distinct Panicoideae genera, a lineage that split from the Pooideae about 60 Mya. Phylogenetic, cytogenetic, and genomic analyses implied that the nonnative sequences were acquired between 1 and 5 Mya after a series of multiple events, with the result that some current Hordeum sp. individuals harbor up to five different panicoid rDNA units in addition to the native Hordeum rDNA copies. There was no evidence that any of the nonnative rDNA units were transcribed; some showed indications of having been silenced via pseudogenization. A single copy of a Panicum sp. rDNA unit present in H. bogdanii had been interrupted by a native transposable element and was surrounded by about 70 kbp of mostly noncoding sequence of panicoid origin. The data suggest that horizontal gene transfer between vascular plants is not a rare event, that it is not necessarily restricted to one or a few genes only, and that it can be selectively neutral.
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MESH Headings
- Cell Nucleus/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Diploidy
- Evolution, Molecular
- Gene Transfer, Horizontal
- Genes, Plant/genetics
- Hordeum/classification
- Hordeum/genetics
- Phylogeny
- Poaceae/classification
- Poaceae/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Václav Mahelka
- Institute of Botany, The Czech Academy of Sciences, Průhonice 25243, Czech Republic;
| | - Karol Krak
- Institute of Botany, The Czech Academy of Sciences, Průhonice 25243, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague 6 16500, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Judith Fehrer
- Institute of Botany, The Czech Academy of Sciences, Průhonice 25243, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Roman Hobza
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
- Institute of Biophysics, The Czech Academy of Sciences, Brno 61265, Czech Republic
| | - Nicolas Blavet
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Frank R Blattner
- Experimental Taxonomy, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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Huang J, Wang Y, Liu W, Shen X, Fan Q, Jian S, Tang T. EARE-1, a Transcriptionally Active Ty1/Copia-Like Retrotransposon Has Colonized the Genome of Excoecaria agallocha through Horizontal Transfer. FRONTIERS IN PLANT SCIENCE 2017; 8:45. [PMID: 28174588 PMCID: PMC5258746 DOI: 10.3389/fpls.2017.00045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/09/2017] [Indexed: 06/06/2023]
Abstract
Long terminal repeat (LTR) retrotransposons constitute the majority of the content of angiosperm genomes, but their evolutionary dynamics remain poorly understood. Here, we report the isolation and characterization of a putative full-length (~9550 bp) Ty1/copia-like retrotransposon in Excoecaria agallocha and its evolution in Euphorbiaceae. The so-called EARE-1 is phylogenetically closely related to RIRE-1 from Oryza australiensis, and has proliferated recently (~7.19 Mya) in the E. agallocha genome. An RT-PCR analysis revealed substantial transcription of EARE-1 in all examined organs (leaves, staminate flowers, pistillate flowers, seeds, and roots) in unstressed E. agallocha plants and indications of elevated expression under stress. We conducted sequence analyses of 256 RT-RH fragments (~860 bp) of EARE-1 from 34 species representing four subfamilies of Euphorbiaceae that exist in China. EARE-1 copies from two Excoecaria species and Phyllanthus urinaria showed incongruent phylogeny with the host species and exhibited high sequence similarity to the host genes, suggesting a horizontal transfer from P. urinaria to the common ancestor of Excoecaria. However, SSAP analysis detected no new insertions of EARE-1 among full-sibling progeny plants of E. agallocha, despite considerable SSAP polymorphisms among half-siblings. EARE-1 is the first transcriptionally active Ty1/copia-like retrotransposon isolated from E. agallocha. Our results provide empirical evidence of the horizontal transfer of LTR retrotransposons in plants, and may suggest a significant role of post-transcriptional host control in the life cycles of transposable elements.
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Affiliation(s)
- Jianhua Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources School of Life Sciences, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
| | - Yushuai Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources School of Life Sciences, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
| | - Wenwen Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources School of Life Sciences, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
| | - Xu Shen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources School of Life Sciences, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources School of Life Sciences, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
| | - Shuguang Jian
- South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Tian Tang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources School of Life Sciences, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
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Konstantinov YM, Dietrich A, Weber-Lotfi F, Ibrahim N, Klimenko ES, Tarasenko VI, Bolotova TA, Koulintchenko MV. DNA import into mitochondria. BIOCHEMISTRY (MOSCOW) 2016; 81:1044-1056. [DOI: 10.1134/s0006297916100035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Knie N, Grewe F, Knoop V. Monilophyte mitochondrial rps1 genes carry a unique group II intron that likely originated from an ancient paralog in rpl2. RNA (NEW YORK, N.Y.) 2016; 22:1338-48. [PMID: 27354706 PMCID: PMC4986890 DOI: 10.1261/rna.056572.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 05/19/2016] [Indexed: 05/10/2023]
Abstract
Intron patterns in plant mitochondrial genomes differ significantly between the major land plant clades. We here report on a new, clade-specific group II intron in the rps1 gene of monilophytes (ferns). This intron, rps1i25g2, is strikingly similar to rpl2i846g2 previously identified in the mitochondrial rpl2 gene of seed plants, ferns, and the lycophyte Phlegmariurus squarrosus Although mitochondrial ribosomal protein genes are frequently subject to endosymbiotic gene transfer among plants, we could retrieve the mitochondrial rps1 gene in a taxonomically wide sampling of 44 monilophyte taxa including basal lineages such as the Ophioglossales, Psilotales, and Marattiales with the only exception being the Equisetales (horsetails). Introns rps1i25g2 and rpl2i846g2 were likewise consistently present with only two exceptions: Intron rps1i25g2 is lost in the genus Ophioglossum and intron rpl2i846g2 is lost in Equisetum bogotense Both intron sequences are moderately affected by RNA editing. The unprecedented primary and secondary structure similarity of rps1i25g2 and rpl2i846g2 suggests an ancient retrotransposition event copying rpl2i846g2 into rps1, for which we suggest a model. Our phylogenetic analysis adding the new rps1 locus to a previous data set is fully congruent with recent insights on monilophyte phylogeny and further supports a sister relationship of Gleicheniales and Hymenophyllales.
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Affiliation(s)
- Nils Knie
- Abteilung Molekulare Evolution, IZMB-Institut für Zelluläre und Molekulare Botanik, Universität Bonn, D-53115 Bonn, Germany
| | - Felix Grewe
- Abteilung Molekulare Evolution, IZMB-Institut für Zelluläre und Molekulare Botanik, Universität Bonn, D-53115 Bonn, Germany
| | - Volker Knoop
- Abteilung Molekulare Evolution, IZMB-Institut für Zelluläre und Molekulare Botanik, Universität Bonn, D-53115 Bonn, Germany
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Filyushin MA, Reshetnikova NM, Kochieva EZ, Skryabin KG. Polymorphism of sequences and the secondary structure of b/c intron of mitochondrial gene nad1 in Monotropa hypopitys and related ericaceae species. BIOL BULL+ 2016. [DOI: 10.1134/s1062359016030043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Conaco C, Tsoulfas P, Sakarya O, Dolan A, Werren J, Kosik KS. Detection of Prokaryotic Genes in the Amphimedon queenslandica Genome. PLoS One 2016; 11:e0151092. [PMID: 26959231 PMCID: PMC4784904 DOI: 10.1371/journal.pone.0151092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/22/2016] [Indexed: 12/20/2022] Open
Abstract
Horizontal gene transfer (HGT) is common between prokaryotes and phagotrophic eukaryotes. In metazoans, the scale and significance of HGT remains largely unexplored but is usually linked to a close association with parasites and endosymbionts. Marine sponges (Porifera), which host many microorganisms in their tissues and lack an isolated germ line, are potential carriers of genes transferred from prokaryotes. In this study, we identified a number of potential horizontally transferred genes within the genome of the sponge, Amphimedon queenslandica. We further identified homologs of some of these genes in other sponges. The transferred genes, most of which possess catalytic activity for carbohydrate or protein metabolism, have assimilated host genome characteristics and are actively expressed. The diversity of functions contributed by the horizontally transferred genes is likely an important factor in the adaptation and evolution of A. queenslandica. These findings highlight the potential importance of HGT on the success of sponges in diverse ecological niches.
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Affiliation(s)
- Cecilia Conaco
- Marine Science Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Pantelis Tsoulfas
- University of Miami School of Medicine, Departments of Neurosurgery and Cell Biology, Miami, Florida, United States of America
| | - Onur Sakarya
- Natera, San Carlos, California, United States of America
| | - Amanda Dolan
- Biology Department, University of Rochester, New York, United States of America
| | - John Werren
- Biology Department, University of Rochester, New York, United States of America
| | - Kenneth S. Kosik
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, United States of America
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Abstract
We report cell-to-cell movement of mitochondria through a graft junction. Mitochondrial movement was discovered in an experiment designed to select for chloroplast transfer from Nicotiana sylvestris into Nicotiana tabacum cells. The alloplasmic N. tabacum line we used carries Nicotiana undulata cytoplasmic genomes, and its flowers are male sterile due to the foreign mitochondrial genome. Thus, rare mitochondrial DNA transfer from N. sylvestris to N. tabacum could be recognized by restoration of fertile flower anatomy. Analyses of the mitochondrial genomes revealed extensive recombination, tentatively linking male sterility to orf293, a mitochondrial gene causing homeotic conversion of anthers into petals. Demonstrating cell-to-cell movement of mitochondria reconstructs the evolutionary process of horizontal mitochondrial DNA transfer and enables modification of the mitochondrial genome by DNA transmitted from a sexually incompatible species. Conversion of anthers into petals is a visual marker that can be useful for mitochondrial transformation.
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Park S, Grewe F, Zhu A, Ruhlman TA, Sabir J, Mower JP, Jansen RK. Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers. THE NEW PHYTOLOGIST 2015; 208:570-83. [PMID: 25989702 DOI: 10.1111/nph.13467] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/15/2015] [Indexed: 05/20/2023]
Abstract
The exchange of genetic material between cellular organelles through intracellular gene transfer (IGT) or between species by horizontal gene transfer (HGT) has played an important role in plant mitochondrial genome evolution. The mitochondrial genomes of Geraniaceae display a number of unusual phenomena including highly accelerated rates of synonymous substitutions, extensive gene loss and reduction in RNA editing. Mitochondrial DNA sequences assembled for 17 species of Geranium revealed substantial reduction in gene and intron content relative to the ancestor of the Geranium lineage. Comparative analyses of nuclear transcriptome data suggest that a number of these sequences have been functionally relocated to the nucleus via IGT. Evidence for rampant HGT was detected in several Geranium species containing foreign organellar DNA from diverse eudicots, including many transfers from parasitic plants. One lineage has experienced multiple, independent HGT episodes, many of which occurred within the past 5.5 Myr. Both duplicative and recapture HGT were documented in Geranium lineages. The mitochondrial genome of Geranium brycei contains at least four independent HGT tracts that are absent in its nearest relative. Furthermore, G. brycei mitochondria carry two copies of the cox1 gene that differ in intron content, providing insight into contrasting hypotheses on cox1 intron evolution.
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Affiliation(s)
- Seongjun Park
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
| | - Felix Grewe
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68588, USA
| | - Andan Zhu
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68588, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
| | - Jamal Sabir
- Department of Biological Science, Biotechnology Research Group, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68588, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
- Department of Biological Science, Biotechnology Research Group, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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Davis CC, Xi Z. Horizontal gene transfer in parasitic plants. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:14-19. [PMID: 26051213 DOI: 10.1016/j.pbi.2015.05.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/08/2015] [Accepted: 05/12/2015] [Indexed: 06/04/2023]
Abstract
Horizontal gene transfer (HGT) between species has been a major focus of plant evolutionary research during the past decade. Parasitic plants, which establish a direct connection with their hosts, have provided excellent examples of how these transfers are facilitated via the intimacy of this symbiosis. In particular, phylogenetic studies from diverse clades indicate that parasitic plants represent a rich system for studying this phenomenon. Here, HGT has been shown to be astonishingly high in the mitochondrial genome, and appreciable in the nuclear genome. Although explicit tests remain to be performed, some transgenes have been hypothesized to be functional in their recipient species, thus providing a new perspective on the evolution of novelty in parasitic plants.
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Affiliation(s)
- Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA.
| | - Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA
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Wu B, Buljic A, Hao W. Extensive Horizontal Transfer and Homologous Recombination Generate Highly Chimeric Mitochondrial Genomes in Yeast. Mol Biol Evol 2015; 32:2559-70. [PMID: 26018571 DOI: 10.1093/molbev/msv127] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The frequency of horizontal gene transfer (HGT) in mitochondrial DNA varies substantially. In plants, HGT is relatively common, whereas in animals it appears to be quite rare. It is of considerable importance to understand mitochondrial HGT across the major groups of eukaryotes at a genome-wide level, but so far this has been well studied only in plants. In this study, we generated ten new mitochondrial genome sequences and analyzed 40 mitochondrial genomes from the Saccharomycetaceae to assess the magnitude and nature of mitochondrial HGT in yeasts. We provide evidence for extensive, homologous-recombination-mediated, mitochondrial-to-mitochondrial HGT occurring throughout yeast mitochondrial genomes, leading to genomes that are highly chimeric evolutionarily. This HGT has led to substantial intraspecific polymorphism in both sequence content and sequence divergence, which to our knowledge has not been previously documented in any mitochondrial genome. The unexpectedly high frequency of mitochondrial HGT in yeast may be driven by frequent mitochondrial fusion, relatively low mitochondrial substitution rates and pseudohyphal fusion to produce heterokaryons. These findings suggest that mitochondrial HGT may play an important role in genome evolution of a much broader spectrum of eukaryotes than previously appreciated and that there is a critical need to systematically study the frequency, extent, and importance of mitochondrial HGT across eukaryotes.
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Affiliation(s)
- Baojun Wu
- Department of Biological Sciences, Wayne State University
| | - Adnan Buljic
- Department of Biological Sciences, Wayne State University
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University
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Wang B, Climent J, Wang XR. Horizontal gene transfer from a flowering plant to the insular pine Pinus canariensis (Chr. Sm. Ex DC in Buch). Heredity (Edinb) 2015; 114:413-8. [PMID: 25604946 PMCID: PMC4359980 DOI: 10.1038/hdy.2014.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/03/2014] [Accepted: 11/10/2014] [Indexed: 11/09/2022] Open
Abstract
Horizontal gene transfer (HGT) is viewed as very common in the plant mitochondrial (mt) genome, but, to date, only one case of HGT has been found in gymnosperms. Here we report a new case of HGT, in which a mt nad5-1 fragment was transferred from an angiosperm to Pinus canariensis. Quantitative assay and sequence analyses showed that the foreign nad5-1 is located in the mt genome of P. canariensis and is nonfunctional. An extensive survey in the genus Pinus revealed that the angiosperm-derived nad5-1 is restricted to P. canariensis and present across the species' range. Molecular dating based on chloroplast DNA suggested that the HGT event occurred in the late Miocene after P. canariensis split from its closest relatives, and that the foreign copy became fixed in P. canariensis owing to drift during its colonization of the Canary Islands. The mechanism of this HGT is unclear but it was probably achieved through either direct cell-cell contact or external vectors. Our discovery provides evidence for an important role of HGT in plant mt genome evolution.
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Affiliation(s)
- B Wang
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - J Climent
- Department of Forest Ecology and Genetics, INIA-CIFOR, Madrid, Spain
| | - X-R Wang
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
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Kannan S, Rogozin IB, Koonin EV. MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes. BMC Evol Biol 2014; 14:237. [PMID: 25421434 PMCID: PMC4256733 DOI: 10.1186/s12862-014-0237-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 11/07/2014] [Indexed: 01/19/2023] Open
Abstract
Background Mitochondria are ubiquitous membranous organelles of eukaryotic cells that evolved from an alpha-proteobacterial endosymbiont and possess a small genome that encompasses from 3 to 106 genes. Accumulation of thousands of mitochondrial genomes from diverse groups of eukaryotes provides an opportunity for a comprehensive reconstruction of the evolution of the mitochondrial gene repertoire. Results Clusters of orthologous mitochondrial protein-coding genes (MitoCOGs) were constructed from all available mitochondrial genomes and complemented with nuclear orthologs of mitochondrial genes. With minimal exceptions, the mitochondrial gene complements of eukaryotes are subsets of the superset of 66 genes found in jakobids. Reconstruction of the evolution of mitochondrial genomes indicates that the mitochondrial gene set of the last common ancestor of the extant eukaryotes was slightly larger than that of jakobids. This superset of mitochondrial genes likely represents an intermediate stage following the loss and transfer to the nucleus of most of the endosymbiont genes early in eukaryote evolution. Subsequent evolution in different lineages involved largely parallel transfer of ancestral endosymbiont genes to the nuclear genome. The intron density in nuclear orthologs of mitochondrial genes typically is nearly the same as in the rest of the genes in the respective genomes. However, in land plants, the intron density in nuclear orthologs of mitochondrial genes is almost 1.5-fold lower than the genomic mean, suggestive of ongoing transfer of functional genes from mitochondria to the nucleus. Conclusions The MitoCOGs are expected to become an important resource for the study of mitochondrial evolution. The nearly complete superset of mitochondrial genes in jakobids likely represents an intermediate stage in the evolution of eukaryotes after the initial, extensive loss and transfer of the endosymbiont genes. In addition, the bacterial multi-subunit RNA polymerase that is encoded in the jakobid mitochondrial genomes was replaced by a single-subunit phage-type RNA polymerase in the rest of the eukaryotes. These results are best compatible with the rooting of the eukaryotic tree between jakobids and the rest of the eukaryotes. The land plants are the only eukaryotic branch in which the gene transfer from the mitochondrial to the nuclear genome appears to be an active, ongoing process. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0237-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sivakumar Kannan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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36
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Knie N, Polsakiewicz M, Knoop V. Horizontal gene transfer of chlamydial-like tRNA genes into early vascular plant mitochondria. Mol Biol Evol 2014; 32:629-34. [PMID: 25415968 DOI: 10.1093/molbev/msu324] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial genomes of lycophytes are surprisingly diverse, including strikingly different transfer RNA (tRNA) gene complements: No mitochondrial tRNA genes are present in the spikemoss Selaginella moellendorffii, whereas 26 tRNAs are encoded in the chondrome of the clubmoss Huperzia squarrosa. Reinvestigating the latter we found that trnL(gag) and trnS(gga) had never before been identified in any other land plant mitochondrial DNA. Sensitive sequence comparisons showed these two tRNAs as well as trnN(guu) and trnS(gcu) to be very similar to their respective counterparts in chlamydial bacteria. We identified homologs of these chlamydial-type tRNAs also in other lycophyte, fern, and gymnosperm DNAs, suggesting horizontal gene transfer (HGT) into mitochondria in the early vascular plant stem lineages. These findings extend plant mitochondrial HGT to affect individual tRNA genes, to include bacterial donors, and suggest that Chlamydiae on top of their recently proposed key role in primary chloroplast establishment may also have participated in early tracheophyte genome evolution.
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Affiliation(s)
- Nils Knie
- Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany
| | - Monika Polsakiewicz
- Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany
| | - Volker Knoop
- Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany
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37
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Redrejo-Rodríguez M, Salas M. Multiple roles of genome-attached bacteriophage terminal proteins. Virology 2014; 468-470:322-329. [PMID: 25232661 DOI: 10.1016/j.virol.2014.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 07/31/2014] [Accepted: 08/04/2014] [Indexed: 11/29/2022]
Abstract
Protein-primed replication constitutes a generalized mechanism to initiate DNA or RNA synthesis in linear genomes, including viruses, gram-positive bacteria, linear plasmids and mobile elements. By this mechanism a specific amino acid primes replication and becomes covalently linked to the genome ends. Despite the fact that TPs lack sequence homology, they share a similar structural arrangement, with the priming residue in the C-terminal half of the protein and an accumulation of positively charged residues at the N-terminal end. In addition, various bacteriophage TPs have been shown to have DNA-binding capacity that targets TPs and their attached genomes to the host nucleoid. Furthermore, a number of bacteriophage TPs from different viral families and with diverse hosts also contain putative nuclear localization signals and localize in the eukaryotic nucleus, which could lead to the transport of the attached DNA. This suggests a possible role of bacteriophage TPs in prokaryote-to-eukaryote horizontal gene transfer.
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Affiliation(s)
- Modesto Redrejo-Rodríguez
- Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas-Universidad de Madrid), Universidad Autónoma, Nicolás Cabrera, 1, Cantoblanco, 28049 Madrid, Spain
| | - Margarita Salas
- Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas-Universidad de Madrid), Universidad Autónoma, Nicolás Cabrera, 1, Cantoblanco, 28049 Madrid, Spain.
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Liu Y, Cox CJ, Wang W, Goffinet B. Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias. Syst Biol 2014; 63:862-78. [PMID: 25070972 DOI: 10.1093/sysbio/syu049] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea for resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to the, perhaps cumulative, effects of saturation, among-taxa compositional (GC content) heterogeneity, or codon-usage bias plaguing the individual nucleotide loci that are concatenated. Here, we provide an example of how these factors affect the inferences of the phylogeny of early land plants based on mitochondrial genomic data. Mitochondrial sequences evolve slowly in plants and hence are thought to be suitable for resolving deep relationships. We newly assembled mitochondrial genomes from 20 bryophytes, complemented these with 40 other streptophytes (land plants plus algal outgroups), compiling a data matrix of 60 taxa and 41 mitochondrial genes. Homogeneous analyses of the concatenated nucleotide data resolve mosses as sister-group to the remaining land plants. However, the corresponding translated amino acid data support the liverwort lineage in this position. Both results receive weak to moderate support in maximum-likelihood analyses, but strong support in Bayesian inferences. Tests of alternative hypotheses using either nucleotide or amino acid data provide implicit support for their respective optimal topologies, and clearly reject the hypotheses that bryophytes are monophyletic, liverworts and mosses share a unique common ancestor, or hornworts are sister to the remaining land plants. We determined that land plant lineages differ in their nucleotide composition, and in their usage of synonymous codon variants. Composition heterogeneous Bayesian analyses employing a nonstationary model that accounts for variation in among-lineage composition, and inferences from degenerated nucleotide data that avoid the effects of synonymous substitutions that underlie codon-usage bias, again recovered liverworts being sister to the remaining land plants but without support. These analyses indicate that the inference of an early-branching moss lineage based on the nucleotide data is caused by convergent compositional biases. Accommodating among-site amino acid compositional heterogeneity (CAT-model) yields no support for the optimal resolution of liverwort as sister to the rest of land plants, suggesting that the robust inference of the liverwort position in homogeneous analyses may be due in part to compositional biases among sites. All analyses support a paraphyletic bryophytes with hornworts composing the sister-group to tracheophytes. We conclude that while genomic data may generate highly supported phylogenetic trees, these inferences may be artifacts. We suggest that phylogenomic analyses should assess the possible impact of potential biases through comparisons of protein-coding gene data and their amino acid translations by evaluating the impact of substitutional saturation, synonymous substitutions, and compositional biases through data deletion strategies and by analyzing the data using heterogeneous composition models. We caution against relying on any one presentation of the data (nucleotide or amino acid) or any one type of analysis even when analyzing large-scale data sets, no matter how well-supported, without fully exploring the effects of substitution models.
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Affiliation(s)
- Yang Liu
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319 Faro, Portugal; and State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Cymon J Cox
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319 Faro, Portugal; and State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wei Wang
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319 Faro, Portugal; and State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA; Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319 Faro, Portugal; and State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Field Supervisory Test of DREB-Transgenic Populus: Salt Tolerance, Long-Term Gene Stability and Horizontal Gene Transfer. FORESTS 2014. [DOI: 10.3390/f5051106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Elliott AG, Delay C, Liu H, Phua Z, Rosengren KJ, Benfield AH, Panero JL, Colgrave ML, Jayasena AS, Dunse KM, Anderson MA, Schilling EE, Ortiz-Barrientos D, Craik DJ, Mylne JS. Evolutionary origins of a bioactive peptide buried within Preproalbumin. THE PLANT CELL 2014; 26:981-95. [PMID: 24681618 PMCID: PMC4001405 DOI: 10.1105/tpc.114.123620] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 01/27/2014] [Accepted: 03/04/2014] [Indexed: 05/25/2023]
Abstract
The de novo evolution of proteins is now considered a frequented route for biological innovation, but the genetic and biochemical processes that lead to each newly created protein are often poorly documented. The common sunflower (Helianthus annuus) contains the unusual gene PawS1 (Preproalbumin with SFTI-1) that encodes a precursor for seed storage albumin; however, in a region usually discarded during albumin maturation, its sequence is matured into SFTI-1, a protease-inhibiting cyclic peptide with a motif homologous to unrelated inhibitors from legumes, cereals, and frogs. To understand how PawS1 acquired this additional peptide with novel biochemical functionality, we cloned PawS1 genes and showed that this dual destiny is over 18 million years old. This new family of mostly backbone-cyclic peptides is structurally diverse, but the protease-inhibitory motif was restricted to peptides from sunflower and close relatives from its subtribe. We describe a widely distributed, potential evolutionary intermediate PawS-Like1 (PawL1), which is matured into storage albumin, but makes no stable peptide despite possessing residues essential for processing and cyclization from within PawS1. Using sequences we cloned, we retrodict the likely stepwise creation of PawS1's additional destiny within a simple albumin precursor. We propose that relaxed selection enabled SFTI-1 to evolve its inhibitor function by converging upon a successful sequence and structure.
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Affiliation(s)
- Alysha G. Elliott
- The University of Queensland, Institute for Molecular Bioscience, Brisbane 4072, Australia
| | - Christina Delay
- The University of Queensland, Institute for Molecular Bioscience, Brisbane 4072, Australia
| | - Huanle Liu
- School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia
| | - Zaiyang Phua
- The University of Queensland, Institute for Molecular Bioscience, Brisbane 4072, Australia
| | - K. Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane 4072, Australia
| | - Aurélie H. Benfield
- The University of Queensland, Institute for Molecular Bioscience, Brisbane 4072, Australia
| | - Jose L. Panero
- Section of Integrative Biology, University of Texas, Austin, Texas 78712
| | | | - Achala S. Jayasena
- The University of Western Australia, School of Chemistry and Biochemistry and ARC Centre of Excellence in Plant Energy Biology, Crawley, Perth 6009, Australia
| | - Kerry M. Dunse
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Marilyn A. Anderson
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Edward E. Schilling
- University of Tennessee, Department of Ecology and Evolutionary Biology, Knoxville, Tennessee 37996
| | | | - David J. Craik
- The University of Queensland, Institute for Molecular Bioscience, Brisbane 4072, Australia
| | - Joshua S. Mylne
- The University of Queensland, Institute for Molecular Bioscience, Brisbane 4072, Australia
- The University of Western Australia, School of Chemistry and Biochemistry and ARC Centre of Excellence in Plant Energy Biology, Crawley, Perth 6009, Australia
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Rice DW, Alverson AJ, Richardson AO, Young GJ, Sanchez-Puerta MV, Munzinger J, Barry K, Boore JL, Zhang Y, dePamphilis CW, Knox EB, Palmer JD. Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Science 2014; 342:1468-73. [PMID: 24357311 DOI: 10.1126/science.1246275] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We report the complete mitochondrial genome sequence of the flowering plant Amborella trichopoda. This enormous, 3.9-megabase genome contains six genome equivalents of foreign mitochondrial DNA, acquired from green algae, mosses, and other angiosperms. Many of these horizontal transfers were large, including acquisition of entire mitochondrial genomes from three green algae and one moss. We propose a fusion-compatibility model to explain these findings, with Amborella capturing whole mitochondria from diverse eukaryotes, followed by mitochondrial fusion (limited mechanistically to green plant mitochondria) and then genome recombination. Amborella's epiphyte load, propensity to produce suckers from wounds, and low rate of mitochondrial DNA loss probably all contribute to the high level of foreign DNA in its mitochondrial genome.
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Affiliation(s)
- Danny W Rice
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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42
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Nikolaidis N, Doran N, Cosgrove DJ. Plant expansins in bacteria and fungi: evolution by horizontal gene transfer and independent domain fusion. Mol Biol Evol 2013; 31:376-86. [PMID: 24150040 DOI: 10.1093/molbev/mst206] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Horizontal gene transfer (HGT) has been described as a common mechanism of transferring genetic material between prokaryotes, whereas genetic transfers from eukaryotes to prokaryotes have been rarely documented. Here we report a rare case of HGT in which plant expansin genes that code for plant cell-wall loosening proteins were transferred from plants to bacteria, fungi, and amoebozoa. In several cases, the species in which the expansin gene was found is either in intimate association with plants or is a known plant pathogen. Our analyses suggest that at least two independent genetic transfers occurred from plants to bacteria and fungi. These events were followed by multiple HGT events within bacteria and fungi. We have also observed that in bacteria expansin genes have been independently fused to DNA fragments that code for an endoglucanase domain or for a carbohydrate binding module, pointing to functional convergence at the molecular level. Furthermore, the functional similarities between microbial expansins and their plant xenologs suggest that these proteins mediate microbial-plant interactions by altering the plant cell wall and therefore may provide adaptive advantages to these species. The evolution of these nonplant expansins represents a unique case in which bacteria and fungi have found innovative and adaptive ways to interact with and infect plants by acquiring genes from their host. This evolutionary paradigm suggests that despite their low frequency such HGT events may have significantly contributed to the evolution of prokaryotic and eukaryotic species.
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Affiliation(s)
- Nikolas Nikolaidis
- Department of Biological Science and Center for Applied Biotechnology Studies, California State University, Fullerton
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Zhang Y, Fernandez-Aparicio M, Wafula EK, Das M, Jiao Y, Wickett NJ, Honaas LA, Ralph PE, Wojciechowski MF, Timko MP, Yoder JI, Westwood JH, Depamphilis CW. Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species. BMC Evol Biol 2013; 13:48. [PMID: 23425243 PMCID: PMC3601976 DOI: 10.1186/1471-2148-13-48] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 02/04/2013] [Indexed: 11/29/2022] Open
Abstract
Background Parasitic plants, represented by several thousand species of angiosperms, use modified structures known as haustoria to tap into photosynthetic host plants and extract nutrients and water. As a result of their direct plant-plant connections with their host plant, parasitic plants have special opportunities for horizontal gene transfer, the nonsexual transmission of genetic material across species boundaries. There is increasing evidence that parasitic plants have served as recipients and donors of horizontal gene transfer (HGT), but the long-term impacts of eukaryotic HGT in parasitic plants are largely unknown. Results Here we show that a gene encoding albumin 1 KNOTTIN-like protein, closely related to the albumin 1 genes only known from papilionoid legumes, where they serve dual roles as food storage and insect toxin, was found in Phelipanche aegyptiaca and related parasitic species of family Orobanchaceae, and was likely acquired by a Phelipanche ancestor via HGT from a legume host based on phylogenetic analyses. The KNOTTINs are well known for their unique “disulfide through disulfide knot” structure and have been extensively studied in various contexts, including drug design. Genomic sequences from nine related parasite species were obtained, and 3D protein structure simulation tests and evolutionary constraint analyses were performed. The parasite gene we identified here retains the intron structure, six highly conserved cysteine residues necessary to form a KNOTTIN protein, and displays levels of purifying selection like those seen in legumes. The albumin 1 xenogene has evolved through >150 speciation events over ca. 16 million years, forming a small family of differentially expressed genes that may confer novel functions in the parasites. Moreover, further data show that a distantly related parasitic plant, Cuscuta, obtained two copies of albumin 1 KNOTTIN-like genes from legumes through a separate HGT event, suggesting that legume KNOTTIN structures have been repeatedly co-opted by parasitic plants. Conclusions The HGT-derived albumins in Phelipanche represent a novel example of how plants can acquire genes from other plants via HGT that then go on to duplicate, evolve, and retain the specialized features required to perform a unique host-derived function.
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Affiliation(s)
- Yeting Zhang
- Intercollege Graduate Program in Genetics, Institute of Molecular Evolutionary Genetics, Penn State University, University Park, PA 16802, USA
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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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Greiner S, Bock R. Tuning a ménage à trois: Co-evolution and co-adaptation of nuclear and organellar genomes in plants. Bioessays 2013; 35:354-65. [DOI: 10.1002/bies.201200137] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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Functional eukaryotic nuclear localization signals are widespread in terminal proteins of bacteriophages. Proc Natl Acad Sci U S A 2012; 109:18482-7. [PMID: 23091024 DOI: 10.1073/pnas.1216635109] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A number of prokaryotic proteins have been shown to contain nuclear localization signals (NLSs), although its biological role remains sometimes unclear. Terminal proteins (TPs) of bacteriophages prime DNA replication and become covalently linked to the genome ends. We predicted NLSs within the TPs of bacteriophages from diverse families and hosts and, indeed, the TPs of Φ29, Nf, PRD1, Bam35, and Cp-1, out of seven TPs tested, were found to localize to the nucleus when expressed in mammalian cells. Detailed analysis of Φ29 TP led us to identify a bona fide NLS within residues 1-37. Importantly, gene delivery into the eukaryotic nucleus is enhanced by the presence of Φ29 TP attached to the 5' DNA ends. These findings show a common feature of TPs from diverse bacteriophages targeting the eukaryotic nucleus and suggest a possible common function by facilitating the horizontal transfer of genes between prokaryotes and eukaryotes.
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Cuenca A, Petersen G, Seberg O, Jahren AH. Genes and processed paralogs co-exist in plant mitochondria. J Mol Evol 2012; 74:158-69. [PMID: 22484699 DOI: 10.1007/s00239-012-9496-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 03/23/2012] [Indexed: 10/28/2022]
Abstract
RNA-mediated gene duplication has been proposed to create processed paralogs in the plant mitochondrial genome. A processed paralog may retain signatures left by the maturation process of its RNA precursor, such as intron removal and no need of RNA editing. Whereas it is well documented that an RNA intermediary is involved in the transfer of mitochondrial genes to the nucleus, no direct evidence exists for insertion of processed paralogs in the mitochondria (i.e., processed and un-processed genes have never been found simultaneously in the mitochondrial genome). In this study, we sequenced a region of the mitochondrial gene nad1, and identified a number of taxa were two different copies of the region co-occur in the mitochondria. The two nad1 paralogs differed in their (a) presence or absence of a group II intron, and (b) number of edited sites. Thus, this work provides the first evidence of co-existence of processed paralogs and their precursors within the plant mitochondrial genome. In addition, mapping the presence/absence of the paralogs provides indirect evidence of RNA-mediated gene duplication as an essential process shaping the mitochondrial genome in plants.
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Affiliation(s)
- Argelia Cuenca
- Botanical Garden, Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83 Opg. S, 1307, Copenhagen K, Denmark.
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48
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49
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Stegemann S, Keuthe M, Greiner S, Bock R. Horizontal transfer of chloroplast genomes between plant species. Proc Natl Acad Sci U S A 2012; 109:2434-8. [PMID: 22308367 PMCID: PMC3289295 DOI: 10.1073/pnas.1114076109] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The genomes of DNA-containing cell organelles (mitochondria, chloroplasts) can be laterally transmitted between organisms, a process known as organelle capture. Organelle capture often occurs in the absence of detectable nuclear introgression, and the capture mechanism is unknown. Here, we have considered horizontal genome transfer across natural grafts as a mechanism underlying chloroplast capture in plants. By grafting sexually incompatible species, we show that complete chloroplast genomes can travel across the graft junction from one species into another. We demonstrate that, consistent with reported phylogenetic evidence, replacement of the resident plastid genome by the alien genome occurs in the absence of intergenomic recombination. Our results provide a plausible mechanism for organelle capture in plants and suggest natural grafting as a path for horizontal gene and genome transfer between sexually incompatible species.
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Affiliation(s)
- Sandra Stegemann
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Mandy Keuthe
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Stephan Greiner
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
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50
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Seed Plant Mitochondrial Genomes: Complexity Evolving. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2012. [DOI: 10.1007/978-94-007-2920-9_8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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