1
|
Zumkeller S, Knoop V. Categorizing 161 plant (streptophyte) mitochondrial group II introns into 29 families of related paralogues finds only limited links between intron mobility and intron-borne maturases. BMC Ecol Evol 2023; 23:5. [PMID: 36915058 PMCID: PMC10012718 DOI: 10.1186/s12862-023-02108-y] [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: 09/20/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
Group II introns are common in the two endosymbiotic organelle genomes of the plant lineage. Chloroplasts harbor 22 positionally conserved group II introns whereas their occurrence in land plant (embryophyte) mitogenomes is highly variable and specific for the seven major clades: liverworts, mosses, hornworts, lycophytes, ferns, gymnosperms and flowering plants. Each plant group features "signature selections" of ca. 20-30 paralogues from a superset of altogether 105 group II introns meantime identified in embryophyte mtDNAs, suggesting massive intron gains and losses along the backbone of plant phylogeny. We report on systematically categorizing plant mitochondrial group II introns into "families", comprising evidently related paralogues at different insertion sites, which may even be more similar than their respective orthologues in phylogenetically distant taxa. Including streptophyte (charophyte) algae extends our sampling to 161 and we sort 104 streptophyte mitochondrial group II introns into 25 core families of related paralogues evidently arising from retrotransposition events. Adding to discoveries of only recently created intron paralogues, hypermobile introns and twintrons, our survey led to further discoveries including previously overlooked "fossil" introns in spacer regions or e.g., in the rps8 pseudogene of lycophytes. Initially excluding intron-borne maturase sequences for family categorization, we added an independent analysis of maturase phylogenies and find a surprising incongruence between intron mobility and the presence of intron-borne maturases. Intriguingly, however, we find that several examples of nuclear splicing factors meantime characterized simultaneously facilitate splicing of independent paralogues now placed into the same intron families. Altogether this suggests that plant group II intron mobility, in contrast to their bacterial counterparts, is not intimately linked to intron-encoded maturases.
Collapse
Affiliation(s)
- Simon Zumkeller
- 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.
| |
Collapse
|
2
|
Kim D, Lee J, Cho CH, Kim EJ, Bhattacharya D, Yoon HS. Group II intron and repeat-rich red algal mitochondrial genomes demonstrate the dynamic recent history of autocatalytic RNAs. BMC Biol 2022; 20:2. [PMID: 34996446 PMCID: PMC8742464 DOI: 10.1186/s12915-021-01200-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 11/29/2021] [Indexed: 11/10/2022] Open
Abstract
Background Group II introns are mobile genetic elements that can insert at specific target sequences, however, their origins are often challenging to reconstruct because of rapid sequence decay following invasion and spread into different sites. To advance understanding of group II intron spread, we studied the intron-rich mitochondrial genome (mitogenome) in the unicellular red alga, Porphyridium. Results Analysis of mitogenomes in three closely related species in this genus revealed they were 3–6-fold larger in size (56–132 kbp) than in other red algae, that have genomes of size 21–43 kbp. This discrepancy is explained by two factors, group II intron invasion and expansion of repeated sequences in large intergenic regions. Phylogenetic analysis demonstrates that many mitogenome group II intron families are specific to Porphyridium, whereas others are closely related to sequences in fungi and in the red alga-derived plastids of stramenopiles. Network analysis of intron-encoded proteins (IEPs) shows a clear link between plastid and mitochondrial IEPs in distantly related species, with both groups associated with prokaryotic sequences. Conclusion Our analysis of group II introns in Porphyridium mitogenomes demonstrates the dynamic nature of group II intron evolution, strongly supports the lateral movement of group II introns among diverse eukaryotes, and reveals their ability to proliferate, once integrated in mitochondrial DNA. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01200-3.
Collapse
Affiliation(s)
- Dongseok Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu, 41566, South Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Eun Jeung Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea.
| |
Collapse
|
3
|
Zumkeller S, Gerke P, Knoop V. A functional twintron, 'zombie' twintrons and a hypermobile group II intron invading itself in plant mitochondria. Nucleic Acids Res 2020; 48:2661-2675. [PMID: 31915815 PMCID: PMC7049729 DOI: 10.1093/nar/gkz1194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/26/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023] Open
Abstract
The occurrence of group II introns in plant mitochondrial genomes is strikingly different between the six major land plant clades, contrasting their highly conserved counterparts in chloroplast DNA. Their present distribution likely reflects numerous ancient intron gains and losses during early plant evolution before the emergence of seed plants. As a novelty for plant organelles, we here report on five cases of twintrons, introns-within-introns, in the mitogenomes of lycophytes and hornworts. An internal group II intron interrupts an intron-borne maturase of an atp9 intron in Lycopodiaceae, whose splicing precedes splicing of the external intron. An invasive, hypermobile group II intron in cox1, has conquered nine further locations including a previously overlooked sdh3 intron and, most surprisingly, also itself. In those cases, splicing of the external introns does not depend on splicing of the internal introns. Similar cases are identified in the mtDNAs of hornworts. Although disrupting a group I intron-encoded protein in one case, we could not detect splicing of the internal group II intron in this ‘mixed’ group I/II twintron. We suggest the name ‘zombie’ twintrons (half-dead, half-alive) for such cases where splicing of external introns does not depend any more on prior splicing of fossilized internal introns.
Collapse
Affiliation(s)
- Simon Zumkeller
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115 Bonn, Germany
| | - Philipp Gerke
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115 Bonn, Germany
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, D-53115 Bonn, Germany
| |
Collapse
|
4
|
Dabbagh N, Bennett MS, Triemer RE, Preisfeld A. Chloroplast genome expansion by intron multiplication in the basal psychrophilic euglenoid Eutreptiella pomquetensis. PeerJ 2017; 5:e3725. [PMID: 28852596 PMCID: PMC5572947 DOI: 10.7717/peerj.3725] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/01/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Over the last few years multiple studies have been published showing a great diversity in size of chloroplast genomes (cpGenomes), and in the arrangement of gene clusters, in the Euglenales. However, while these genomes provided important insights into the evolution of cpGenomes across the Euglenales and within their genera, only two genomes were analyzed in regard to genomic variability between and within Euglenales and Eutreptiales. To better understand the dynamics of chloroplast genome evolution in early evolving Eutreptiales, this study focused on the cpGenome of Eutreptiella pomquetensis, and the spread and peculiarities of introns. METHODS The Etl. pomquetensis cpGenome was sequenced, annotated and afterwards examined in structure, size, gene order and intron content. These features were compared with other euglenoid cpGenomes as well as those of prasinophyte green algae, including Pyramimonas parkeae. RESULTS AND DISCUSSION With about 130,561 bp the chloroplast genome of Etl. pomquetensis, a basal taxon in the phototrophic euglenoids, was considerably larger than the two other Eutreptiales cpGenomes sequenced so far. Although the detected quadripartite structure resembled most green algae and plant chloroplast genomes, the gene content of the single copy regions in Etl. pomquetensis was completely different from those observed in green algae and plants. The gene composition of Etl. pomquetensis was extensively changed and turned out to be almost identical to other Eutreptiales and Euglenales, and not to P. parkeae. Furthermore, the cpGenome of Etl. pomquetensis was unexpectedly permeated by a high number of introns, which led to a substantially larger genome. The 51 identified introns of Etl. pomquetensis showed two major unique features: (i) more than half of the introns displayed a high level of pairwise identities; (ii) no group III introns could be identified in the protein coding genes. These findings support the hypothesis that group III introns are degenerated group II introns and evolved later.
Collapse
Affiliation(s)
- Nadja Dabbagh
- Faculty of Mathematics and Natural Sciences, Zoology and Didactics of Biology, Bergische Universität Wuppertal, Wuppertal, Germany
| | - Matthew S Bennett
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
| | - Richard E Triemer
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
| | - Angelika Preisfeld
- Faculty of Mathematics and Natural Sciences, Zoology and Didactics of Biology, Bergische Universität Wuppertal, Wuppertal, Germany
| |
Collapse
|
5
|
Ebenezer TE, Carrington M, Lebert M, Kelly S, Field MC. Euglena gracilis Genome and Transcriptome: Organelles, Nuclear Genome Assembly Strategies and Initial Features. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 979:125-140. [PMID: 28429320 DOI: 10.1007/978-3-319-54910-1_7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Euglena gracilis is a major component of the aquatic ecosystem and together with closely related species, is ubiquitous worldwide. Euglenoids are an important group of protists, possessing a secondarily acquired plastid and are relatives to the Kinetoplastidae, which themselves have global impact as disease agents. To understand the biology of E. gracilis, as well as to provide further insight into the evolution and origins of the Kinetoplastidae, we embarked on sequencing the nuclear genome; the plastid and mitochondrial genomes are already in the public domain. Earlier studies suggested an extensive nuclear DNA content, with likely a high degree of repetitive sequence, together with significant extrachromosomal elements. To produce a list of coding sequences we have combined transcriptome data from both published and new sources, as well as embarked on de novo sequencing using a combination of 454, Illumina paired end libraries and long PacBio reads. Preliminary analysis suggests a surprisingly large genome approaching 2 Gbp, with a highly fragmented architecture and extensive repeat composition. Over 80% of the RNAseq reads from E. gracilis maps to the assembled genome sequence, which is comparable with the well assembled genomes of T. brucei and T. cruzi. In order to achieve this level of assembly we employed multiple informatics pipelines, which are discussed here. Finally, as a preliminary view of the genome architecture, we discuss the tubulin and calmodulin genes, which highlight potential novel splicing mechanisms.
Collapse
Affiliation(s)
- ThankGod Echezona Ebenezer
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.,School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Michael Lebert
- Cell Biology Division, Department of Biology, University of Erlangen-Nuremberg, Staudtstraβe 5, Erlangen, 91058, Germany
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
| |
Collapse
|
6
|
Dabbagh N, Preisfeld A. The Chloroplast Genome of Euglena mutabilis-Cluster Arrangement, Intron Analysis, and Intrageneric Trends. J Eukaryot Microbiol 2016; 64:31-44. [PMID: 27254767 DOI: 10.1111/jeu.12334] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 04/06/2016] [Accepted: 05/25/2016] [Indexed: 11/28/2022]
Abstract
A comparative analysis of the chloroplast genome of Euglena mutabilis underlined a high diversity in the evolution of plastids in euglenids. Gene clusters in more derived Euglenales increased in complexity with only a few, but remarkable changes in the genus Euglena. Euglena mutabilis differed from other Euglena species in a mirror-inverted arrangement of 12 from 15 identified clusters, making it very likely that the emergence at the base of the genus Euglena, which has been considered a long branch artifact, is truly a probable position. This was corroborated by many similarities in gene arrangement and orientation with Strombomonas and Monomorphina, rendering the genome organization of E. mutabilis in certain clusters as plesiomorphic feature. By RNA analysis exact exon-intron boundaries and the type of the 77 introns identified were mostly determined unambiguously. A detailed intron study of psbC pointed at two important issues: First, the number of introns varied even between species, and no trend from few to many introns could be observed. Second, mat1 was localized in Eutreptiales exclusively in intron 1, and mat2 was not identified. With the emergence of Euglenaceae in most species, a new intron containing mat2 inserted in front of the previous intron 1 and thereby became intron 2 with mat1.
Collapse
Affiliation(s)
- Nadja Dabbagh
- Bergische University Wuppertal, Faculty of Mathematics and Natural Sciences, Zoology and Didactics of Biology, Wuppertal, Germany
| | - Angelika Preisfeld
- Bergische University Wuppertal, Faculty of Mathematics and Natural Sciences, Zoology and Didactics of Biology, Wuppertal, Germany
| |
Collapse
|
7
|
Bicudo CEDM, Menezes M. Phylogeny and Classification of Euglenophyceae: A Brief Review. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
8
|
Kim JI, Linton EW, Shin W. Taxon-rich multigene phylogeny of the photosynthetic euglenoids (Euglenophyceae). Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00098] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
|
9
|
Karnkowska A, Bennett MS, Watza D, Kim JI, Zakryś B, Triemer RE. Phylogenetic Relationships and Morphological Character Evolution of Photosynthetic Euglenids (Excavata) Inferred from Taxon-rich Analyses of Five Genes. J Eukaryot Microbiol 2014; 62:362-73. [DOI: 10.1111/jeu.12192] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Anna Karnkowska
- Department of Plant Systematics and Geography; Faculty of Biology; University of Warsaw; Warsaw Poland
- Department of Parasitology; Faculty of Science; Charles University in Prague; Prague Czech Republic
| | - Matthew S. Bennett
- Department of Plant Biology; Michigan State University; East Lansing Michigan USA
| | - Donovan Watza
- Department of Plant Biology; Michigan State University; East Lansing Michigan USA
| | - Jong Im Kim
- Department of Biology; Chungnam National University; Daejeon Korea
| | - Bożena Zakryś
- Department of Plant Systematics and Geography; Faculty of Biology; University of Warsaw; Warsaw Poland
| | - Richard E. Triemer
- Department of Plant Biology; Michigan State University; East Lansing Michigan USA
| |
Collapse
|
10
|
A small portion of plastid transcripts is polyadenylated in the flagellate Euglena gracilis. FEBS Lett 2014; 588:783-8. [PMID: 24492004 DOI: 10.1016/j.febslet.2014.01.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 12/21/2022]
Abstract
Euglena gracilis possesses secondary plastids of green algal origin. In this study, E. gracilis expressed sequence tags (ESTs) derived from polyA-selected mRNA were searched and several ESTs corresponding to plastid genes were found. PCR experiments failed to detect SL sequence at the 5'-end of any of these transcripts, suggesting plastid origin of these polyadenylated molecules. Quantitative PCR experiments confirmed that polyadenylation of transcripts occurs in the Euglena plastids. Such transcripts have been previously observed in primary plastids of plants and algae as low-abundance intermediates of transcript degradation. Our results suggest that a similar mechanism exists in secondary plastids.
Collapse
|
11
|
Flipphi M, Fekete E, Ag N, Scazzocchio C, Karaffa L. Spliceosome twin introns in fungal nuclear transcripts. Fungal Genet Biol 2013; 57:48-57. [PMID: 23792080 DOI: 10.1016/j.fgb.2013.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 06/07/2013] [Accepted: 06/09/2013] [Indexed: 10/26/2022]
Abstract
The spliceosome is an RNA/protein complex, responsible for intron excision from eukaryotic nuclear transcripts. In bacteria, mitochondria and plastids, intron excision does not involve the spliceosome, but occurs through mechanisms dependent on intron RNA secondary and tertiary structure. For group II/III chloroplast introns, "twintrons" (introns within introns) have been described. The excision of the external intron, and thus proper RNA maturation, necessitates prior removal of the internal intron, which interrupts crucial sequences of the former. We have here predicted analogous instances of spliceosomal twintrons ("stwintrons") in filamentous fungi. In two specific cases, where the internal intron interrupts the donor of the external intron after the first or after the second nucleotide, respectively, we show that intermediates with the sequence predicted by the "stwintron" hypothesis, are produced in the splicing process. This implies that two successive rounds of RNA scanning by the spliceosome are necessary to produce the mature mRNA. The phylogenetic distributions of the stwintrons we have identified suggest that they derive from "late" events, subsequent to the appearance of the host intron. They may well not be limited to fungal nuclear transcripts, and their generation and eventual disappearance in the evolutionary process are relevant to hypotheses of intron origin and alternative splicing.
Collapse
Affiliation(s)
- Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4010 Debrecen, Hungary.
| | | | | | | | | |
Collapse
|
12
|
Kim JI, Shin W, Triemer RE. Cryptic Speciation in the Genus Cryptoglena (Euglenaceae) Revealed by Nuclear and Plastid SSU and LSU rRNA Gene. JOURNAL OF PHYCOLOGY 2013; 49:92-102. [PMID: 27008392 DOI: 10.1111/jpy.12032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Accepted: 08/27/2012] [Indexed: 05/23/2023]
Abstract
The photosynthetic euglenoid genus Cryptoglena is differentiated from other euglenoid genera by having a longitudinal sulcus, one chloroplast, two large trough-shaped paramylon plates positioned between the chloroplast and pellicle, and lack of metaboly. The genus contains only two species. To understand genetic diversity and taxonomy of Cryptoglena species, we analyzed molecular and morphological data from 25 strains. A combined data set of nuclear SSU and LSU and plastid SSU and LSU rRNA genes was analyzed using Bayesian, maximum likelihood, maximum parsimony, and distance (neighbor joining) methods. Although morphological data of all strains showed no significant species-specific pattern, molecular data segregated the taxa into five clades, two of which represented previously known species: C. skujae and C. pigra, and three of which were designated as the new species, C. soropigra, C. similis, and C. longisulca. Each species had unique molecular signatures that could be found in the plastid SSU rRNA Helix P23_1 and LSU rRNA H2 domain. The genetic similarity of intraspecies based on nr SSU rDNA ranged from 97.8% to 100% and interspecies ranged from 95.3% to 98.9%. Therefore, we propose three new species based on specific molecular signatures and gene divergence of the nr SSU rDNA sequences.
Collapse
Affiliation(s)
- Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon, 305-764, Korea
| | - Woongghi Shin
- Department of Biology, Chungnam National University, Daejeon, 305-764, Korea
| | - Richard E Triemer
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| |
Collapse
|
13
|
Evidence for transitional stages in the evolution of euglenid group II introns and twintrons in the Monomorphina aenigmatica plastid genome. PLoS One 2012; 7:e53433. [PMID: 23300929 PMCID: PMC3534033 DOI: 10.1371/journal.pone.0053433] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 11/28/2012] [Indexed: 11/19/2022] Open
Abstract
Background Photosynthetic euglenids acquired their plastid by secondary endosymbiosis of a prasinophyte-like green alga. But unlike its prasinophyte counterparts, the plastid genome of the euglenid Euglena gracilis is riddled with introns that interrupt almost every protein-encoding gene. The atypical group II introns and twintrons (introns-within-introns) found in the E. gracilis plastid have been hypothesized to have been acquired late in the evolution of euglenids, implying that massive numbers of introns may be lacking in other taxa. This late emergence was recently corroborated by the plastid genome sequences of the two basal euglenids, Eutreptiella gymnastica and Eutreptia viridis, which were found to contain fewer introns. Methodology/Principal Findings To gain further insights into the proliferation of introns in euglenid plastids, we have characterized the complete plastid genome sequence of Monomorphina aenigmatica, a freshwater species occupying an intermediate phylogenetic position between early and late branching euglenids. The M. aenigmatica UTEX 1284 plastid genome (74,746 bp, 70.6% A+T, 87 genes) contains 53 intron insertion sites, of which 41 were found to be shared with other euglenids including 12 of the 15 twintron insertion sites reported in E. gracilis. Conclusions The pattern of insertion sites suggests an ongoing but uneven process of intron gain in the lineage, with perhaps a minimum of two bursts of rapid intron proliferation. We also identified several sites that represent intermediates in the process of twintron evolution, where the external intron is in place, but not the internal one, offering a glimpse into how these convoluted molecular contraptions originate.
Collapse
|
14
|
Hrdá Š, Fousek J, Szabová J, Hampl V, Hampl V, Vlček Č. The plastid genome of Eutreptiella provides a window into the process of secondary endosymbiosis of plastid in euglenids. PLoS One 2012; 7:e33746. [PMID: 22448269 PMCID: PMC3308993 DOI: 10.1371/journal.pone.0033746] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 02/16/2012] [Indexed: 11/18/2022] Open
Abstract
Euglenids are a group of protists that comprises species with diverse feeding modes. One distinct and diversified clade of euglenids is photoautotrophic, and its members bear green secondary plastids. In this paper we present the plastid genome of the euglenid Eutreptiella, which we assembled from 454 sequencing of Eutreptiella gDNA. Comparison of this genome and the only other available plastid genomes of photosynthetic euglenid, Euglena gracilis, revealed that they contain a virtually identical set of 57 protein coding genes, 24 genes fewer than the genome of Pyramimonas parkeae, the closest extant algal relative of the euglenid plastid. Searching within the transcriptomes of Euglena and Eutreptiella showed that 6 of the missing genes were transferred to the nucleus of the euglenid host while 18 have been probably lost completely. Euglena and Eutreptiella represent the deepest bifurcation in the photosynthetic clade, and therefore all these gene transfers and losses must have happened before the last common ancestor of all known photosynthetic euglenids. After the split of Euglena and Eutreptiella only one additional gene loss took place. The conservation of gene content in the two lineages of euglenids is in contrast to the variability of gene order and intron counts, which diversified dramatically. Our results show that the early secondary plastid of euglenids was much more susceptible to gene losses and endosymbiotic gene transfers than the established plastid, which is surprisingly resistant to changes in gene content.
Collapse
Affiliation(s)
- Štěpánka Hrdá
- Charles University in Prague, Faculty of Science, Department of Parasitology, Prague, Czech Republic
| | | | | | | | | | | |
Collapse
|
15
|
Wiegert KE, Bennett MS, Triemer RE. Evolution of the chloroplast genome in photosynthetic euglenoids: a comparison of Eutreptia viridis and Euglena gracilis (Euglenophyta). Protist 2012; 163:832-43. [PMID: 22364772 DOI: 10.1016/j.protis.2012.01.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 01/05/2012] [Accepted: 01/06/2012] [Indexed: 11/27/2022]
Abstract
The chloroplast genome of Eutreptia viridis Perty, a basal taxon in the photosynthetic euglenoid lineage, was sequenced and compared with that of Euglena gracilis Ehrenberg, a crown species. Several common gene clusters were identified and gene order, conservation, and sequence similarity was assessed through comparisons with Euglena gracilis. Significant gene rearrangements were present between Eutreptia viridis and Euglena gracilis chloroplast genomes. In addition, major expansion has occurred in the Euglena gracilis chloroplast accounting for its larger size. However, the key chloroplast genes are present and differ only in the absence of psaM and roaA in Eutreptia viridis, and psaI in Euglena gracilis, suggesting a high level of gene conservation within the euglenoid lineage. Further comparisons with the plastid genomes of closely related green algal taxa have provided additional support for the hypothesis that a Pyramimonas-like alga was the euglenoid chloroplast donor via secondary endosymbiosis.
Collapse
Affiliation(s)
- Krystle E Wiegert
- Michigan State University, Department of Plant Biology, East Lansing, MI 48824, USA
| | | | | |
Collapse
|
16
|
Transcriptome analysis of the Euglena gracilis plastid chromosome. Curr Genet 2009; 55:425-38. [DOI: 10.1007/s00294-009-0256-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 05/12/2009] [Accepted: 05/15/2009] [Indexed: 11/26/2022]
|
17
|
Kim E, Archibald JM. Diversity and Evolution of Plastids and Their Genomes. PLANT CELL MONOGRAPHS 2008. [DOI: 10.1007/978-3-540-68696-5_1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
18
|
Kim JI, Shin W. PHYLOGENY OF THE EUGLENALES INFERRED FROM PLASTID LSU rDNA SEQUENCES(1). JOURNAL OF PHYCOLOGY 2008; 44:994-1000. [PMID: 27041618 DOI: 10.1111/j.1529-8817.2008.00536.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
To gain insights into the phylogeny of the Euglenales, we analyzed the plastid LSU rDNA sequences from 101 strains of the photosynthetic euglenoids belonging to nine ingroup genera (Euglena, Trachelomonas, Strombomonas, Monomorphina, Cryptoglena, Colacium, Discoplastis, Phacus, and Lepocinclis) and two outgroup genera (Eutreptia and Eutreptiella). Bayesian and maximum-likelihood (ML) analyses resulted in trees of similar topologies and four major clades: a Phacus and Lepocinclis clade; a Colacium clade; a Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade; and a Euglena clade. The Phacus and Lepocinclis clade was the sister group of all other euglenalian genera, followed by Discoplastis spathirhyncha (Skuja) Triemer and the Colacium clade, respectively, which was inconsistent with their placement based on nuclear rDNA genes. The Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade was sister to the Euglena clade. The loricate genera, Trachelomonas and Strombomonas, were closely related to each other, while Monomorphina and Cryptoglena also grouped together. The Euglena clade formed a monophyletic lineage comprising most species from taxa formerly allocated to the subgenera Calliglena and Euglena. However, within this genus, none of the subgenera was monophyletic.
Collapse
Affiliation(s)
- Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon 305-764, South Korea
| | - Woongghi Shin
- Department of Biology, Chungnam National University, Daejeon 305-764, South Korea
| |
Collapse
|
19
|
|
20
|
Rice DW, Palmer JD. An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters. BMC Biol 2006; 4:31. [PMID: 16956407 PMCID: PMC1570145 DOI: 10.1186/1741-7007-4-31] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Accepted: 09/06/2006] [Indexed: 11/30/2022] Open
Abstract
Background Horizontal gene transfer (HGT) to the plant mitochondrial genome has recently been shown to occur at a surprisingly high rate; however, little evidence has been found for HGT to the plastid genome, despite extensive sequencing. In this study, we analyzed all genes from sequenced plastid genomes to unearth any neglected cases of HGT and to obtain a measure of the overall extent of HGT to the plastid. Results Although several genes gave strongly supported conflicting trees under certain conditions, we are confident of HGT in only a single case beyond the rubisco HGT already reported. Most of the conflicts involved near neighbors connected by long branches (e.g. red algae and their secondary hosts), where phylogenetic methods are prone to mislead. However, three genes – clpP, ycf2, and rpl36 – provided strong support for taxa moving far from their organismal position. Further taxon sampling of clpP and ycf2 resulted in rejection of HGT due to long-branch attraction and a serious error in the published plastid genome sequence of Oenothera elata, respectively. A single new case, a bacterial rpl36 gene transferred into the ancestor of the cryptophyte and haptophyte plastids, appears to be a true HGT event. Interestingly, this rpl36 gene is a distantly related paralog of the rpl36 type found in other plastids and most eubacteria. Moreover, the transferred gene has physically replaced the native rpl36 gene, yet flanking genes and intergenic regions show no sign of HGT. This suggests that gene replacement somehow occurred by recombination at the very ends of rpl36, without the level and length of similarity normally expected to support recombination. Conclusion The rpl36 HGT discovered in this study is of considerable interest in terms of both molecular mechanism and phylogeny. The plastid acquisition of a bacterial rpl36 gene via HGT provides the first strong evidence for a sister-group relationship between haptophyte and cryptophyte plastids to the exclusion of heterokont and alveolate plastids. Moreover, the bacterial gene has replaced the native plastid rpl36 gene by an uncertain mechanism that appears inconsistent with existing models for the recombinational basis of gene conversion.
Collapse
Affiliation(s)
- Danny W Rice
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
21
|
Abstract
Evidence is presented for the recent, horizontal transfer of a self-splicing, homing group II intron from a cyanobacteria to the chloroplast genome of Euglena myxocylindracea. The psbA gene of E.myxocylindracea was found to contain a single 2566 nt group II intron with a gene in domain 4 for a 575 amino acid maturase. The predicted secondary structure and tertiary interactions of the group II intron, as well as the derived maturase primary sequence, most closely resemble the homing intron of the cyanobacterium Calothrix and the rnl introns of Porphyra purpurea mitochondria, while being only distantly related to all other Euglena plastid introns and maturases. All main functional domains of the intron-encoded proteins of known homing introns are conserved, including reverse transcriptase domains 1-7, the zinc finger domain and domain X. The close relationship with cyanobacterial introns was confirmed by phylogenetic analysis. Both the full-length psbA intron and a Delta-maturase variant self-splice in vitro in two independent assays. The psbA intron is the first example of a self-splicing chloroplast group II intron from any organism. These results support the conclusion that the psbA intron is the result of a recent horizontal transfer into the E.myxocylindracea chloroplast genome from a cyanobacterial donor and should prompt a reconsideration of horizontal transfer mechanisms to account for the origin of other chloroplast genetic elements.
Collapse
Affiliation(s)
- Elena V Sheveleva
- Department of Biochemistry and Molecular Biophysics, The University of Arizona, 1041 East Lowell Street, Tucson, AZ 85721-0088, USA
| | | |
Collapse
|
22
|
Brosnan S, Shin W, Kjer KM, Triemer RE. Phylogeny of the photosynthetic euglenophytes inferred from the nuclear SSU and partial LSU rDNA. Int J Syst Evol Microbiol 2003; 53:1175-1186. [PMID: 12892147 DOI: 10.1099/ijs.0.02518-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Previous studies using the nuclear SSU rDNA have indicated that the photosynthetic euglenoids are a monophyletic group; however, some of the genera within the photosynthetic lineage are not monophyletic. To test these results further, evolutionary relationships among the photosynthetic genera were investigated by obtaining partial LSU nuclear rDNA sequences. Taxa from each of the external clades of the SSU rDNA-based phylogeny were chosen to create a combined dataset and to compare the individual LSU and SSU rDNA datasets. Conserved areas of the aligned sequences for both the LSU and SSU rDNA were used to generate parsimony, log-det, maximum-likelihood and Bayesian trees. The SSU and LSU rDNA consistently generated the same seven terminal clades; however, the relationship among those clades varied depending on the type of analysis and the dataset used. The combined dataset generated a more robust phylogeny, but the relationships among clades still varied. The addition of the LSU rDNA dataset to the euglenophyte phylogeny supports the view that the genera Euglena, Lepocinclis and Phacus are not monophyletic and substantiates the existence of several well-supported clades. A secondary structural model for the D2 region of the LSU rDNA was proposed on the basis of compensatory base changes found in the alignment.
Collapse
Affiliation(s)
- Stacy Brosnan
- Division of Life Sciences, Rutgers University, Nelson Hall, 604 Allison Road, Piscataway, NJ 08854, USA
| | - Woongghi Shin
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Karl M Kjer
- Department of Entomology, Rutgers University, Cook College, Blake Hall, 93 Lipman Drive, New Brunswick, NJ 08901, USA
| | - Richard E Triemer
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
23
|
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
|
24
|
Cavalier-Smith T. Genomic reduction and evolution of novel genetic membranes and protein-targeting machinery in eukaryote-eukaryote chimaeras (meta-algae). Philos Trans R Soc Lond B Biol Sci 2003; 358:109-33; discussion 133-4. [PMID: 12594921 PMCID: PMC1693104 DOI: 10.1098/rstb.2002.1194] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Chloroplasts originated just once, from cyanobacteria enslaved by a biciliate protozoan to form the plant kingdom (green plants, red and glaucophyte algae), but subsequently, were laterally transferred to other lineages to form eukaryote-eukaryote chimaeras or meta-algae. This process of secondary symbiogenesis (permanent merger of two phylogenetically distinct eukaryote cells) has left remarkable traces of its evolutionary role in the more complex topology of the membranes surrounding all non-plant (meta-algal) chloroplasts. It took place twice, soon after green and red algae diverged over 550 Myr ago to form two independent major branches of the eukaryotic tree (chromalveolates and cabozoa), comprising both meta-algae and numerous secondarily non-photosynthetic lineages. In both cases, enslavement probably began by evolving a novel targeting of endomembrane vesicles to the perialgal vacuole to implant host porter proteins for extracting photosynthate. Chromalveolates arose by such enslavement of a unicellular red alga and evolution of chlorophyll c to form the kingdom Chromista and protozoan infrakingdom Alveolata, which diverged from the ancestral chromalveolate chimaera. Cabozoa arose when the common ancestor of euglenoids and cercozoan chlorarachnean algae enslaved a tetraphyte green alga with chlorophyll a and b. I suggest that in cabozoa the endomembrane vesicles originally budded from the Golgi, whereas in chromalveolates they budded from the endoplasmic reticulum (ER) independently of Golgi-targeted vesicles, presenting a potentially novel target for drugs against alveolate Sporozoa such as malaria parasites and Toxoplasma. These hypothetical ER-derived vesicles mediated fusion of the perialgal vacuole and rough ER (RER) in the ancestral chromist, placing the former red alga within the RER lumen. Subsequently, this chimaera diverged to form cryptomonads, which retained the red algal nucleus as a nucleomorph (NM) with approximately 464 protein-coding genes (30 encoding plastid proteins) and a red or blue phycobiliprotein antenna pigment, and the chromobiotes (heterokonts and haptophytes), which lost phycobilins and evolved the brown carotenoid fucoxanthin that colours brown seaweeds, diatoms and haptophytes. Chromobiotes transferred the 30 genes to the nucleus and lost the NM genome and nuclear-pore complexes, but retained its membrane as the periplastid reticulum (PPR), putatively the phospholipid factory of the periplastid space (former algal cytoplasm), as did the ancestral alveolate independently. The chlorarachnean NM has three minute chromosomes bearing approximately 300 genes riddled with pygmy introns. I propose that the periplastid membrane (PPM, the former algal plasma membrane) of chromalveolates, and possibly chlorarachneans, grows by fusion of vesicles emanating from the NM envelope or PPR. Dinoflagellates and euglenoids independently lost the PPM and PPR (after diverging from Sporozoa and chlorarachneans, respectively) and evolved triple chloroplast envelopes comprising the original plant double envelope and an extra outermost membrane, the EM, derived from the perialgal vacuole. In all metaalgae most chloroplast proteins are coded by nuclear genes and enter the chloroplast by using bipartite targeting sequences--an upstream signal sequence for entering the ER and a downstream chloroplast transit sequence. I present a new theory for the four-fold diversification of the chloroplast OM protein translocon following its insertion into the PPM to facilitate protein translocation across it (of both periplastid and plastid proteins). I discuss evidence from genome sequencing and other sources on the contrasting modes of protein targeting, cellular integration, and evolution of these two major lineages of eukaryote "cells within cells". They also provide powerful evidence for natural selection's effectiveness in eliminating most functionless DNA and therefore of a universally useful non-genic function for nuclear non-coding DNA, i.e. most DNA in the biosphere, and dramatic examples of genomic reduction. I briefly argue that chloroplast replacement in dinoflagellates, which happened at least twice, may have been evolutionarily easier than secondary symbiogenesis because parts of the chromalveolate protein-targeting machinery could have helped enslave the foreign plastids.
Collapse
Affiliation(s)
- T Cavalier-Smith
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
| |
Collapse
|
25
|
. Famà P, Jousson O, Zaninetti L, Meinesz A, Dini F, Di Giuseppe G, Millar AJK, Pawlowski J. Genetic polymorphism inCaulerpa taxifolia(Ulvophyceae) chloroplast DNA revealed by a PCR-based assay of the invasive Mediterranean strain. J Evol Biol 2002. [DOI: 10.1046/j.1420-9101.2002.00418.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
26
|
Sheveleva EV, Giordani NV, Hallick RB. Identification and comparative analysis of the chloroplast alpha-subunit gene of DNA-dependent RNA polymerase from seven Euglena species. Nucleic Acids Res 2002; 30:1247-54. [PMID: 11861918 PMCID: PMC101230 DOI: 10.1093/nar/30.5.1247] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
When the sequence of the Euglena gracilis chloroplast genome was reported in 1993 the alpha-subunit gene (rpoA) of RNA polymerase appeared to be missing, based on a comparison of all putative reading frames to the then known rpoA loci. Since there has been a large increase in known rpoA sequences, the question of a Euglena chloroplast rpoA gene was re-examined. A previously described unknown reading frame of 161 codons was found to be part of an rpoA gene split by a single group III intron. This rpoA gene, which is highly variable from species to species, was then isolated and characterized in five other euglenoid species, Euglena anabaena, Euglena granulata, Euglena myxocylindracea, Euglena stellata and Euglena viridis, and in the Astasia longa plastid genome. All seven Euglena rpoA genes have either one or three group III introns. The rpoA gene products in Euglena spp. appear to be the most variable in this gene family when compared to the rpoA gene in other species of bacteria, algae and plants. Additionally, Euglena rpoA proteins lack a C-terminal domain required for interaction with some regulatory proteins, a feature shared only with some chlorophyte green algae. The E.gracilis rpoA gene is the distal cistron of a multigene cluster that includes genes for carbohydrate biosynthesis, photosynthetic electron transport, an antenna complex and ribosomal proteins. This study provides new insights into the transcription system of euglenoid plastids, the organization of the plastid genome, group III intron evolution and euglenoid phylogeny.
Collapse
Affiliation(s)
- Elena V Sheveleva
- Department of Biochemistry and Molecular Biophysics, The University of Arizona, 1041 East Lowell Street, Tucson, AZ 85721-0088, USA
| | | | | |
Collapse
|
27
|
Abstract
Trends in the evolution of the euglenid pellicle were described using phylogenetic methods on 18S rDNA, morphological, and combined data from 25 mostly phototrophic taxa. The tree topology from a total-evidence analysis formed a template for a synthetic tree that took into account conflicting results derived from the partitioned datasets. Pellicle character states that can only be observed with the assistance of transmission and scanning electron microscopy were phylogenetically mapped onto the synthetic tree to test a set of previously established homology statements (inferences made independently from a cladogram). The results permitted us to more confidently infer the ancestral-derived polarities of character state transformations and provided a framework for understanding the key cytoskeletal innovations associated with the evolution of phototrophic euglenids. We specifically addressed the character evolution of (1) the maximum number of pellicle strips around the cell periphery; (2) the patterns of terminating strips near the cell posterior end; (3) the substructural morphology of pellicle strips; (4) the morphology of the cell posterior tip; and (5) patterns of pellicle pores on the cell surface.
Collapse
Affiliation(s)
- B S Leander
- Center for Ultrastructural Research, The University of Georgia, Athens 30602, USA.
| | | | | |
Collapse
|
28
|
|
29
|
Leander BS, Farmer MA. Comparative morphology of the euglenid pellicle. I. Patterns of strips and pores. J Eukaryot Microbiol 2000; 47:469-79. [PMID: 11001144 DOI: 10.1111/j.1550-7408.2000.tb00076.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In anticipation that improved knowledge of euglenid morphology will provide robust apomorphy-based definitions for clades, transmission and scanning electron microscopy were used to reveal novel morphological patterns associated with the euglenid pellicle. In some taxa, the number of pellicle strips around the cell periphery reduces as discrete whorls at the anterior and posterior ends of the cell. The number of whorls at either end varies between selected euglenid taxa but is invariant within a taxon. The pattern of strip reduction associated with these whorls is shown to have at least three evolutionarily linked states: exponential, pseudoexponential, and linear. Two general equations describe these states near the posterior end of euglenid cells. Exponential patterns of strip reduction near the anterior end are described by a third equation. In addition, several euglenid taxa were found to possess conspicuous pellicle pores. These pores are arranged in discrete rows that follow the articulation zones between adjacent strips. The number of strips between rows of pores varies between taxa and displays a series of consecutive character states that differ by a power of two. The patterns of pores may not only have phylogenetical and taxonomical value but may provide morphological markers for following strip maturation during cytoskeletal reproduction.
Collapse
Affiliation(s)
- B S Leander
- Center for Advanced Ultrastructural Research, The University of Georgia, Athens 30602, USA.
| | | |
Collapse
|
30
|
Chen WM, Hsieh HM, Huang PC. Type 2 rice metallothionein-like gene has two introns. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1998; 8:223-8. [PMID: 10520450 DOI: 10.3109/10425179809008455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A type 2 rice metallothionein-like gene was isolated from root by PCR and sequenced. The PCR fragment was designated as pcr1460, which overlaps with OsMT-2, a cDNA sequence previously characterized, with the presence of two additional segments, 583 and 613 bp in length. These segments are recognized as introns which divide the coding sequence into three exons, 65, 78 and 106 base pairs in length. The sequences flanking the introns conform with the GT/AG rule for splice junctions, and one exonic open reading frame can be identified in each of the introns. The observation that MT-like gene has two introns is the first of such a finding obtained from monocotyledonous plants.
Collapse
Affiliation(s)
- W M Chen
- Department of Life Science, National Tsing Hua University, Taiwan, ROC
| | | | | |
Collapse
|
31
|
Hankeln T, Friedl H, Ebersberger I, Martin J, Schmidt ER. A variable intron distribution in globin genes of Chironomus: evidence for recent intron gain. Gene 1997; 205:151-60. [PMID: 9461389 DOI: 10.1016/s0378-1119(97)00518-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The intron positions found in globin genes of plants, protozoa and invertebrates have been interpreted as evidence for a three-intron-four-exon structure of the ancestral globin gene. In particular, the so-called 'central' introns, which are not found in vertebrate globin genes but are present in a variety of invertebrate and plant species, have been used as an argument for an ancestral gene structure featuring three introns. We have analyzed the presence or absence of central introns in the Gb genes 2beta, 9 and 7A of various European and Australasian species of the insect Chironomus. We find unrelated central introns at different positions in some of the species investigated, while other species completely lack introns in these genes. This variable distribution of introns is parsimoniously explained by independent intron additions. Such a gain of introns may occur convergently at identical positions in unrelated taxa. Insertion by gene conversion may be a viable mechanism to explain intron gain.
Collapse
Affiliation(s)
- T Hankeln
- Institute of Molecular Genetics and Biosafety Research, Johannes Gutenberg University Mainz, Germany
| | | | | | | | | |
Collapse
|
32
|
Wakasugi T, Nagai T, Kapoor M, Sugita M, Ito M, Ito S, Tsudzuki J, Nakashima K, Tsudzuki T, Suzuki Y, Hamada A, Ohta T, Inamura A, Yoshinaga K, Sugiura M. Complete nucleotide sequence of the chloroplast genome from the green alga Chlorella vulgaris: the existence of genes possibly involved in chloroplast division. Proc Natl Acad Sci U S A 1997; 94:5967-72. [PMID: 9159184 PMCID: PMC20890 DOI: 10.1073/pnas.94.11.5967] [Citation(s) in RCA: 170] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The complete nucleotide sequence of the chloroplast genome (150,613 bp) from the unicellular green alga Chlorella vulgaris C-27 has been determined. The genome contains no large inverted repeat and has one copy of rRNA gene cluster consisting of 16S, 23S, and 5S rRNA genes. It contains 31 tRNA genes, of which the tRNALeu(GAG) gene has not been found in land plant chloroplast DNAs analyzed so far. Sixty-nine protein genes and eight ORFs conserved with those found in land plant chloroplasts have also been found. The most striking is the existence of two adjacent genes homologous to bacterial genes involved in cell division, minD and minE, which are arranged in the same order in Escherichia coli. This finding suggests that the mechanism of chloroplast division is similar to bacterial division. Other than minD and minE homologues, genes encoding ribosomal proteins L5, L12, L19, and S9 (rpl5, rpl12, rpl19, and rps9); a chlorophyll biosynthesis Mg chelating subunit (chlI); and elongation factor EF-Tu (tufA), which have not been reported from land plant chloroplast DNAs, are present in this genome. However, many of the new chloroplast genes recently found in red and brown algae have not been found in C. vulgaris. Furthermore, this algal species possesses two long ORFs related to ycf1 and ycf2 that are exclusively found in land plants. These observations suggest that C. vulgaris is closer to land plants than to red and brown algae.
Collapse
Affiliation(s)
- T Wakasugi
- Center for Gene Research, Nagoya University, Nagoya 464-01, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|