Comparison of Chloroplast and Mitochondrial Genome Evolution in Plants

Palmer, Jeffrey D.

doi:10.1007/978-3-7091-9138-5_3

Cited by 90 publications

(61 citation statements)

References 157 publications

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“…The phylogenetic translocation of genes from plastids to the nucleus -undisputable from the comparison of equivalent prokaryotic and eukaryotic genes and of operons in prokaryotes and plastid chromosomes [25] -must have been accompanied by the acquisition of DNA segments ensuring a proper expression in the nucleo/cytosolic compartment and import of the resulting protein into the organelle. The observation that functionally equivalent plastid import sequences [ 17] and the promotors of the corresponding genes [2,26] reins and genes respectively, but relatively conserved for the same protein/gene in different organisms is indicative of separate phylogenetic transiocation events.…”

Section: Resultsmentioning

confidence: 99%

The single‐copy gene psbS codes for a phylogenetically intriguing 22 kDa polypeptide of photosystem II

et al. 1992

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Recombine,It phages that encode the complete precursor polypeptide for the 22 kDa pol~cpeptide associated with photosystem it have been serologically selected fi'om two Agtll expression libraries made from polyadenylated RNA of spinach seedlings, The eDNAs hybridize to a 1.3 kb RNA species. The precursor protein is comprised of 274 amino acid residues and carries an N-terminal transit peptide of probably 69 amino acid residues, The mature protein exhibits Ibm' predicted transmembrane segments and is shown to be an integral component ofphotosystem It originating in a single-copy gene, The unique characteristics of this protein are: (i) it is the result of a eerie-internal duplication of an arJcestot with two ,rtembraqe spans, (it) a striking resemblance to LHC i/11, CP24/CP29 apoproteins, and ELIPs, although it does not bind chlorophyll and is p,'esent in cyanobacteria, mad. as these proteins, (iii) it integrates into the membrane with uncleared routing signals that display remarkable resemblance to patterns found in bipartite transit peptides, 22 kDa polypeptide

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Section: Resultsmentioning

confidence: 99%

The single‐copy gene psbS codes for a phylogenetically intriguing 22 kDa polypeptide of photosystem II

et al. 1992

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“…However, the rate of nucleotide substitutions is very low in plant mitochondria (about 10-fold lower than in the nucleus), which should counterbalance the effects of Muller's ratchet (44,45) and negate (for plants) the hypothesis (46) that a nuclear location is favored because it provides relief from the effects of oxygen free radical damage incurred by organellar genes. Selection for a small, compact genome, although perhaps operating in other eukaryotes, is unlikely to be a factor favoring continued gene transfer in plants, because plant mt genomes readily incorporate and retain foreign DNA (8,10,11,47,48) and are very large and mostly noncoding (7)(8)(9)(10)(11). Finally, there is the possibility that genes for some organellar proteins may be better regulated in the nucleus (33).…”

Section: Roles Of Selection and Chance In Mitochondrial Gene Transfermentioning

confidence: 99%

“…Angiosperms have by far the largest mtDNAs, at least 200 kb to over 2,000 kb in size (larger than some bacterial genomes) (7,8). These genomes grow and shrink relatively rapidly; for example, within the cucumber family, mt genome size varies by more than six-fold (9).…”

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confidence: 99%

“…These most commonly result in small (2-10 members) repeat families whose elements range up to a few hundred base pairs in size, although large duplications and triplications of up to 20 kb are almost always found at least once and sometimes several times within a genome. Angiosperm mtDNAs also grow promiscuously via the relatively frequent capture of sequences from the chloroplast and nucleus (8,10,11). The functional significance of this foreign DNA seems entirely limited to chloroplast-derived tRNA genes, which provide many of the tRNAs used in plant mt protein synthesis (12).…”

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Dynamic evolution of plant mitochondrial genomes: Mobile genes and introns and highly variable mutation rates

Palmer

Adams

Cho

et al. 2000

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

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305

242

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We summarize our recent studies showing that angiosperm mitochondrial (mt) genomes have experienced remarkably high rates of gene loss and concomitant transfer to the nucleus and of intron acquisition by horizontal transfer. Moreover, we find substantial lineage-specific variation in rates of these structural mutations and also point mutations. These findings mostly arise from a Southern blot survey of gene and intron distribution in 281 diverse angiosperms. These blots reveal numerous losses of mt ribosomal protein genes but, with one exception, only rare loss of respiratory genes. Some lineages of angiosperms have kept all of their mt ribosomal protein genes whereas others have lost most of them. These many losses appear to reflect remarkably high (and variable) rates of functional transfer of mt ribosomal protein genes to the nucleus in angiosperms. The recent transfer of cox2 to the nucleus in legumes provides both an example of interorganellar gene transfer in action and a starting point for discussion of the roles of mechanistic and selective forces in determining the distribution of genetic labor between organellar and nuclear genomes. Plant mt genomes also acquire sequences by horizontal transfer. A striking example of this is a homing group I intron in the mt cox1 gene. This extraordinarily invasive mobile element has probably been acquired over 1,000 times separately during angiosperm evolution via a recent wave of cross-species horizontal transfers. Finally, whereas all previously examined angiosperm mtDNAs have low rates of synonymous substitutions, mtDNAs of two distantly related angiosperms have highly accelerated substitution rates.

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“…Because they capture the complete genome, gene-order data do not suffer from the gene tree vs. species tree problem; and because rearrangements of genes are rare genomic events [19], gene-order data enable the reconstruction of evolutionary events far back in time. Many biologists have embraced this new source of data in their phylogenetic work [7,17,18], while computer scientists are slowly solving the difficult problems posed by the manipulations of these gene orders [16]. Studies conducted by our group [15,26,[29][30][31] confirm that gene-order data support very accurate reconstructions.…”

Section: Introductionmentioning

confidence: 99%

Quartet-Based Phylogeny Reconstruction from Gene Orders

Liu

Tang

Moret

2005

Lecture Notes in Computer Science

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Abstract. Phylogenetic reconstruction based on gene rearrangements is attracting increasing attention from biologists and computer scientists. Methods used in reconstruction include distance-based methods, parsimony methods using sequence encodings, and direct optimization. The latter, pioneered by Sankoff and extended by us with the software suite GRAPPA, is the most accurate approach; however, its exhaustive nature means that it can be applied only to small datasets (of fewer than 15 taxa). While we have successfully scaled it up to 1,000 taxa by integrating it with a disk-covering method, yielding DCM-GRAPPA, the recursive decomposition in the DCM may require many levels of recursion to handle datasets with 1,000 or more taxa. In order to handle larger datasets and reduce the need for recursive decomposition, we investigate quartet-based approaches, which directly decompose the datasets into subsets of four taxa each. Such approaches have been well studied for sequence data, but not for gene-order data. We give an optimization algorithm for the NP-hard problem of computing optimal trees for each quartet, present a variation of the dyadic method (using heuristics to choose suitable short quartets), and use both in simulation studies. We find that our quartet-based method can handle more taxa than the base version of GRAPPA, thus enabling us to reduce the number of levels of recursion in DCM-GRAPPA, but is more sensitive to the rate of evolution, with error rates rapidly increasing when saturation is approached.

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Comparison of Chloroplast and Mitochondrial Genome Evolution in Plants

Cited by 90 publications

References 157 publications

The single‐copy gene psbS codes for a phylogenetically intriguing 22 kDa polypeptide of photosystem II

The single‐copy gene psbS codes for a phylogenetically intriguing 22 kDa polypeptide of photosystem II

Dynamic evolution of plant mitochondrial genomes: Mobile genes and introns and highly variable mutation rates

Quartet-Based Phylogeny Reconstruction from Gene Orders

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