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At least 19 recordsLinked to original sources

PubMed1994

The structure of the small mitochondrial DNA of Kluyveromyces thermotolerans is likely to reflect the ancestral gene order in fungi.

Mapping the 23-kb circular mitochondrial DNA from the yeast Kluyveromyces thermotolerans has shown that only one change occurs in the gene order in comparison to the 19-kb mtDNA of Candida (Torulopsis) glabrata. Sequence analysis of the mitochondrially encoded cytochrome oxidase subunit 2 gene reveals that despite their conserved gene order, the two small genomes are more distantly related than larger mtDNA molecules with multiple rearrangements. This result supports a previous observation that larger mitochondrial genomes are more prone to rearrange than smaller forms and suggests that the architecture of the two small molecules is likely to represent the structure of an ancestor.

Amino Acid Sequence↗

PubMed2002

Genome-scale evolution: reconstructing gene orders in the ancestral species.

Recent progress in genome-scale sequencing and comparative mapping raises new challenges in studies of genome rearrangements. Although the pairwise genome rearrangement problem is well-studied, algorithms for reconstructing rearrangement scenarios for multiple species are in great need. The previous approaches to multiple genome rearrangement problem were largely based on the breakpoint distance rather than on a more biologically accurate rearrangement (reversal) distance. Another shortcoming of the existing software tools is their inability to analyze rearrangements (inversions, translocations, fusions, and fissions) of multichromosomal genomes. This paper proposes a new multiple genome rearrangement algorithm that is based on the rearrangement (rather than breakpoint) distance and that is applicable to both unichromosomal and multichromosomal genomes. We further apply this algorithm for genome-scale phylogenetic tree reconstruction and deriving ancestral gene orders. In particular, our analysis suggests a new improved rearrangement scenario for a very difficult Campanulaceae cpDNA dataset and a putative rearrangement scenario for human, mouse and cat genomes.

Algorithms↗

PubMed2003

Complete mtDNA sequence of the North American freshwater mussel, Lampsilis ornata (Unionidae): an examination of the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca).

Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. Two factors inhibiting our understanding the evolution of gene rearrangement in bivalves are inadequate taxonomic sampling and failure to examine gene order in a phylogenetic framework. Here, we report the first complete nucleotide sequence (16,060 bp) of the mitochondrial (mt) genome of a North American freshwater bivalve, Lampsilis ornata (Mollusca: Paleoheterodonta: Unionidae). Gene order and mt genome content is examined in a comparative phylogenetic framework for Lampsilis and five other bivalves, representing five families. Mitochondrial genome content is shown to vary by gene duplication and loss among taxa and between male and female mitotypes within a species. Although mt gene arrangement is highly variable among bivalves, when optimized on an independently derived phylogenetic hypothesis, it allows for the reconstruction of ancestral gene order states and indicates the potential phylogenetic utility of the data. However, the interpretation of reconstructed ancestral gene order states must take in to account both the accuracy of the phylogenetic estimation and the probability of character state change across the topology, such as the presence/absence of atp8 in bivalve lineages. We discuss what role, if any, doubly uniparental inheritance (DUI) and recombination between sexual mitotypes may play in influencing gene rearrangement of the mt genome in some bivalve lineages.

Animals↗

PubMed2004

Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha).

BACKGROUND: With some exceptions, mitochondria within the class Insecta have the same gene content, and generally, a similar gene order allowing the proposal of an ancestral gene order. The principal exceptions are several orders within the Hemipteroid assemblage including the order Thysanoptera, a sister group of the order Hemiptera. Within the Hemiptera, there are available a number of completely sequenced mitochondrial genomes that have a gene order similar to that of the proposed ancestor. None, however, are available from the suborder Sternorryncha that includes whiteflies, psyllids and aphids. RESULTS: We have determined the complete nucleotide sequence of the mitochondrial genomes of six species of whiteflies, one psyllid and one aphid. Two species of whiteflies, one psyllid and one aphid have mitochondrial genomes with a gene order very similar to that of the proposed insect ancestor. The remaining four species of whiteflies had variations in the gene order. In all cases, there was the excision of a DNA fragment encoding for cytochrome oxidase subunit III(COIII)-tRNAgly-NADH dehydrogenase subunit 3(ND3)-tRNAala-tRNAarg-tRNAasn from the ancestral position between genes for ATP synthase subunit 6 and NADH dehydrogenase subunit 5. Based on the position in which all or part of this fragment was inserted, the mitochondria could be subdivided into four different gene arrangement types. PCR amplification spanning from COIII to genes outside the inserted region and sequence determination of the resulting fragments, indicated that different whitefly species could be placed into one of these arrangement types. A phylogenetic analysis of 19 whitefly species based on genes for mitochondrial cytochrome b, NADH dehydrogenase subunit 1, and 16S ribosomal DNA as well as cospeciating endosymbiont 16S and 23S ribosomal DNA indicated a clustering of species that corresponded to the gene arrangement types. CONCLUSIONS: In whiteflies, the region of the mitochondrial genome consisting of genes encoding for COIII-tRNAgly-ND3-tRNAala-tRNAarg-tRNAasn can be transposed from its ancestral position to four different locations on the mitochondrial genome. Related species within clusters established by phylogenetic analysis of host and endosymbiont genes have the same mitochondrial gene arrangement indicating a transposition in the ancestor of these clusters.

Animals↗

PubMed2005

Alignments of mitochondrial genome arrangements: applications to metazoan phylogeny.

Mitochondrial genomes provide a valuable dataset for phylogenetic studies, in particular of metazoan phylogeny because of the extensive taxon sample that is available. Beyond the traditional sequence-based analysis it is possible to extract phylogenetic information from the gene order. Here we present a novel approach utilizing these data based on cyclic list alignments of the gene orders. A progressive alignment approach is used to combine pairwise list alignments into a multiple alignment of gene orders. Parsimony methods are used to reconstruct phylogenetic trees, ancestral gene orders, and consensus patterns in a straightforward approach. We apply this method to study the phylogeny of protostomes based exclusively on mitochondrial genome arrangements. We, furthermore, demonstrate that our approach is also applicable to the much larger genomes of chloroplasts.

Algorithms↗

PubMed2000

Early eukaryote evolution based on mitochondrial gene order breakpoints.

The comparison of the gene orders in a set of genomes can be used to infer their phylogenetic relationships and to reconstruct ancestral gene orders. For three genomes this is done by solving the "median problem for breakpoints"; this solution can then be incorporated into a routine for estimating optimal gene orders for all the ancestral genomes in a fixed phylogeny. For the difficult (and most prevalent) case where the genomes contain partially different sets of genes, we present a general heuristic for the median problem for induced breakpoints. A fixed-phylogeny optimization based on this is applied in a phylogenetic study of a set of completely sequenced protist mitochondrial genomes, confirming some of the recent sequence-based groupings which have been proposed and, conversely, confirming the usefulness of the breakpoint method as a phylogenetic tool even for small genomes.

Biological Evolution↗

PubMed1999

Phenotypic consequences of rearranging the P, M, and G genes of vesicular stomatitis virus.

The nonsegmented negative-strand RNA viruses (order Mononegavirales) include many important human pathogens. The order of their genes, which is highly conserved, is the major determinant of the relative levels of gene expression, since genes that are close to the single promoter site at the 3' end of the viral genome are transcribed at higher levels than those that occupy more distal positions. We manipulated an infectious cDNA clone of the prototypic vesicular stomatitis virus (VSV) to rearrange three of the five viral genes, using an approach which left the viral nucleotide sequence otherwise unaltered. The central three genes in the gene order, which encode the phosphoprotein P, the matrix protein M, and the glycoprotein G, were rearranged into all six possible orders. Viable viruses were recovered from each of the rearranged cDNAs. The recovered viruses were examined for their levels of gene expression, growth potential in cell culture, and virulence in mice. Gene rearrangement changed the expression levels of the encoded proteins in concordance with their distance from the 3' promoter. Some of the viruses with rearranged genomes replicated as well or slightly better than wild-type virus in cultured cells, while others showed decreased replication. All of the viruses were lethal for mice, although the time to symptoms and death following inoculation varied. These data show that despite the highly conserved gene order of the Mononegavirales, gene rearrangement is not lethal or necessarily even detrimental to the virus. These findings suggest that the conservation of the gene order observed among the Mononegavirales may result from immobilization of the ancestral gene order due to the lack of a mechanism for homologous recombination in this group of viruses. As a consequence, gene rearrangement should be irreversible and provide an approach for constructing viruses with novel phenotypes.

Animals↗

PubMed2005

Comparative genomics of Gossypium and Arabidopsis: unraveling the consequences of both ancient and recent polyploidy.

Both ancient and recent polyploidy, together with post-polyploidization loss of many duplicated gene copies, complicates angiosperm comparative genomics. To explore an approach by which these challenges might be mitigated, genetic maps of extant diploid and tetraploid cottons (Gossypium spp.) were used to infer the approximate order of 3016 loci along the chromosomes of their hypothetical common ancestor. The inferred Gossypium gene order corresponded more closely than the original maps did to a similarly inferred ancestral gene order predating an independent paleopolyploidization (alpha) in Arabidopsis. At least 59% of the cotton map and 53% of the Arabidopsis transcriptome showed correspondence in multilocus gene arrangements based on one or both of two software packages (CrimeStatII, FISH). Genomic regions in which chromosome structural rearrangement has been rapid (obscuring gene order correspondence) have also been subject to greater divergence of individual gene sequences. About 26%-44% of corresponding regions involved multiple Arabidopsis or cotton chromosomes, in some cases consistent with known, more ancient, duplications. The genomic distributions of multiple-locus probes provided early insight into the consequences for chromosome structure of an ancient large-scale duplication in cotton. Inferences that mitigate the consequences of ancient duplications improve leveraging of genomic information for model organisms in the study of more complex genomes.

Arabidopsis↗

PubMed2002

Molecular phylogenetics and mitochondrial genomic evolution in the chamaeleonidae (Reptilia, Squamata).

A phylogenetic hypothesis for the lizard family Chamaeleonidae is generated from 1503 aligned base positions (883 parsimony-informative) of mitochondrial DNA for specimens representing 59 species (57 ingroup and two outgroup). Sequences are reported for a genomic segment encoding eight transfer RNAs, NADH dehydrogenase component 2 (ND2), and portions of NADH dehydrogenase component 1 (ND1) and cytochrome c oxidase subunit 1 (COI). Newly reported genomic rearrangements and duplications support the hypothesis that mitochondrial gene order and content are destabilized by phylogenetic loss of a functional origin for light-strand replication between the genes encoding tRNA(Asn) and tRNA(Cys). A novel gene order characterizes all sampled Brookesia except B. nasus. Brookesia nasus, the apparent sister taxon of a clade formed by all other Brookesia, has the ancestral gene order but contains a large tandem duplication. An apparently noncoding 220 base pair insertion between the genes encoding ND2 and tRNA(Trp) is reported for Bradypodion tavetanum. Phylogenetic analysis identifies nine clades whose ancestral lineages diverged early in chamaeleonid evolutionary history: (1) Brookesia (possibly excluding B. nasus), (2) Chamaeleo subgenus Chamaeleo (excluding C. namaquensis), (3) Chamaeleo subgenus Trioceros, (4) viviparous Bradypodion, (5) oviparous Bradypodion, (6) genus Furcifer (except F. balteatus), and (7-9) three distinct clades of Calumma. Chamaeleo namaquensis, Brookesia nasus, Furcifer balteatus, Rhampholeon brevicaudatus, and R. spectrum represent ancient lineages dating to approximately the same time. Multiple independent losses and a possible secondary gain of horns are inferred for Trioceros. Viviparity has at least two separate origins in chameleons, one in Bradypodion and

Animals↗

PubMed2002

A mapping and evolutionary study of porcine sex chromosome genes.

A combination of FISH and RH mapping was used to study the evolution of sex chromosome genes in the pig. In total, 19 genes were identified, including 3 PAR genes (STS, KAL, PRK). The gene order of the porcine X Chromosome (Chr) closely resembled the human X Chr (PRK/STS/KAL-AMELX-EIF2s3X/ZFX-USP9X-DBX-SMCX), suggesting that the porcine X has undergone very little rearrangement during evolution. For the porcine Y Chr, two linkage groups of 10 NRY genes were found, and the following order was established: Ypter-(AMELY-EIF2S3Y/ZFY-USP9Y-DBY/UTY)-(TSPY-SMCY-UBE1Y-SRY)-CEN. This gene order showed greater conservation with the murine Y than with the human Y Chr. In addition, all porcine Y Chr genes mapped to Yp, which is similar to the mouse and included EIF2s3Y and UBE1Y, which are not present in humans. Interestingly, complete conservation of X/Y homologous gene order was found between the pig X and Y Chrs, indicating that the porcine Y Chr has not undergone extensive reorganisation with respect to the X. This suggests that the order of the X/Y homologous genes of the porcine X and Y Chrs may closely resemble the ancestral gene order of the eutherian sex chromosomes.

Animals↗

PubMedDate not supplied

Genome rearrangement based on reversals that preserve conserved intervals.

The order of genes in the genomes of species can change during evolution and can provide information about their phylogenetic relationship. An interesting method to infer the phylogenetic relationship from the gene orders is to use different types of rearrangement operations and to find possible rearrangement scenarios using these operations. One of the most common rearrangement operations is reversals, which reverse the order of a subset of neighbored genes. In this paper, we study the problem to find the ancestral gene order for three species represented by their gene orders. The rearrangement scenario should use a minimal number of reversals and no other rearrangement operations. This problem is called the Median problem and is known to be NP-complete. In this paper, we describe a heuristic algorithm for finding solutions to the Median problem that searches for rearrangement scenarios with the additional property that gene groups should not be destroyed by reversal operations. The concept of conserved intervals for signed permutations is used to describe such gene groups. We show experimentally, for different types of test problems, that the proposed algorithm produces very good results compared to other algorithms for the Median problem. We also integrate our reversal selection procedure into the well-known MGR and GRAPPA algorithms and show that they achieve a significant speedup while obtaining solutions of the same quality as the original algorithms on the test problems.

Algorithms↗

PubMed2003

Tests for gene clustering.

Comparing chromosomal gene order in two or more related species is an important approach to studying the forces that guide genome organization and evolution. Linked clusters of similar genes found in related genomes are often used to support arguments of evolutionary relatedness or functional selection. However, as the gene order and the gene complement of sister genomes diverge progressively due to large scale rearrangements, horizontal gene transfer, gene duplication and gene loss, it becomes increasingly difficult to determine whether observed similarities in local genomic structure are indeed remnants of common ancestral gene order, or are merely coincidences. A rigorous comparative genomics requires principled methods for distinguishing chance commonalities, within or between genomes, from genuine historical or functional relationships. In this paper, we construct tests for significant groupings against null hypotheses of random gene order, taking incomplete clusters, multiple genomes, and gene families into account. We consider both the significance of individual clusters of prespecified genes and the overall degree of clustering in whole genomes.

Algorithms↗

PubMed1998

Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi.

The extent to which the order of genes along chromosomes is conserved between Saccharomyces cerevisiae and related species was studied by analysing data from DNA sequence database. As expected, the extent of gene order conservation decreases with increasing evolutionary distance. About 59% of adjacent gene pairs in Kluyveromyces lactis or K. marxianus are also adjacent in S. cerevisiae, and a further 16% of Kluyveromyces neighbours can be explained in terms of the inferred ancestral gene order in Saccharomyces prior to the occurrence of an ancient whole-genome duplication. Only 13% of Candida albicans linkages, and no Schizosaccharomyces pombe linkages, are conserved. Analysis of gene order arrangements, chromosome numbers, and ribosomal RNA sequences suggests that genome duplication occurred before the divergence of the four species in Saccharomyces sensu stricto (all of which have 16 chromosomes), but after this lineage had diverged from Saccharomyces kluyveri and the Kluyveromyces lactislmarxianus species assemblage.

Ascomycota↗

PubMed2004

Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): a novel gene order revealed.

The complete mitochondrial DNA sequence was determined for the Australian freshwater crayfish Cherax destructor (Crustacea: Decapoda: Parastacidae). The 15,895-bp genome is circular with the same gene composition as that found in other metazoans. However, we report a novel gene arrangement with respect to the putative arthropod ancestral gene order and all other arthropod mitochondrial genomes sequenced to date. It is apparent that 11 genes have been translocated (ND1, ND4, ND4L, Cyt b, srRNA, and tRNAs Ser(UGA), Leu(CUN), Ile, Cys, Pro, and Val), two of which have also undergone inversions (tRNAs Pro and Val). The 'duplication/random loss' mechanism is a plausible model for the observed translocations, while 'intramitochondrial recombination' may account for the gene inversions. In addition, the arrangement of rRNA genes is incompatible with current mitochondrial transcription models, and suggests that a different transcription mechanism may operate in C. destructor.

Animals↗

PubMed2006

Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach.

BACKGROUND: Genome rearrangements influence gene order and configuration of gene clusters in all genomes. Most land plant chloroplast DNAs (cpDNAs) share a highly conserved gene content and with notable exceptions, a largely co-linear gene order. Conserved gene orders may reflect a slow intrinsic rate of neutral chromosomal rearrangements, or selective constraint. It is unknown to what extent observed changes in gene order are random or adaptive. We investigate the influence of natural selection on gene order in association with increased rate of chromosomal rearrangement. We use a novel parametric bootstrap approach to test if directional selection is responsible for the clustering of functionally related genes observed in the highly rearranged chloroplast genome of the unicellular green alga Chlamydomonas reinhardtii, relative to ancestral chloroplast genomes. RESULTS: Ancestral gene orders were inferred and then subjected to simulated rearrangement events under the random breakage model with varying ratios of inversions and transpositions. We found that adjacent chloroplast genes in C. reinhardtii were located on the same strand much more frequently than in simulated genomes that were generated under a random rearrangement processes (increased sidedness; p < 0.0001). In addition, functionally related genes were found to be more clustered than those evolved under random rearrangements (p < 0.0001). We report evidence of co-transcription of neighboring genes, which may be responsible for the observed gene clusters in C. reinhardtii cpDNA. CONCLUSION: Simulations and experimental evidence suggest that both selective maintenance and directional selection for gene clusters are determinants of chloroplast gene order.

Adaptation, Physiological↗

PubMed2004

Detailed four-way comparative mapping and gene order analysis of the canine ctvm locus reveals evolutionary chromosome rearrangements.

Canine tricuspid valve malformation (CTVM) maps to canine chromosome 9 (CFA9), in a region syntenic with gene-dense human chromosome 17q. To define synteny blocks, we analyzed 148 markers on CFA9 using radiation hybrid mapping and established a four-way comparative map for human, mouse, rat, and dog. We identified a large number of rearrangements, allowing us to reconstruct the evolutionary history of individual synteny blocks and large chromosomal segments. A most parsimonious rearrangement scenario for all four species reveals that human chromosome 17q differs from CFA9 and the syntenic rodent chromosomes through two macroreversals of 9.2 and 23 Mb. Compared to a recovered ancestral gene order, CFA9 has undergone 11 reversals of <3 Mb and 2 reversals of >3 Mb. Interspecies reuse of breakpoints for micro- and macrorearrangements was observed. Gene order and content of the ctvm interval are best extrapolated from murine data, showing that multispecies genome rearrangement scenarios contribute to identifying gene content in canine mapping studies.

Animals↗

PubMed2003

Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events.

Conservation of gene order in vertebrates is evident after hundreds of millions of years of divergence, but comparisons of the Arabidopsis thaliana sequence to partial gene orders of other angiosperms (flowering plants) sharing common ancestry approximately 170-235 million years ago yield conflicting results. This difference may be largely due to the propensity of angiosperms to undergo chromosomal duplication ('polyploidization') and subsequent gene loss ('diploidization'); these evolutionary mechanisms have profound consequences for comparative biology. Here we integrate a phylogenetic approach (relating chromosomal duplications to the tree of life) with a genomic approach (mitigating information lost to diploidization) to show that a genome-wide duplication post-dates the divergence of Arabidopsis from most dicots. We also show that an inferred ancestral gene order for Arabidopsis reveals more synteny with other dicots (exemplified by cotton), and that additional, more ancient duplication events affect more distant taxonomic comparisons. By using partial sequence data for many diverse taxa to better relate the evolutionary history of completely sequenced genomes to the tree of life, we foster comparative approaches to the study of genome organization, consequences of polyploidy, and the molecular basis of quantitative traits.

Arabidopsis↗

PubMed2006

The complete mitochondrial genome of the mantid shrimp Harpiosquilla harpax, and a phylogenetic investigation of the Decapoda using mitochondrial sequences.

The complete mitochondrial DNA sequence was determined for the mantid shrimp Harpiosquilla harpax. These data demonstrate that the H. harpax mitochondrial genome is a 15,714 bp circular molecule and encodes the typical 37 metazoan mitochondrial genes (13 protein-coding, 22 tRNA, and two rRNA genes). The gene arrangement of H. harpax is consistent with that of the putative arthropod ancestral gene order as depicted by Limulus polyphemus. H. harpax was employed as an outgroup taxon for a phylogenetic investigation of the Decapoda using sequences from complete mitochondrial genomes. Whilst our results are largely in agreement with current taxonomic treatments, the relationships indicated among the reptantian decapods are novel. Our results provide strong statistical support for a sister-group relationship between the Achelata and the Astacida. These findings not only refute previous phylogenetic hypotheses, but also have serious implications for the interpretation of morphological and developmental evolution in the Decapoda. In addition we also investigated the effects of outgroup selection on the resolution of ingroup relationships. We found outgroup choice to significantly influence tree topology thus reinforcing the importance of appropriate outgroup selection in phylogenetic studies.

Animals↗