The Mitochondrial CoxII Intron has Been Lost in Two Different Lineages of Dicots and Altered in Others

Rabbi, Mohammed F.; Wilson, Kenneth G.

doi:10.2307/2445551

Cited by 7 publications

(9 citation statements)

References 21 publications

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“…Because our primary emphasis was on eudicots, the monocots and basal angio- Note. The primer sequences were taken from Rabbi and Wilson (1993). sperms were less extensively sampled (only one representative per order).…”

Section: Methodsmentioning

confidence: 99%

“…To investigate the presence or absence of the intron, we amplified the intron region using two primers corresponding to the 5 and 3 exon coding sequences. The primers used were those designed by Rabbi and Wilson (1993); their sequences are given in table 1. The coxII-A primer is located 178 bp upstream from the intron, while the coxII-Icr primer is 89 bp downstream from the site of excision.…”

Section: Methodsmentioning

confidence: 99%

“…A subsequent study supported the hypothesis that the intron loss is characteristic of the rosids but 1 Author for correspondence; e-mail jolysi@magellan.umontreal.ca. introduced evidence for a further intron loss in two closely related genera of Apocynaceae, Vinca and Catharanthus (Rabbi and Wilson 1993). More recently, Qiu and Palmer (1997) suggested that the loss of the coxII.i3 intron occurred in the common ancestor of rosids I and II.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenetic Implications of the Multiple Losses of the Mitochondrial coxII.i3 Intron in the Angiosperms

Joly¹,

Brouillet²,

Bruneau³

2001

International Journal of Plant Sciences

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Previous studies have shown that the mitochondrial coxII.i3 intron is absent in all rosids examined, in Philadelphus (Hydrangeaceae, Cornales), and in Catharanthus and Vinca (Apocynaceae, Gentianales). We surveyed for the presence or absence of this intron in 177 species representing all orders of angiosperms, where it is primitively present. The intron appears to have been lost independently in Gnetales, Laurales, Zingiberales, Ranunculales, Saxifragales, rosids, Santalales, Caryophyllales, Ericales, Cornales, Gentianales, Lamiales, Boraginales, Aquifoliales, Asterales, Dipsacales, as well as in the genus Escallonia. Depending upon the phylogenies used to interpret the losses, and due to lack of resolution in some groups, the intron could have been lost up to 27 times in the angiosperms (excluding the loss in Gnetales). The losses sometimes corroborate the monophyly of groups (rosids and Lamiales) or of subgroups within orders (in the Ranunculales, Caryophyllales, Cornales, Gentianales, and Asterales). In other groups, such as the Saxifragales, Ericales, and Dipsacales, the patterns of losses are more complex and would require further study. The presence or absence of the coxII.i3 mitochondrial intron seems a useful phylogenetic marker in some groups, but caution in interpretation is needed as multiple parallel losses have occurred throughout the angiosperms.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Phylogenetic Implications of the Multiple Losses of the Mitochondrial coxII.i3 Intron in the Angiosperms

Joly¹,

Brouillet²,

Bruneau³

2001

International Journal of Plant Sciences

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“…In particular, the highly variable intron content of the gene has made the cox2 locus a preferred object of studies on the dynamics of intron evolution in higher plant mitochondria (Hiesel and Brennicke 1983;Laroche et al 1997;Qiu et al 1998;Rabbi and Wilson 1993;Albrizio et al 1994;Kudla et al 2002). The picture that has emerged from these studies is that the cox2 locus gained two introns in the moss lineage ).…”

Section: A Large Intron In the Cox2 Locus Of Ginkgo Bilobamentioning

confidence: 99%

“…The picture that has emerged from these studies is that the cox2 locus gained two introns in the moss lineage ). Subsequently, the two introns have undergone multiple independent loss events during seed-plant evolution (Hiesel and Brennicke 1983;Rabbi and Wilson 1993;Albrizio et al 1994;Kudla et al 2002). We have conducted a systematic analysis of intron evolution in mitochondrial cox2 genes of seed plants (Albertazzi et al 1998;Kudla et al 2002;and our unpublished results).…”

Section: A Large Intron In the Cox2 Locus Of Ginkgo Bilobamentioning

confidence: 99%

Evolutionary origin of a plant mitochondrial group II intron from a reverse transcriptase/maturase-encoding ancestor

et al. 2006

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Group II introns are widespread in plant cell organelles. In vivo, most if not all plant group II introns do not self-splice but require the assistance of proteinaceous splicing factors. In some cases, a splicing factor (also referred to as maturase) is encoded within the intronic sequence and produced by translation of the (excised) intron RNA. However, most present-day group II introns in plant organellar genomes do not contain open reading frames (ORFs) for splicing factors, and their excision may depend on proteins encoded by other organellar introns or splicing factors encoded in the nuclear genome. Whether or not the ancestors of all of these noncoding organellar introns originally contained ORFs for maturases is currently unknown. Here we show that a noncoding intron in the mitochondrial cox2 gene of seed plants is likely to be derived from an ancestral reverse transcriptase/maturase-encoding form. We detected remnants of maturase and reverse transcriptase sequences in the 2.7 kb cox2 intron of Ginkgo biloba, the only living species of an ancient gymnosperm lineage, suggesting that the intron originally harbored a splicing factor. This finding supports the earlier proposed hypothesis that the ancient group II introns that invaded organellar genomes were autonomous genetic entities in that they encoded the factor(s) required for their own excision and mobility.

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cpDNA and mtDNA Primers in Plants

Petit¹,

Demesure²,

Dumolin³

1998

Molecular Tools for Screening Biodiversity

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This document provides a set of primer sequences for amplifying and sequencing the entire avian mitochondrial DNA. Most of the primers were originally developed as part of earlier studies (see refs) but many have since been revised or replaced with primers in different locations. All of the primers have been designed to work with most or all birds and most perform very well in this regard. This document is intended as a resource for those interested in using mtDNA for avian population genetics and systematics, whether that work involves sequencing complete mitochondrial genomes or single genes. A second goal is to encourage the use of genes other than cytochrome b, which is a poor choice for studies in which only one mitochondrial gene will be sequenced. If I'm going to sequence only one gene, which one should I choose? ND2! Why not cyt b? All mitochondrial protein genes have similarly high rates of substitution at 3 rd codon positions, but they vary greatly in the rate of amino acid substitution. Therefore, all mt protein genes provide similar information (per base pair sequenced) for very closely related taxa (e.g., individuals within a species) that differ primarily at degenerate 3 rd codon positions. For somewhat more distantly related taxa (including species within a genus, for example, and everything else up to and including comparisons between avian orders), more variable mt genes accumulate more informative variation at 1 st and 2 nd codon positions, whereas 3 rd positions increasingly accumulate multiple substitutions (i.e., homoplasy) in all genes. With cyt b, you get all of the noise and none of the signal!-with other mt genes, you get a little signal along with the noise. Why ND2? In terms of amino acid sequence, ND2 is the 3 rd most variable gene after ATPase 8, which is very short (~165-168 bp) and therefore provides relatively little information, and ND6, which is also relatively short (~519-522 bp) and is generally more difficult to amplify and sequence, given its unusual base composition and location near the control region. In contrast, the complete ND2 gene can be amplified in either one or two pieces with primers that have worked well on essentially all birds (L5216-H6313 for the whole gene; L5216-H5766 and L5758-H6313 for two pieces). We routinely amplify the gene in two pieces and run four sequencing reactions (both strands of each PCR product). What are all those Y's and R's in the primer sequences? Many of the primers listed below have several and as many as six or more "degenerate" positions. What this means is that there are actually different versions of the primer that have

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The Mitochondrial CoxII Intron has Been Lost in Two Different Lineages of Dicots and Altered in Others

Cited by 7 publications

References 21 publications

Phylogenetic Implications of the Multiple Losses of the Mitochondrial coxII.i3 Intron in the Angiosperms

Phylogenetic Implications of the Multiple Losses of the Mitochondrial coxII.i3 Intron in the Angiosperms

Evolutionary origin of a plant mitochondrial group II intron from a reverse transcriptase/maturase-encoding ancestor

cpDNA and mtDNA Primers in Plants

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