Larger rearranged mitochondrial genomes in Dekkera/Brettanomyces yeasts are more closely related than smaller genomes with a conserved gene order

Summary Mitochondrial genomes from yeasts in the Dekkera/Brettanomyces/Eeniella group vary in size from 28 to 101 kb. Mapping of genes has shown that the three smallest genomes, of 28–42 kb, have the same gene order, whereas the three larger mitochondrial DNAs of 57–101 kb are rearranged relative to the smaller molecules and between themselves. To examine the relationships between these genomes, a phylogenetic tree has been constructed by sequence comparison of the mitochondrialencoded cytochrome oxidase subunit gene (COX2) from the six species. Contrary to expectation, the tree shows that the larger rearranged genomes are more closely related than the smaller mtDNAs. This result indicates that the gene order of the smaller mtDNAs (28–42 kb) is ancestral and that larger mtDNA molecules (57–101 kb) are more prone to rearrangement than smaller forms.Offprint requests to: G.D. Clark-Walker     

Genome evolution: the dynamics of static genomes

A random survey of a microsporidian genome has revealed some striking features. Although the genomes of microsporidians are among the smallest known for eukaryotes, their organisation appears to be well conserved.     

A comparative study of duplications in bacteria and eukaryotes: the importance of telomeres

The genomes of three bacteria (Haemophilus influenzae, Mycoplasma genitalium, and Escherichia coli) and two eukaryotes (Saccharomyces cerevisiae and Caenorhabditis elegans) were compared. The distribution of their putative open reading frames (ORFs) was studied, and several conclusions were drawn: (1) All of these genomes, even the smallest, exhibit a significant proportion (7%-30%) of duplicated ORFs. This proportion is a function of genome size and appears unrelated to the bacteria/eukaryote division. (2) Some of these ORFs constitute families of up 20 or more members. (3) The levels of sequence similarity within these families are highly variable and their distribution is different among bacteria and eukaryotes. (4) In yeast, there are topological relationships between members of the same family. The paired ORFs are frequently in the same orientation with regard to their respective telomeres and located at comparable distances from them.      

B chromosomes in Stylidium crossocephalum (Angiospermae:Stylidiaceae)

Populations of Stylidium crossocephalum contain two common types of B chromosomes, macro B chromosomes and micro B chromosomes. The macro B chromosomes are telocentric, slightly smaller than the smallest A chromosomes and mitotically unstable. They have so far been found associated with 6 of the 16 stable genomes known in S. crossocephalum, occurring in populations covering a substantial portion of the species range. Micro B chromosomes are about one third the length of the smallest A chromosome, acrocentric and show some mitotic instability. They occur associated with 3 stable genomes in populations found in the more medial regions of the species range. Both types of B chromosomes generally show regular behaviour during meiosis, although when two or more are present their pairing efficiency is reduced when compared to the A chromosomes. In addition a single very large mega chromosome was found in a single cell of one heterokaryotypic plant. Its origin although conjectural at this stage may be of relevance in understanding the origin of macro and micro B chromosomes in this species.     

Bacterial and archaeal globins — A revised perspective

A bioinformatics survey of putative globins in over 2200 bacterial and some 140 archaeal genomes revealed that over half the bacterial and approximately one fifth of archaeal genomes contain genes encoding globins that were classified into three families: the M (myoglobin-like), and S (sensor) families all exhibiting the canonical 3/3 myoglobin fold, and the T family (truncated myoglobin fold). Although the M family comprises 2 subfamilies, flavohemoglobins (FHbs) and single domain globins (SDgbs), the S family encompasses chimeric globin-coupled sensors (GCSs), single domain Pgbs (protoglobins) and SSDgbs (sensor single domain globins). The T family comprises three classes TrHb1s, TrHb2s and TrHb3s, characterized by the abbreviated 2/2 myoglobin fold. The Archaea contain only Pgbs, GCSs and TrHb1s. The smallest globin-bearing genomes are the streamlined genomes (~ 1.3 Mbp) of the SAR11 clade of alphaproteobacteria and the slightly larger (ca. 1.7 Mbp) genomes of Aquificae. The smallest genome with members of all three families is the 2.3 Mbp genome of the extremophile Methylacidiphilum infernorum (Verrumicrobia). Of the 147 possible combinations of the eight globin subfamilies, only 83 are observed. Although binary combinations are infrequent and ternary combinations are rare, the FHb + TrHb2 combination is the most commonly observed. Of the possible functions of bacterial globins we discuss the two principal ones — nitric oxide detoxification via the NO dioxygenase or denitrosylase activities and the sensing of oxygen concentration in the environmental niche. In only few cases has a physiological role been demonstrated in vivo. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.     

Giant viruses in the oceans: the 4th Algal Virus Workshop

Giant double-stranded DNA viruses (such as record breaking Acanthamoeba polyphaga Mimivirus), with particle sizes of 0.2 to 0.6 μm, genomes of 300 kbp to 1.200 kbp, and commensurate complex gene contents, constitute an evolutionary mystery. They challenge the common vision of viruses, traditionally seen as highly streamlined genomes optimally fitted to the smallest possible -filterable- package. Such giant viruses are now discovered in increasing numbers through the systematic sampling of ocean waters as well as freshwater aquatic environments, where they play a significant role in controlling phyto- and bacterio- plankton populations. The 4^th algal virus workshop showed that the study of these ecologically important viruses is now massively entering the genomic era, promising a better understanding of their diversity and, hopefully, some insights on their origin and the evolutionary forces that shaped their genomes.     

Jam packed genomes--a preliminary,comparative analysis of nucleomorphs

There are two ways eukaryotic cells can permanently acquire chloroplasts. They can take up a cyanobacterium and turn it into a chloroplast or they can engulf an alga that already has a chloroplast. The second method is far more common and there are at least seven major groups of protists that have obtained their chloroplasts, this way. In most cases little remains of the engulfed alga apart from its chloroplast, but in two groups, the cryptomonads and chlorarachniophytes, a small remnant nucleus of the engulfed alga is still present. These tiny nuclei, called nucleomorphs, are the smallest and most compact eukaryotic genomes known and recently the nucleomorph of the cryptomonad alga Guillardia theta, was completely sequenced (551 kilobases). The nucleomorph of the chlorarachniophyte Bigellowiella natans (380 kilobases), is also being sequenced and is about half complete. We discuss some of the similarities and differences that are emerging between these two nucleomorph genomes. Both genomes contain just three chromosomes that encode mainly housekeeping genes and a few proteins for chloroplast functions. The bulk of nucleomorph gene coding capacity, therefore, appears to be devoted to self perpetuation and creating gene and protein expression machineries to make a small number of essential chloroplast proteins. We discuss reasons why both nucleomorphs are extraordinarily compact and why their gene sequences are evolving rapidly.     

A first assessment of genome size diversity in Monogonont rotifers

This study provides the first analysis of genome size diversity in Monogonont rotifers. Measurements were made using flow cytometry, with Drosophila melanogaster and chicken erythrocytes as internal standards. Nuclear DNA content (??2C????assuming diploid genomes) in eight different species of four different genera ranged almost fourfold, from 0.12 to 0.46 pg. A comparison with previously published values for Bdelloid rotifers suggested that the genomes of Monogononts are significantly smaller than those of Bdelloids. When compared to other Metazoans, Monogonont rotifers seem to have relatively small genomes. For instance, the C-values of the two species with the smallest genomes, Brachionus dimidiatus and Synchaeta pectinata, were only 0.06 and 0.085 pg, respectively. Various explanations for genome size diversity within Monogononta are discussed.     

Physical mapping of the mitochondrial genome of Arabidopsis thaliana by cosmid and YAC clones

As part of the worldwide efforts at molecular analysis of Arabidopsis thaliana as a model plant the complete structure of the mitochondrial genome has been determined. The mitochondrial DNA molecules were mapped by restriction fragment analysis of more than 300 cosmid clones and purified mitochondrial DNA. The entire genome of 372 kb is contained in three different configurations of circular molecules and is split into two additional subgenomic molecules of 234 kb and 138 kb, respectively. These arrangements result from recombinations of the two sets of repeats present in combinations of inverted and/or direct orientation. Alignment of YAC clones confirms the in vivo presence of continuous DNA molecules of more than 300 kb in A. thaliana mitochondria. The presence of this comparatively large mitochondrial genome in a plant with one of the smallest nuclear genomes shows that different size constraints act upon the different genomes in plant cells.     

Ostreococcus tauri: seeing through the genes to the genome

The marine green alga Ostreococcus tauri is the smallest-known free-living eukaryote. The recent sequencing of its genome extends this distinction, because it also has one of the smallest and most compact nuclear genomes. For other highly compacted genomes (e.g. those of microsporidian parasites and relic endosymbiont nucleomorphs), compaction is associated with severe gene loss. By contrast, O. tauri has retained a large complement of genes. Studying O. tauri should shed light on forces, other than parasitism and endosymbiosis, that result in densely packed genomes.     

Characterization of two new thermoacidophilic microalgae: Genome organization and comparison with Galdieria sulphuraria

Abstract Thermoacidophilic algae ( Cyanidiaceae ) constitute a taxonomic group with interesting phylogenetic and ecological implications. In this report, we have classified three thermoacidophilic microalgal isolates from Rio Tinto (Spain) using a combination of classical analysis of phenotypic features and the characterization of their electrophoretically determined karyotypes by means of pulsed-field gel electrophoresis. Using this technique, we have been able to demonstrate that thermoacidophilic algae genomes have the smallest genomes of all photosynthetic eukaryotes studied so far. In addition, we show that two of these Rio Tinto isolates may constitute new species within the genus Galdieria .     

Inverted terminal repeats and terminal proteins of the genomes of pneumococcal phages

The nucleotide (nt) sequence at the ends of the genomes of the Streptococcus pneumoniae phages Cp-5 and Cp-7 has been determined and compared with the corresponding sequence of phage Cp-1. The genomes of phages Cp-5 and Cp-7 have inverted terminal repeats (ITRs) 343 and 347 bp long, respectively. In Cp-1 DNA the ITR is 236 bp long and the following 116 bp are 93% homologous. Some regions within the ITRs are conserved in the three genomes although the complete sequence of the ITRs is no more conserved than the rest of their genomes. The chromatographic behavior of their tryptic peptides suggests that the terminal proteins (TPs) of at least two of the phages are similar and that the TPs of the three pneumococcal phages differ markedly from that of the Bacillus subtilis phage psi 29.     

Complete mitochondrial genome sequences of three Nakaseomyces species reveal invasion by palindromic GC clusters and considerable size expansion

Here we report the sequence of three mitochondrial genomes from yeasts of the Nakaseomyces clade that includes the pathogenic yeast Candida glabrata , namely, that of Kluyveromyces delphensis, Candida castellii and Kluyveromyces bacillisporus . The gene content is equivalent to that of C. glabrata , but reveals the existence of new group I introns in COX1 and CYTB and new potential intronic endonucleases. Gene order is highly rearranged in these genomes, which contain numerous palindromic GC clusters. The more GC nucleotides these elements contain, the longer and more AT-rich are the intergenes containing them, leading to a direct relationship between the number of Gs and Cs within the elements and the size of the genomes. Thus, there is a fivefold difference in size between the smallest and the largest mitochondrial genome, with the largest being the most AT-rich overall. Sequences are available under EMBL accession numbers FM995164 , FM995165 , and FM995166 .     

Twenty-fold difference in evolutionary rates between the mitochondrial and plastid genomes of species with secondary red plastids

Within plastid-bearing species, the relative rates of evolution between mitochondrial and plastid genomes are poorly studied, but for the few lineages in which they have been explored, including land plants and green algae, the mitochondrial DNA mutation rate is nearly always estimated to be lower than or equal to that of the plastid DNA. Here, we show that in protists from three distinct lineages with secondary, red algal-derived plastids, the opposite is true: their mitochondrial genomes are evolving 5-30 times faster than their plastid genomes, even when the plastid is nonphotosynthetic. These findings have implications for understanding the origins and evolution of organelle genome architecture and the genes they encode.     

Genome size of Mycoplasma genitalium.

The genome size of Mycoplasma genitalium was determined by using restriction enzymes that infrequently cut its DNA. The calculated value of 577 to 590 kilobases is one-fourth smaller than the genome of Mycoplasma pneumoniae, which is considered among the smallest genomes of self-replicating organisms.     

Extrachromosomal DNA in the Apicomplexa.

Malaria and related apicomplexan parasites have two highly conserved organellar genomes: one is of plastid (pl) origin, and the other is mitochondrial (mt). The organization of both organellar DNA molecules from the human malaria parasite Plasmodium falciparum has been determined, and they have been shown to be tightly packed with genes. The 35-kb circular DNA is the smallest known vestigial plastid genome and is presumed to be functional. All but two of its recognized genes are involved with genetic expression: one of the two encodes a member of the clp family of molecular chaperones, and the other encodes a conserved protein of unknown function found both in algal plastids and in eubacterial genomes. The possible evolutionary source and intracellular location of the plDNA are discussed. The 6-kb tandemly repeated mt genome is the smallest known and codes for only three proteins (cytochrome b and two subunits of cytochrome oxidase) as well as two bizarrely fragmented rRNAs. The organization of the mt genome differs somewhat among genera. The mtDNA sequence provides information not otherwise available about the structure of apicomplexan cytochrome b as well as the unusually fragmented rRNAs. The malarial mtDNA has a phage-like replication mechanism and undergoes extensive recombination like the mtDNA of some other lower eukaryotes.     

Nucleomorph genome diversity and its phylogenetic implications in cryptomonad algae

The relationship between phylogeny and nucleomorph genome size was examined in 16 strains of cryptomonad algae using pulsed‐field gel electrophoresis, Southern hybridization and phylogenetic analyses. Our results suggest that all cryptomonads examined in this study contain three nucleomorph chromosomes and their total genome size ranges from 495 to 750 kb. In addition, we estimated the plastid genome size of the respective organisms. The plastid genomes of photosynthetic strains were approximately 120–160 kb in size, whereas the non‐photosynthetic Cryptomonas paramecium NIES715 possesses a genome of approximately 70 kb. Phylogenetic analysis of the nuclear small subunit ribosomal DNA (SSU rDNA) gene showed that nucleomorph genome size varies considerably within closely related strains. This result indicates that the reduction of nucleomorph genomes is a rapid phenomenon that occurred multiple times independently during cryptomonad evolution. The nucleomorph genome sizes of Cryptomonas rostratiformis NIES277 appeared to be approximately 495 kb. This is smaller than that of Guillardia theta CCMP327, which until now was thought to have the smallest known nucleomorph genome size among photosynthetic cryptomonads.     

Bacteriophage genomics

The past three years have seen an escalation in the number of sequenced bacteriophage genomes with more than 500 now in the NCBI phage database, representing a more than threefold increase since 2005. These span at least 70 different bacterial hosts, with two-thirds of the sequenced genomes of phages representing only eight bacterial hosts. Three key features emerge from the comparative analysis of these genomes. First, they span a very high degree of genetic diversity, suggesting early evolutionary origins. Second, the genome architectures are mosaic, reflecting an unusually high degree of horizontal genetic exchange in their evolution. Third, phage genomes contain a very high proportion of novel genetic sequences of unknown function, and probably represent the largest reservoir of unexplored genes. With an estimated 10(31) bacterial and archael viruses in the biosphere, our view of the virosphere will draw into sharper focus as further bacteriophage genomes are characterized.     

Compositional correlation studies among the three different codon positions in 12 bacterial genomes

Compositional distributions in the three codon positions of the coding sequences of 12 fully sequenced prokaryotic genomes, which are publicly available, were investigated. A universal compositional correlation was observed in most of the genomes under investigation irrespective of their overall genomic GC contents. In all the genomes, the GC contents at the first codon positions are always greater than the overall GC contents of the genomes whereas the reverse is true in the case of second codon positions. GC contents at the third codon positions are higher than the overall genomic GC contents in high GC containing genomes, and the opposite situation was found in case of low GC genomes except for Helicobacter pylori. In high-GC rich genomes, the GC contents at the first + second codon positions are less than the GC contents at the third codon positions, and they are low in low-GC genomes except for Helicobacter pylori. The distributions of four bases at the three different positions were also investigated for all 12 organisms. It was observed that in high-GC genomes G is the most dominant base and in low-GC genomes A is the most dominant base in the first codon positions. But purine bases, i.e., (A + G), predominantly occur in the first codon position. In the second codon position, A is the most dominant base in most of the organisms and G is the least dominant base in all the organisms. There is no unique regular pattern of individual bases at the third codon positions; however, there are significant differences in the occurrences of (G + C) contents in the third codon positions among the different organisms. Calculations of dinucleotide frequencies in 12 different organisms indicate that in GC-rich genomes GG, GC, CC, and CG dinucleotides are the most dominant whereas the reverse is true in case of low-GC genomes. Biological implications of these results are discussed in this paper.