Structural divergence among genomes of closely related baculoviruses and its implications for baculovirus evolution

Baculoviruses are members of a large, well-characterized family of dsDNA viruses that have been identified from insects of the orders Lepidoptera, Hymenoptera, and Diptera. Baculovirus genomes from different virus species generally exhibit a considerable degree of structural diversity. However, some sequenced baculovirus genomes from closely related viruses are structurally very similar and share overall nucleotide sequence identities in excess of 95%. This review focuses on the comparative analysis of partial and complete nucleotide sequences from two groups of closely related baculoviruses with broad host ranges: (a) group I multiple nucleopolyhedroviruses (MNPVs) from a cluster including Autographa californica (Ac)MNPV, Rachiplusia ou (Ro)MNPV, and Plutella xylostella (Plxy)MNPV; and (b) granuloviruses (GVs) from a cluster including Xestia c-nigrum (Xecn)GV and Helicoverpa armigera (Hear)GV. Even though the individual viruses in these clusters share high nucleotide sequence identities, a significant degree of genomic rearrangement (in the form of insertions, deletions, and homologous recombination resulting in allelic replacement) is evident from alignments of their genomes. These observations suggest an important role for recombination in the early evolution and biological characteristics of baculoviruses of these two groups.     

Repeating DNA sequences of closely related species of mosquitoes]

Repeated DNA sequences of mosquitoes were studied by using of reassociation kinetics, molecular hybridization, restriction analysis and Southern blot-hybridization. Mosquitoes of two genera, the species of one of them being sibling species, were investigated. The content of all repeated families is the same both in sibling species and in species of different genera DNA. The percent of homologous sequences is low as compared to the high thermal stability of heterologous duplexes both in sibling species DNA and in different genera DNA. Restriction analysis of DNA and blot-hybridization with 35S repeated fraction revealed certain specific families of repeated sequences in the DNA of sibling species and of different genera of mosquitoes.     

High divergence rate of sequences located on different DNA strands in closely related bacterial genomes

One of the common features of bacterial genomes is a strong compositional asymmetry between differently replicating DNA strands (leading and lagging). The main cause of the observed bias is the mutational pressure associated with replication. This suggests that genes translocated between differently replicating DNA strands are subjected to a higher mutational pressure, which may influence their composition and divergence rate. Analyses of groups of completely sequenced bacterial genomes have revealed that the highest divergence rate is observed for the DNA sequences that in closely related genomes are located on different DNA strands in respect to their role in replication. Paradoxically, for this group of sequences the absolute values of divergence rate are higher for closely related species than for more diverged ones. Since this effect concerns only the specific group of orthologs, there must be a specific mechanism introducing bias into the structure of chromosome by enriching the set of homologs in trans position in newly diverged species in relatively highly diverged sequences. These highly diverged sequences may be of varied nature: (1) paralogs or other fast-evolving genes under weak selection; or (2) pseudogenes that will probably be eliminated from the genome during further evolution; or (3) genes whose history after divergence is longer than the history of the genomes in which they are found. The use of these highly diverged sequences for phylogenetic analyses may influence the topology and branch length of phylogenetic trees. The changing mutational pressure may contribute to arising of genes with new functions as well.     

Amount of repeated and non-repeated DNA in the genomes of closely related fish species with varying genome sizes.

1. Within the teleostean family Cyprinidae, diploid species occur with wide variation in genome size. There also exist species which were anciently tetraploid. 2. The quantitative changes of DNA content in the diploids are primarily due to differences in the amount of intermediately repeated DNA. DNA sequence composition of the ancient tetraploid genomes suggests that the species derived from diploid ancestors of small genome size. 3. The average base composition and the base compositional heterogeneity are similar in all the species examined.     

Mapping contacts between gRNA and mRNA in trypanosome RNA editing.

All guide RNAs (gRNAs) identified to date have defined 5' anchor sequences, guiding sequences and a non-encoded 3' uridylate tail. The 5' anchor is required for in vitro editing and is thought to be responsible for selection and binding to the pre-edited mRNA. Little is known, however, about how the gRNAs are used to direct RNA editing. Utilizing the photo-reactive crosslinking agent, azidophenacyl (APA), attached to the 5'- or 3'-terminus of the gRNA, we have begun to map the structural relationships between the different defined regions of the gRNA with the pre-edited mRNA. Analyses of crosslinked conjugates produced with a 5'-terminal APA group confirm that the anchor of the gRNA is correctly positioning the interacting molecules. 3' Crosslinks (X-linker placed at the 3'-end of a U10tail) have also been mapped for three different gRNA/mRNA pairs. In all cases, analyses indicate that the U-tail can interact with a range of nucleotides located upstream of the first edited site. It appears that the U-tail prefers purine-rich sites, close to the first few editing sites. These results suggest that the U-tail may act in concert with the anchor to melt out secondary structure in the mRNA in the immediate editing domain, possibly increasing the accessibility of the editing complex to the proper editing sites.     

DNA reassociation kinetics of closely related species

The kinetics of reassociation of the DNA of three groups of closely related organisms were examined. The laboratory mouse was compared to an Asiatic mouse, whose chromosome number is the same but whose chromosome organization is different. Chinese hamster (2N=22) was compared to Syrian hamster (2N=44), and Haplopappus gracilis (2N=4) was compared to H. ravenit (2N=8). It was found that the most highly repeated DNA fractions of the three comparative sets of organisms differ in their reaction rates. However, these fractions of the related hamsters, haplopappi, and probably the mice, do not differ in the amount of DNA composing the fractions. The intermediately fast reassociating DNA and the unique DNA do not differ between members of related pairs of organisms. The implication of these results is that a short sequence of DNA may be highly copied in one organism, while in a related organism a longer DNA sequence is repeated a fewer number of times, and the total amount of repeated DNA may be the same in both related organisms.     

A model for RNA editing in kinetoplastid mitochondria: "guide" RNA molecules transcribed from maxicircle DNA provide the edited information.

A class of small RNA molecules possibly involved in RNA editing is present in the mitochondrion of Leishmania tarentolae. These "guide" RNA (gRNA) molecules are encoded in intergenic regions of the mitochondrial maxicircle DNA and contain sequences that represent precise complementary versions of the mature mRNAs within the edited regions. In addition, the 5' portions of several gRNAs can form hybrids with mRNAs just 3' of the preedited region. A model is presented in which a partial hybrid formed between the gRNA and preedited mRNA is substrate for multiple cycles of cleavage, addition or deletion of uridylates, and religation, eventually resulting in a complete hybrid between the gRNA and the mature edited mRNA.     

Distribution and evolution of short tandem repeats in closely related bacterial genomes

Simultaneous identification and comparison of perfect and imperfect microsatellites within a genome is a valuable tool both to overcome the lack of a consensus definition of SSRs and to assess repeat history. Detailed analysis of the overall distribution of perfect and imperfect microsatellites in closely related bacterial taxa is expected to give new insight into the evolution of prokaryotic genomes. We have performed a genome-wide analysis of microsatellite distribution in four Escherichia coli and seven Chlamydial strains. Chlamydial strains generally have a higher density of SSRs and show greater intra-group differences of SSR distribution patterns than E. coli genomes. In most investigated genomes the distribution of the total lengths of matching perfect and imperfect trinucleotide repeats are highly similar, with the notable exception of C. muridarum. Closely related strains show more similar repeat distribution patterns than strains separated by a longer divergence time. The discrepancy between the preferred classes of perfect and imperfect repeats in C. muridarum implies accelerated evolution of SSRs in this particular strain. Our results suggest that microsatellites, although considerably less abundant than in eukaryotic genomes, may nevertheless play an important role in the evolution of prokaryotic genomes and several gene families.     

Inversions in evolution of man and closely related species

By the comparative study of the karyotypes of many Primates, 35 inversions (25 peri- and 10 paracentric) having accumulated during evolution of species related to man were reconstructed. Some of them originated human chromosomes from more ancestral chromosomes still present in other primate species. Their detection in man would indicate the occurrence of reverse mutations. Other inversions occurred in ancestral chromosomes identical to those of man, and originated chromosomes of other Primates species. Their detection in man would indicate the occurrence of a convergent mutation. It is shown that such reverse and convergent mutations do occur. They are too frequently observed than by mere chance among patients ascertained in human cytogenetic laboratories. Their excess is still larger among radiation induced inversions in human cells. This demonstrates the nonrandom occurrence of inversions. In addition, it is concluded that inversions which have accumulated during evolution are more representative of mutagenesis than those detected in human cytogenetic laboratories.     

The systematics of Porphyra: character evolution in closely related species

Isozymes, vegetative and reproductive morphology, seasonality, vertical and geographic distributions and chromosomes were compared for six pairs of putative sibling species of Porphyra (P. abbottae/P. torta, P. fallax subsp. fallax/P. fallax subsp. conwayae, P. amplissima/P. cuneiformis, P. fucicola/P. leucostica, P. miniata/P. variegata, P. umbilicalis/P. umbilicalis) and among five species in a complex (P. brumalis, P. kurogii, P. linearis, P. pseudolinearis, and P. purpurea.) Geographic distribution and zymograms for certain proteins showed the greatest change between species pairs: only one pair of species had identical distributions, and most species pairs were disjunct; every species had a different allozyme for GOT-1, whereas all species had apparently identical proteins for phycoerythrin. Seasonality and habitat exhibited moderate differentiation: Northeast Pacific sibling species were characterized by a high intertidal winter species pairing with a mid intertidal spring species, whereas all but one of the other species pairs exhibited nearly identical vertical distributions and seasonalities. There were few changes in morphology: most species pairs had essentially identical morphologies and coloration and the same arrangement of reproductive cells. Chromosome numbers and karyotypes were identical for species pairs and in the species complex. These results provide evidence for different rates of evolution of different characters in the genus Porphyra.     

Detection and resolution of closely related satellite DNA sequences by molecular cloning.

Highly repeated satellite DNAs often consist of mixtures of DNAs with closely related repeating sequences. By cloning individual molecules we have resolved the 1.705 g/cm³ satellite DNA of Drosophila melanogaster into two distinct components: poly$\text{d}\text{A-A-G-A-G}\text{T-T-C-T-C}$ and poly$\text{d}\text{A-A-G-A-G-A-G}\text{T-T-C-T-C-T-C}$. The presence of two distinct sequences within this physically homogeneous satellite DNA had not previously been detected by standard physical, chemical, or sequencing techniques. Both cloning and direct sequence analysis suggest that the five-base-pair and seven-base-pair repeating units reside on separate molecules and are not interspersed with each other.     

Conservation of sequences in related genomes of Apodemus: constraints on the maintenance of satellite DNA sequences.

Satellites from two related species of the Apodemus genus, A. sylvaticus and A. flavicollis, have been analysed with restriction enzymes Taq I, Alu I and Hind III. The restriction maps are closely conserved between species and show a novel feature of two differing internal periodicities within a 375 base pair repeating unit detected by two different restriction enzymes. This places constraints on the introduction of the observed restriction sites according to current models such as unequal crossing-over. The implications of such a conserved sequence and its presence in other species are discussed.     

Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes

In order to explore microevolutionary trends in bacteria and archaea, we constructed a data set of 41 alignable tight genome clusters (ATGCs). We show that the ratio of the medians of nonsynonymous to synonymous substitution rates (dN/dS) that is used as a measure of the purifying selection pressure on protein sequences is a stable characteristic of the ATGCs. In agreement with previous findings, parasitic bacteria, notwithstanding the sometimes dramatic genome shrinkage caused by gene loss, are typically subjected to relatively weak purifying selection, presumably owing to relatively small effective population sizes and frequent bottlenecks. However, no evidence of genome streamlining caused by strong selective pressure was found in any of the ATGCs. On the contrary, a significant positive correlation between the genome size, as well as gene size, and selective pressure was observed, although a variety of free-living prokaryotes with very close selective pressures span nearly the entire range of genome sizes. In addition, we examined the connections between the sequence evolution rate and other genomic features. Although gene order changes much faster than protein sequences during the evolution of prokaryotes, a strong positive correlation was observed between the “rearrangement distance” and the amino acid distance, suggesting that at least some of the events leading to genome rearrangement are subjected to the same type of selective constraints as the evolution of amino acid sequences.     

Phylogeny of the Cucurbitales based on DNA sequences of nine loci from three genomes: implications for morphological and sexual system evolution

The Cucurbitales are a clade of rosids with a worldwide distribution and a striking heterogeneity in species diversity among its seven family members: the Anisophylleaceae (29-40 species), Begoniaceae (1400 spp.), Coriariaceae (15 spp.), Corynocarpaceae (6 spp.), Cucurbitaceae (800 spp.), Datiscaceae (2 spp.), and Tetramelaceae (2 spp.). Most Cucurbitales have unisexual flowers, and species are monoecious, dioecious, andromonoecious, or androdioecious. To resolve interfamilial relationships within the order and to polarize morphological character evolution, especially of flower sexual systems, we sequenced nine plastids (atpB, matK, ndhF, rbcL, the trnL-F region, and the rpl20-rps12 spacer), nuclear (18S and 26S rDNA), and mitochondrial (nad1 b/c intron) genes (together approximately 12,000 bp) of 26 representatives of the seven families plus eight outgroup taxa from six other orders of the Eurosids I. Cucurbitales are strongly supported as monophyletic and are closest to Fagales, albeit with moderate support; both together are sister to Rosales. The deepest split in the Cucurbitales is that between the Anisophylleaceae and the remaining families; next is a clade of Corynocarpaceae and Coriariaceae, followed by Cucurbitaceae, which are sister to a clade of Begoniaceae, Datiscaceae, and Tetramelaceae. Based on this topology, stipulate leaves, inferior ovaries, parietal placentation, and one-seeded fruits are inferred as ancestral in Cucurbitales; exstipulate leaves, superior ovaries, apical placentation, and many-seeded fruits evolved within the order. Bisexual flowers are reconstructed as ancestral, but dioecy appears to have evolved already in the common ancestor of Begoniaceae, Cucurbitaceae, Datiscaceae, and Tetramelaceae, and then to have been lost repeatedly in Begoniaceae and Cucurbitaceae. Both instances of androdioecy (Datisca glomerata and Schizopepon bryoniifolius) evolved from dioecious ancestors, corroborating recent hypotheses about androdioecy often evolving from dioecy.     

Rates of DNA change and phylogeny from the DNA sequences of the alcohol dehydrogenase gene for five closely related species of Hawaiian Drosophila

The sequence of 1.6 kb of DNA surrounding the alcohol dehydrogenase (Adh) gene from five species of the Planitibia subgroup of the Hawaiian picture-winged Drosophila, with estimated divergence times of 0.4-5.1 Myr, has been determined. The gene trees which were found by using the sequence divergence from different regions of the sequences are generally in accord with the phylogeny proposed for these species when chromosomal inversions and island of origin are used. One of the species (D. picticornis) appears to be more distant from the other species in this group than they are from a member of the Grimshawi group (D. affinidisjuncta) which is chromosomally more distant. Two of the species (D. differens and D. plantibia) show heterogeneity in the nucleotide changes in the Adh coding region, heterogeneity which is interpreted to be due to a gene conversion or recombination after hybridization between the two species. The minimal rate of nucleotide substitution of synonymous nucleotides and of nontranscribed nucleotides downstream from the coding region is estimated as 1.5 x 10(-8) and 1.1 x 10(-8) substitutions/nucleotide/year, respectively. This rate is two to three times the maximal rate estimated for mammalian synonymous substitutions.     

Ancient repeated sequences in the pea and mung bean genomes and implications for genome evolution

Essentially all of the sequences in the pea (Pisum sativum) genome which reassociate with single copy kinetics at standard (T_m -25°C) criterion follow repetitive kinetics at lower temperatures (about T_m-35°C). Analysis of thermal stability profiles for presumptive single copy duplexes show that they contain substantial mismatch even when formed at standard criterion. Thus most of the sequences in the pea genome which are conventionally defined as single copy are actually fossil repeats — that is, they are members of extensively diverged (mutuated) and thus presumably ancient families of repeated sequences. Coding sequences as represented by a cDNA probe prepared from poly-somal poly(A) + mRNA reassociate with single copy kinetics regardless of criterion and do not form mismatched duplexes. The coding regions thus appear to be composed of true single copy sequences but they cannot represent more than a few percent of the pea genome. Ancient diverged repeats are present, but not a prominent feature of the smaller mung bean (Vigna radiata) genome. An extension of a simple evolutionary model is proposed in which these and other differences in genome organization are considered to reflect different rates of sequence amplification or genome turnover during evolution. The model accounts for some of the differences between typical plant and animal genomes.     

Periodicity in DNA coding sequences: implications in gene evolution

In this paper we have employed Fourier analysis of DNA coding and non-coding sequences in an attempt to identify possible patterns in gene sequences. It was found that while intronic sequences show a rather random pattern, coding sequences show periodicities and in particular a periodicity of 3. We were able to reconstruct such patterns by assuming a gene having one codon occurring in about 40% of the sequence. This could indicate that the predominant presence of codons all starting from the same base could confer the observed periodicities. Indeed, it was found that proteins do obey this rule. Implications of this finding in gene evolution are discussed.     

Discrimination of the closely related A and B genomes in AABB tetraploid species of Avena

Fluorescent in situ (FISH) and Southern hybridization procedures were used to investigate the chromosomal distribution and genomic organization of the satellite DNA sequence As120a (specific to the A-genome chromosomes of hexaploid oats) in two tetraploid species, Avena barbata and Avena vaviloviana. These species have AB genomes. In situ hybridization of pAs120a to tetraploid oat species revealed elements of this repeated family to be distributed over both arms of 14 of the 28 chromosomes of these species. Genomes A and B were subsequently distinguished, indicating an allopolyploid origin for A. barbata. This was confirmed by assigning the satellited chromosomes to individual genomes, using the satellite itself and two ribosomal probes in simultaneous and sequential in situ hybridization analyses. Differences between A. barbata and A. vaviloviana genomes were also revealed by both FISH and Southern techniques using pAs120a probes. Whereas two B-genome chromosome pairs were found to be involved in intergenomic translocations in A. vaviloviana, FISH detected no intergenomic rearrangements in A. barbata. When using pAs120a as a probe, Southern hybridization also revealed differences in the hybridization patterns of the two genomes. A 1300-bp EcoRV fragment was present in A. barbata but absent in A. vaviloviana. This fragment was also detected in Southern analyses of A-genome diploid and hexaploid oat species. Received: 27 November 2000 / Accepted: 28 February 2001