1
|
Liu X, Wu X, Tan H, Xie B, Deng Y. Large inverted repeats identified by intra-specific comparison of mitochondrial genomes provide insights into the evolution of Agrocybe aegerita. Comput Struct Biotechnol J 2020; 18:2424-2437. [PMID: 33005305 PMCID: PMC7508693 DOI: 10.1016/j.csbj.2020.08.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 11/29/2022] Open
Abstract
Genomic structure and content of Agrocybe aegerita mitochondrial DNA contain essential information regarding the evolution of this gourmet mushroom. In this study, eight isolates of A. aegerita were sequenced and assembled into complete mitochondrial genomes. The mtDNA of the isolate Ag0067 contained two genotypes, both of which were quadripartite architecture consisting of two identical inverted repeats, separated by a small single-copy region and a large single-copy region. The only difference was opposite directions of the small single-copy region. The mtDNAs ranged from 116,329 bp to 134,035 bp, harboring two large identical inverted repeats. Genes of plasmid-origin were present in regions flanked by inverted repeat ID2. Most of the core genes evolved at a relatively low rate, whereas five tRNA genes located in corresponding regions of Ag0002:1-14000 and Ag0002:50001-61000 showed higher diversity. A long fragment inversion (10 Kb) was suggested to have occurred during the differentiation of two main clades, leading to two different gene orders. The number and distribution of the introns varied greatly among the A. aegerita mtDNAs. Fast invasion of short insertions likely resulted in the diversity of introns as well as other non-coding regions, increasing the variation of the mtDNAs. We raised a model about the evolution of the large repeats to explain the unusual features of A. aegerita mtDNAs. This study constructed quadripartite architecture of A. aegerita mtDNAs analogous to chloroplast DNA, proposed an interconversion model of the divergent mitochondrial genotypes with large inverted repeats. The findings could increase our knowledge of fungal evolution.
Collapse
Affiliation(s)
- Xinrui Liu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiaoping Wu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Hao Tan
- Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
- School of Bioengineering, Jiangnan University, Wuxi 214062, China
| | - Baogui Xie
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Youjin Deng
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| |
Collapse
|
2
|
Schoenle A, Živaljić S, Prausse D, Voß J, Jakobsen K, Arndt H. New phagotrophic euglenids from deep sea and surface waters of the Atlantic Ocean (Keelungia nitschei, Petalomonas acorensis, Ploeotia costaversata). Eur J Protistol 2019; 69:102-116. [DOI: 10.1016/j.ejop.2019.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 10/27/2022]
|
3
|
Lax G, Lee WJ, Eglit Y, Simpson A. Ploeotids Represent Much of the Phylogenetic Diversity of Euglenids. Protist 2019; 170:233-257. [PMID: 31102975 DOI: 10.1016/j.protis.2019.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/19/2019] [Accepted: 03/01/2019] [Indexed: 11/26/2022]
Abstract
Ploeotids are an assemblage of rigid phagotrophic euglenids that have 10-12 pellicular strips and glide on their posterior flagellum. Molecular phylogenies place them as a poorly resolved, likely paraphyletic assemblage outside the Spirocuta clade of flexible euglenids, which includes the well-known phototrophs and primary osmotrophs. Here, we report SSU rRNA gene sequences from 38 ploeotids, using both single-cell and culture-based methods. Several contain group I or non-canonical introns. Our phylogenetic analyses place ploeotids in 8 distinct clades: Olkasia n. gen., Hemiolia n. gen., Liburna n. gen., Lentomonas, Decastava, Keelungia, Ploeotiidae, and Entosiphon. Ploeotia vitrea, the type of Ploeotia, is closely related to P. oblonga and Serpenomonas costata, but not to Lentomonas. Ploeotia cf. vitrea sensu Lax and Simpson 2013 is not related to P. vitrea and has a different pellicle strip architecture (as imaged by scanning electron microscopy): it instead represents a novel genus and species, Olkasia polycarbonata. We also describe new genera, Hemiolia and Liburna, for the morphospecies Anisonema trepidum and A. glaciale. A recent system proposing 13 suprafamilial taxa that include ploeotids is not supported by our phylogenies. The exact relationships between ploeotid groups remain unresolved and multigene phylogenetics or phylogenomics are needed to address this uncertainty.
Collapse
Affiliation(s)
- Gordon Lax
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Won Je Lee
- Department of Environment and Energy Engineering, Kyungnam University, Changwon, Republic of Korea
| | - Yana Eglit
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Alastair Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada.
| |
Collapse
|
4
|
New phagotrophic euglenoid species (new genus Decastava; Scytomonas saepesedens; Entosiphon oblongum), Hsp90 introns, and putative euglenoid Hsp90 pre-mRNA insertional editing. Eur J Protistol 2016; 56:147-170. [DOI: 10.1016/j.ejop.2016.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 07/29/2016] [Accepted: 08/03/2016] [Indexed: 11/19/2022]
|
5
|
Chan YF, Chiang KP, Chang J, Moestrup Ø, Chung CC. Strains of the Morphospecies Ploeotia costata
(Euglenozoa) Isolated from the Western North Pacific (Taiwan) Reveal Substantial Genetic Differences. J Eukaryot Microbiol 2014; 62:318-26. [DOI: 10.1111/jeu.12183] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 08/13/2014] [Accepted: 08/28/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Ya-Fan Chan
- Institute of Marine Environmental Chemistry and Ecology; National Taiwan Ocean University; Keelung Taiwan
| | - Kuo-Ping Chiang
- Institute of Marine Environmental Chemistry and Ecology; National Taiwan Ocean University; Keelung Taiwan
- Center of Excellence for the Oceans; National Taiwan Ocean University; Keelung Taiwan
| | - Jeng Chang
- Center of Excellence for the Oceans; National Taiwan Ocean University; Keelung Taiwan
- Institute of Marine Biology; National Taiwan Ocean University; Keelung Taiwan
| | - Øjvind Moestrup
- Biological Institute; University of Copenhagen; Copenhagen K Denmark
| | - Chih-Ching Chung
- Institute of Marine Environmental Chemistry and Ecology; National Taiwan Ocean University; Keelung Taiwan
- Center of Excellence for the Oceans; National Taiwan Ocean University; Keelung Taiwan
| |
Collapse
|
6
|
Torres-Machorro AL, Hernández R, Cevallos AM, López-Villaseñor I. Ribosomal RNA genes in eukaryotic microorganisms: witnesses of phylogeny? FEMS Microbiol Rev 2010; 34:59-86. [DOI: 10.1111/j.1574-6976.2009.00196.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
7
|
Haugen P, Bhattacharya D. The spread of LAGLIDADG homing endonuclease genes in rDNA. Nucleic Acids Res 2004; 32:2049-57. [PMID: 15069127 PMCID: PMC390371 DOI: 10.1093/nar/gkh520] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Group I introns that encode homing endonuclease genes (HEGs) are highly invasive genetic elements. Their movement into a homologous position in an intron-less allele is termed homing. Although the mechanism of homing is well understood, the evolutionary relationship between HEGs and their intron partners remains unclear. Here we have focused on the largest family of HEGs (encoding the protein motif, LAGLIDADG) to understand how HEGs and introns move in rDNA. Our analysis shows the phylogenetic clustering of HEGs that encode a single copy of the LAGLIDADG motif in neighboring, but often evolutionarily distantly related, group I introns. These endonucleases appear to have inserted into existing introns independent of ribozymes. In contrast, our data support a common evolutionary history for a large family of heterologous introns that encode HEGs with a duplicated LAGLIDADG motif. This finding suggests that intron/double-motif HEG elements can move into heterologous sites as a unit. Our data also suggest that a subset of the double-motif HEGs in rDNA originated from the duplication and fusion of a single-motif HEG encoded by present-day ribozymes in LSU rDNA.
Collapse
Affiliation(s)
- Peik Haugen
- Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, 210 Old Biology Building, Iowa City, IA 52242-1324, USA
| | | |
Collapse
|
8
|
Sandegren L, Sjöberg BM. Distribution, sequence homology, and homing of group I introns among T-even-like bacteriophages: evidence for recent transfer of old introns. J Biol Chem 2004; 279:22218-27. [PMID: 15026408 DOI: 10.1074/jbc.m400929200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Self-splicing group I introns are being found in an increasing number of bacteriophages. Most introns contain an open reading frame coding for a homing endo-nuclease that confers mobility to both the intron and the homing endonuclease gene (HEG). The frequent occurrence of intron/HEG has raised questions whether group I introns are spread via horizontal transfer between phage populations. We have determined complete sequences for the known group I introns among T-even-like bacteriophages together with sequences of the intron-containing genes td, nrdB, and nrdD from phages with and without introns. A previously uncharacterized phage isolate, U5, is shown to contain all three introns, the only phage besides T4 found with a "full set" of these introns. Sequence analysis of td and nrdB genes from intron-containing and intronless phages provides evidence that recent horizontal transmission of introns has occurred among the phages. The fact that several of the HEGs have suffered deletions rendering them non-functional implies that the homing endonucleases are of no selective advantage to the phage and are rapidly degenerating and probably dependent upon frequent horizontal transmissions for maintenance within the phage populations. Several of the introns can home to closely related intronless phages during mixed infections. However, the efficiency of homing varies and is dependent on homology in regions flanking the intron insertion site. The occurrence of optional genes flanking the respective intron-containing gene can strongly affect the efficiency of homing. These findings give further insight into the mechanisms of propagation and evolution of group I introns among the T-even-like bacteriophages.
Collapse
Affiliation(s)
- Linus Sandegren
- Department of Molecular Biology & Functional Genomics, Stockholm University, Svante Arrhenius vag 16, F3. SE-10691 Stockholm, Sweden
| | | |
Collapse
|
9
|
Marin B, Palm A, Klingberg M, Melkonian M. Phylogeny and taxonomic revision of plastid-containing euglenophytes based on SSU rDNA sequence comparisons and synapomorphic signatures in the SSU rRNA secondary structure. Protist 2003; 154:99-145. [PMID: 12812373 DOI: 10.1078/143446103764928521] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sequence comparisons and a revised classification of the Euglenophyceae were based on 92 new SSU rDNA sequences obtained from strains of Euglena, Astasia, Phacus, Trachelomonas, Colacium, Cryptoglena, Lepocinclis, Eutreptia, Eutreptiella and Tetreutreptia. Sequence data also provided molecular signatures for taxa from genus to class level in the SSU rRNA secondary structure, revealed by a novel approach (search for non-homoplasious synapomorphies) and used for taxonomic diagnoses. Photosynthetic euglenoids and secondary heterotrophs formed a clade, designated as Euglenophyceae (emend.) with two orders: Euglenales and Eutreptiales. The mostly marine Eutreptiales (Eutreptia, Eutreptiella; not Distigma) comprised taxa with two or four emergent flagella (the quadriflagellate Tetreutreptia was integrated within Eutreptiella). The Euglenales (freshwater genera with < or = one emergent flagellum) formed nine clades and two individual branches (single strains); however, only two clades were congruent with traditional genera: Trachelomonas (incl. Strombomonas) and Colacium. Euglena was polyphyletic and diverged into four independent clades (intermixed with Astasia, Khawkinea and Lepocinclis) and two individual branches (e.g. E. polymorpha). Phacus was also subdivided into Phacus s. str. and two combined lineages (mixed with Lepocinclis spp. or Cryptoglena). In consequence, Euglena (s. str.), Phacus and other genera were emended and one lineage (mixed Phacus/Lepocinclis-clade) was recognized as the previously neglected genus Monomorphina Mereschkowsky (1877). The sister clade of Phacus s. str. (mixed Euglena/Lepocinclis-clade) was identified as Lepocinclis Perty (emended).
Collapse
Affiliation(s)
- Birger Marin
- Botanisches Institut, Lehrstuhl I, Universität zu Köln, Gyrhofstr. 15, D-50931 Köln, Germany.
| | | | | | | |
Collapse
|