Distribution of cognates of group II introns detected in mitochondrial cox1 genes of a diatom and a haptophyte

Ehara, Megumi; Watanabe, Kazuo; Ohama, Takeshi

doi:10.1016/s0378-1119(00)00359-0

Cited by 25 publications

(26 citation statements)

References 31 publications

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“…This raises the possibility that a gymnosperm-type intron 2 was lost in the common ancestor of Gnetum and Welwitschia, and regained within Gnetum. Although the retrohoming͞homing and coconversion of group II introns have been reported for yeast (34,35) and horizontal transfer of group II introns has been reported from marine unicellular flagellates (20), we know of no case from seed plants in which a group II intron was lost and then regained (see also ref. 19).…”

Section: Discussionmentioning

confidence: 98%

“…Because of these characteristics and the presence of reverse transcriptase ORFs, they are believed to be the ancestors of spliceosomal introns and non-long-terminal repeat retroelements (13, 15). Unlike group I introns, at least one of which appears to have been traded within flowering plants (16), group II introns in plants have been thought to be strictly vertically inherited (17)(18)(19), and the only known horizontal transfer of a group II intron in eukaryotes occurred in haptophytes, marine unicellular flagellates (20).During work on the phylogeny of Gnetum, we developed specific primers to amplify the second intron in the nad1 gene, plus flanking exons, from numerous previously unstudied species of Gnetum. We discovered that Gnetum harbors two copies of nad1 intron 2 and reasoned that a larger-scale survey of complete nad1 intron 2 sequences should allow identification of the source of the different copies because major seed plant lineages have specific intron signatures.…”

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Horizontal gene transfer from flowering plants to Gnetum

Won

Renner²

2003

Proc. Natl. Acad. Sci. U.S.A.

206

131

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Although horizontal gene transfer is well documented in microbial genomes, no case has been reported in higher plants. We discovered horizontal transfer of the mitochondrial nad1 intron 2 and adjacent exons b and c from an asterid to Gnetum (Gnetales, gymnosperms). Gnetum has two copies of intron 2, a group II intron, that differ in their exons, nucleotide composition, domain lengths, and structural characteristics. One of the copies, limited to an Asian clade of Gnetum, is almost identical to the homologous locus in angiosperms, and partial sequences of its exons b and c show characteristic substitutions unique to angiosperms. Analyses of 70 seed plant nad1 exons b and c and intron 2 sequences, including representatives of all angiosperm clades, support that this copy originated from a euasterid and was horizontally transferred to Gnetum. Molecular clock dating, using calibrations provided by gnetalean macrofossils, suggests an age of 5 to 2 million years for the Asian clade that received the horizontal transfer.H orizontal gene transfer is the basis for the genetic engineering of commercially important crops, and natural horizontal gene transfers across kingdoms have been documented between Agrobacterium and Nicotiana (1), Wolbachia and its insect host Callosobruchus (2), and bacteria and land plants (3, 4). Among eukaryotic lineages, however, very few natural horizontal transfers have been reported, and none of them involve transfers across groups of seed plants. As part of an investigation of the phylogeny of Gnetum (Gnetales, gymnosperms), we studied the distribution of a group II intron in the mitochondrial (mt) nad1 gene, which encodes subunit 1 of the respiratory chain NADH dehydrogenase. The nad1 gene consists of five exons that are cisor trans-located and separated by 7-294 kb . The intervening introns are cis-or trans-spliced accordingly (9, 10). The second intron of the nad1 gene, located between exons b and c, is a group II intron (ref. 11 and Fig. 1 A). Group II introns are self-splicing RNAs that are typical components of contemporary organellar genomes in plants, algae, fungi, protists, and eubacteria (10,(12)(13)(14). They are characterized by a uniform structure of six major domains radiating from a central wheel (Fig. 1B), with domains I and V most crucial for the introns' enzymatic activity (12, 14) and ribozymic function (11,12). Because of these characteristics and the presence of reverse transcriptase ORFs, they are believed to be the ancestors of spliceosomal introns and non-long-terminal repeat retroelements (13, 15). Unlike group I introns, at least one of which appears to have been traded within flowering plants (16), group II introns in plants have been thought to be strictly vertically inherited (17)(18)(19), and the only known horizontal transfer of a group II intron in eukaryotes occurred in haptophytes, marine unicellular flagellates (20).During work on the phylogeny of Gnetum, we developed specific primers to amplify the second intron in the nad1 gene, plus flanking exons, from n...

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Section: Discussionmentioning

confidence: 98%

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confidence: 99%

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confidence: 99%

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Horizontal gene transfer from flowering plants to Gnetum

Won

Renner²

2003

Proc. Natl. Acad. Sci. U.S.A.

206

131

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“…genera, and use group-specific primers (Chantangsi et al 2007;Evans et al 2007Evans et al , 2008. In diatoms this high variability of the cox1 locus could be due to the occurrence of intron events and introgression of bacterial genes, both common in diatoms (Armbrust et al 2004;Bowler et al 2008;Ehara et al 2000;Imanian et al 2007;Ravin et al 2010).…”

Section: Molecular Species Identification Inmentioning

confidence: 99%

Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols

2011

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Diatoms are present in all types of water bodies and their species diversity is influenced greatly by environmental conditions. This means that diatom occurrence and abundances are suitable indicators of water quality. Furthermore, continuous screening of algal biodiversity can provide information about diversity changes in ecosystems. Thus, diatoms represent a desirable group for which to develop an easy to use, quick, efficient, and standardised organism identification tool to serve routine water quality assessments. Because conventional morphological identification of diatoms demands specialised indepth knowledge, we have established standard laboratory procedures for DNA barcoding in diatoms. We (1) identified a short segment (about 400 bp) of the SSU (18S) rRNA gene which is applicable for the identification of diatom taxa, and (2) elaborated a routine protocol including standard primers for this group of microalgae. To test the universality of the primer binding sites and the discriminatory power of the proposed barcode region, 123 taxa, representing limnic diatom diversity, were included in the study and identified at species level. The effectiveness of the barcode was also scrutinised within a closely related species group, namely the Sellaphora pupula taxon complex and relatives.

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“…Group II introns are found in the genomes of prokaryotes (bacteria and archaebacteria), as well as mitochondria and plastids, 1 , 2 which are derived from an α-proteobacterium 3 and a cyanobacterium, 4 respectively. So far, gII introns have been identified in mt genomes from members of phylogenetically diverse eukaryotic assemblages such as Metazoa, 5 , 6 Jakobida, 7 , 8 Archaeplastida, 9 - 11 Fungi, 12 , 13 Cryptophyta, 14 Haptophyta, 15 , 16 and Stramenopiles 17 - 19 . These gII introns possess features at both the primary and secondary structure levels.…”

Section: Introductionmentioning

confidence: 99%

An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyteChrysochromulinasp. NIES-1333

Nishimura¹,

Kamikawa²,

Hashimoto³

et al. 2014

Mobile Genetic Elements

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Mitochondrial (mt) genome sequences, which often bear introns, have been sampled from phylogenetically diverse eukaryotes. Thus, we can anticipate novel insights into intron evolution from previously unstudied mt genomes. We here investigated the origins and evolution of three introns in the mt genome of the haptophyte Chrysochromulina sp. NIES-1333, which was sequenced completely in this study. All the three introns were characterized as group II, on the basis of predicted secondary structure, and the conserved sequence motifs at the 5′ and 3′ termini. Our comparative studies on diverse mt genomes prompt us to propose that the Chrysochromulina mt genome laterally acquired the introns from mt genomes in distantly related eukaryotes. Many group II introns harbor intronic open reading frames for the proteins (intron-encoded proteins or IEPs), which likely facilitate the splicing of their host introns. However, we propose that a “free-standing,” IEP-like protein, which is not encoded within any introns in the Chrysochromulina mt genome, is involved in the splicing of the first cox1 intron that lacks any open reading frames.

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Distribution of cognates of group II introns detected in mitochondrial cox1 genes of a diatom and a haptophyte

Cited by 25 publications

References 31 publications

Horizontal gene transfer from flowering plants to Gnetum

Horizontal gene transfer from flowering plants to Gnetum

Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols

An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyteChrysochromulinasp. NIES-1333

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