Molecular diversity in the primary and secondary gene pools of genus Oryza

The objective of the present investigation was to assess the genetic relationships among the species of Oryza that belong to the primary gene pool (sativa complex) and the secondary gene pool (officinalis complex) using three marker systems such as RAPDs, ISSRs and SSRs. A total of 432 clear and reproducible bands were amplified from 18 RAPD primers; 113 bands were detected from 8 ISSR primers and 78 alleles were found to be amplified across the Oryza species from 13 SSR primer pairs. All the three dendrograms constructed, using UPGMA from the genetic similarity matrices based on the three marker data sets, were similar in their groupings. In all the three trees, two accessions of Oryza sativa formed an exclusive group indicating its genomic differentiation from its wild ancestors through the process of domestication. Distinctness between the wild species of the sativa and officinalis complexes was evident in all the trees derived from different markers. The groupings obtained among the species of the sativa complex were in perfect concordance with the species relationships established through classical crossability and cytogenetic analysis. This study has brought out some information on the species relationship between the diploid and tetraploid genomes of the officinalis complex possessing BB, CC and DD genomes. The higher level of similarity observed between the species possessing C and D genomes supports the view of many earlier authors that these two genomes might have originated from a single hybridization event. The results of this study also show that the diploid species possessing C genomes such as Oryza officinalis, Oryza rhizomatis and Oryza eichingeri are distinct from their allotetraploid counterparts possessing BBCC and CCDD genomes indicating a wider genomic differentiation in their evolutionary process.     

Relationship between genome similarity and DNA-DNA hybridization among closely related bacteria

DNA-DNA hybridization has been established as an important technology in bacterial species taxonomy and phylogenetic analysis. In this study, we analyzed how the efficiency with which the genomic DNA from one species hybridizes to the genomic DNA of another species (DNA-DNA hybridization) in microarray analysis relates to the similarity between two genomes. We found that the predicted DNA-DNA hybridization based on genome sequence similarity correlated well with the experimentally determined microarray hybridization. Between closely related strains, significant numbers of highly divergent genes (<55% identity) and/or the accumulation of mismatches between conserved genes lowered the DNA-DNA hybridization signal, and this reduced the hybridization signals to below 70% for even bacterial strains with over 97% 16S rRNA gene identity. In addition, our results also suggest that a DNA-DNA hybridization signal intensity of over 40% indicates that two genomes at least shared 30% conserved genes (>60% gene identity). This study may expand our knowledge of DNA-DNA hybridization based on genomic sequence similarity comparison and further provide insights for bacterial phylogeny analyses.     

Interspezifische Variabilität bei hypotrichen Ciliaten1

Interspecific variability in hypotrichous ciliates The genome organization of hypotrichous ciliates differs fundamentally from those of most other eukaryotic organisms. Every cell has two kinds of nuclei as is characteristic for ciliatese small generative micronuclei (Mi) whose DNA has a high molecular weight and which is organized in chromosomes, and vegetative macronuclei (Ma) which are very rich in DNA. The macronuclear DNA consists of so-called “gene-sized” DNA pieces, an organization which is not found in any other organism. This extraordinary genome organization offers a convenient experimental approach for studying evolutionary divergence at different molecular levels: 1. whole genomes, 2. subfractions of genomes, and 3. enzyme proteins. The comparison of unfractionated genomic DNA of hypotrichous ciliates by Dna-DNA hybridizations has yielded an unsuspected result: species that are closely related according to their morphology show an unusually low amount of sequence homology. The underlying reason might be that hypotrichous species separated early in eukaryotic evolution. Whereas the morphology of “closely related” species has changed only little, molecular evolution has led to major genomic changes that reflect the great evolutionary age of the species. The separation of native macronuclear DNA by gel electrophoresis produces species-specific DNA banding patterns based on different copy numbers of individual “gene-sized” DNA pieces in different species. These banding patterns allow the discrimination of sibling species which are morphologically very similar or even undistinguishable. Higher taxa can also be identified by means of DNA banding patterns. Cloned α- and β-tubulin genes were used in hybridization experiments to study the evolutionary divergence of individual DNA sequences in different hypotrichous species. The unusual Magenome organization makes such an analysis especially convenient. Characteristics of individual genes such as length number of sequence variants, copy number, and pattern of restriction sites can be compared with this method. The digestion of Mi-DNA with restriction endonucleases reveals differences in the repetitive DNA fraction of those genomes. Specific differences can be detected between closely related species and even between different populations of one species. The comparison of evolutionary divergence at the DNA level was supplemented by a comparison at the protein level. Enzyme electrophoresis proved to be a suitable method for the identification of otherwise indistinguishable species. Genetic ivergency (D-values) was estimated on the basis of allozyme data and a dendrogram was constructed reflecting the amount of genetic similarity between the species investigated. The discussion considers advantages and disadvantages of molecular characteristics for attacking taxonomic, phylogenetic, and evolutionary problems.     

Sequences homologous to the suffix from the Drosophila melanogaster genome in the DNA of other organisms]

Sequences homologous to the suffix repeat involved in 3'maturation of many Drosophila melanogaster genes have been searched in various organisms by molecular hybridization technique. Several species from evolutionary close and distant to Drosophila melanogaster taxons have been found to contain homology with the suffix in their genomes.     

Genetic relationship between Sarcina ureae and members of the genus Bacillus

Deoxyribonucleic acid-ribonucleic acid (DNA-RNA) and DNA-DNA hybridization studies were performed to determine the degree of genetic relatedness between Sarcina ureae and several members of the genus Bacillus. DNA-RNA hybridization showed a high degree of homology between S. ureae RNA and DNA from Bacillus species having a similar guanine plus cytosine content. The DNA from other genera of the family Micrococcaceae showed less homology with S. ureae RNA than did that of the Bacillus species tested; however, this homology was not found between the DNA of S. ureae and DNA from these Bacillus species or DNA from the other Micrococcaceae tested. Transformation with Bacillus DNA, infection with representatives from several major classes of Bacillus phages, and electrophoretic analysis of proteins in crude extracts of these strains were also attempted as a further test of the genetic relationship between the genera. These experiments did not support the belief that the two groups are closely related genetically.     

Untangling complex histories of genome mergings in high polyploids

Polyploidy, the duplication of entire genomes, plays a major role in plant evolution. In allopolyploids, genome duplication is associated with hybridization between two or more divergent genomes. Successive hybridization and polyploidization events can build up species complexes of allopolyploids with complicated network-like histories, and the evolutionary history of many plant groups cannot be adequately represented by phylogenetic trees because of such reticulate events. The history of complex genome mergings within a high-polyploid species complex in the genus Cerastium (Caryophyllaceae) is here untangled by the use of a network algorithm and noncoding sequences of a low-copy number gene. The resulting network illustrates how hybridization and polyploidization have acted as key evolutionary processes in creating a plant group where high-level allopolyploids clearly outnumber extant parental genomes.     

Diversity of European spined loaches (genus Cobitis L.): an update of the geographic distribution of the Cobitis taenia hybrid complex with a description of new molecular tools for species and hybrid determination

Although the unique features of asexual reproduction and hybridization among European spined loaches (genus Cobitis ) have recently attracted the attention of conservation biologists, faunists and evolutionary biologists, the research has suffered from uncertain identification of specimens and their genomes because of the extreme morphological similarity of all the species within the hybrid complex. In this article, a Europe-wide study is reported, which was performed on samples collected by several research teams. Several complementary methodologies, such as allozyme analysis, karyotyping, flow cytometry and DNA sequencing allowed us to confirm or reject the existence of all previously reported species and their hybrids as well as to uncover several new hybrid biotypes. The biogeography of all the known biotypes, that is, parental species and hybrid biotypes, has been summarized here and the taxonomic position of two undescribed putative species mentioned in previous publications has been established. New polymerase chain reaction restriction fragment length polymorphism markers for species determination have further been developed and applied, which would allow the unambiguous identification of parental species and their genomes in the known hybrid biotypes within the complex.     

A genetic similarity rule determines arthropod community structure

We define a genetic similarity rule that predicts how genetic variation in a dominant plant affects the structure of an arthropod community. This rule applies to hybridizing cottonwood species where plant genetic variation determines plant-animal interactions and structures a dependent community of leaf-modifying arthropods. Because the associated arthropod community is expected to respond to important plant traits, we also tested whether plant chemical composition is one potential intermediate link between plant genes and arthropod community composition. Two lines of evidence support our genetic similarity rule. First, in a common garden experiment we found that trees with similar genetic compositions had similar chemical compositions and similar arthropod compositions. Second, in a wild population, we found a similar relationship between genetic similarity in cottonwoods and the dependent arthropod community. Field data demonstrate that the relationship between genes and arthropods was also significant when the hybrids were analysed alone, i.e. the pattern is not dependent upon the inclusion of both parental species. Because plant-animal interactions and natural hybridization are common to diverse plant taxa, we suggest that a genetic similarity rule is potentially applicable, and may be extended, to other systems and ecological processes. For example, plants with similar genetic compositions may exhibit similar litter decomposition rates. A corollary to this genetic similarity rule predicts that in systems with low plant genetic variability, the environment will be a stronger factor structuring the dependent community. Our findings argue that the genetic composition of a dominant plant can structure higher order ecological processes, thus placing community and ecosystem ecology within a genetic and evolutionary framework. A genetic similarity rule also has important conservation implications because the loss of genetic diversity in one species, especially dominant or keystone species that define many communities, may cascade to negatively affect the rest of the dependent community.     

Immunochemical characterization of seed proteins of some species of the genusArachis L.

Relationships between seed protein patterns of 16 species ofArachis were studied by means of immunochemical methods (immunoelectrophoresis and double diffusion). The broad similarity of these patterns suggests that protein patterns are conservative in this genus from an evolutionary viewpoint. The differences which have evolved support recent schemes for classifying the genus, particularly the breakdown into sections. It also suggests thatA. villosa andA. correntina should probably be recognized as distinct species. The strong relationship indicated betweenA. hypogaea andA. batizocoi supports the hypothesis that the latter may be source of one of the genomes ofA. hypogaea. The possibility thatA. cardenasii might be the source of the other genome did not receive such strong positive support.     

Subgenome evolution in allotetraploid plants

Polyploidization is a well-known speciation and adaptation mechanism. Traces of former polyploidization events were discovered within many genomes, and especially in plants. Allopolyploidization by interspecific hybridization between two species is common. Among hybrid plants, many are domesticated species of agricultural interest and many of their genomes and of their presumptive parents have been sequenced. Hybrid genomes remain challenging to analyse because of the presence of multiple subgenomes. The genomes of hybrids often undergo rearrangement and degradation over time. Based on 10 hybrid plant genomes from six different genera, with hybridization dating from 10,000 to 5 million years ago, we assessed subgenome degradation, subgenomic intermixing and biased subgenome fractionation. The restructuring of hybrid genomes does not proceed proportionally with the age of the hybrid. The oldest hybrids in our data set display completely different fates: whereas the subgenomes of the tobacco plant Nicotiana benthamiana are in an advanced stage of degradation, the subgenomes of quinoa (Chenopodium quinoa) are exceptionally well conserved by structure and sequence. We observed statistically significant biased subgenome fractionation in seven out of 10 hybrids, which had different ages and subgenomic intermixing levels. Hence, we conclude that no correlation exists between biased fractionation and subgenome intermixing. Lastly, domestication may encourage or hinder subgenome intermixing, depending on the evolutionary context. In summary, comparative analysis of hybrid genomes and their presumptive parents allowed us to determine commonalities and differences between their evolutionary fates. In order to facilitate the future analysis of further hybrid genomes, we automated the analysis steps within manticore , which is publicly available at https://github.com/MatteoSchiavinato/manticore.git .     

Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea)

Arabica coffee (Coffea arabica L.) is a self-compatible perennial allotetraploid species (2n=4x=44), whereas Robusta coffee (C. canephora L.) is a self-incompatible perennial diploid species (2n=2x=22). C. arabica (C(a) C(a) E(a) E(a) ) is derived from a spontaneous hybridization between two closely related diploid coffee species, C. canephora (CC) and C. eugenioides (EE). To investigate the patterns and degree of DNA sequence divergence between the Arabica and Robusta coffee genomes, we identified orthologous bacterial artificial chromosomes (BACs) from C. arabica and C. canephora, and compared their sequences to trace their evolutionary history. Although a high level of sequence similarity was found between BACs from C. arabica and C. canephora, numerous chromosomal rearrangements were detected, including inversions, deletions and insertions. DNA sequence identity between C. arabica and C. canephora orthologous BACs ranged from 93.4% (between E(a) and C(a) ) to 94.6% (between C(a) and C). Analysis of eight orthologous gene pairs resulted in estimated ages of divergence between 0.046 and 0.665 million years, indicating a recent origin of the allotetraploid species C. arabica. Analysis of transposable elements revealed differential insertion events that contributed to the size increase in the C(a) sub-genome compared to its diploid relative. In particular, we showed that insertion of a Ty1-copia LTR retrotransposon occurred specifically in C. arabica, probably shortly after allopolyploid formation. The two sub-genomes of C. arabica, C(a) and E(a) , showed sufficient sequence differences, and a whole-genome shotgun approach could be suitable for sequencing the allotetraploid genome of C. arabica.     

Foraging behaviour and diet in two sympatric shrike species during autumn migration across the Arabian Peninsula

In situations of restricted food supply, the trophic niches of closely-related species of animals should be separate. For sit-and-wait hunters, such as shrikes, this is associated with competition for food and hunting sites. In the present study, the foraging behaviour of two shrike species – Red-tailed Shrike Lanius phoenicuroides and Red-backed Shrike Lanius collurio – was studied in a desert habitat in Oman. The fieldwork was carried out in September 2019, during the peak migration of these birds. Their behaviour was recorded in detail during 30-minute observation bouts. A General Linear Mixed Model with logit link function and binomial error variance was used to compare their behaviour. The type of perch and its height did not differ between them, but there were significant differences in their use of look-out posts only in the mean duration of a single perching event, which was more than twice as long in Red-backed Shrike. No differences in prey size were found between the species and hunting success (the ratio of successful attacks to all attacks) was similar in both (RtS-RbS: 46 vs. 61%). Dietary diversity was twice as great in Red-tailed Shrike as in Red-backed Shrike, but in general, their diets did not differ very much. Dietary overlap between the species at this level of prey identification was 92%. This absence of differences in some aspects of behaviour and diet may be due to the similarity of the two species, above all their same body size, and even the possibility of hybridization. If the species compared are so similar due to body size, behaviour and evolutionary relationship their food niches may overlap.     

A CHROMATOGRAPHIC INVESTIGATION OF INTERSPECIFIC RELATIONSHIPS IN PINUS (SUBSECTION SYLVESTRES)

The foliage polyphenols of 16 Pinus species were compared by two-dimensional paper chromatography. The general patterns of chemical similarity were correlated with the geographic distributions of the species; sympatric species generally had greater chemical affinity than did allotropic species. This relationship did not always correspond to hybridization patterns and morphological similarities. The distinctive chromatographic patterns of the Southeast Asian species (P. insularis, P. luchuensis, P. merkusii) and their generally low affinities with species of Europe and the Asian mainland suggest that further investigation of the morphological relationships and the genetic compatibility of these species with other Sylvestres species is warranted. The chemical relationships of P. halepensis and P. heldreichii to other Sylvestres species were also unclear. The qualitative differences in polyphenols among species are consistent and of sufficient magnitude to enable the application of chromatographic analysis to studies of interspecific hybridization in Pinus.     

The cotton centromere contains a Ty3-gypsy-like LTR retroelement

The centromere is a repeat-rich structure essential for chromosome segregation; with the long-term aim of understanding centromere structure and function, we set out to identify cotton centromere sequences. To isolate centromere-associated sequences from cotton, (Gossypium hirsutum) we surveyed tandem and dispersed repetitive DNA in the genus. Centromere-associated elements in other plants include tandem repeats and, in some cases, centromere-specific retroelements. Examination of cotton genomic survey sequences for tandem repeats yielded sequences that did not localize to the centromere. However, among the repetitive sequences we also identified a gypsy-like LTR retrotransposon (Centromere Retroelement Gossypium, CRG) that localizes to the centromere region of all chromosomes in domestic upland cotton, Gossypium hirsutum, the major commercially grown cotton. The location of the functional centromere was confirmed by immunostaining with antiserum to the centromere-specific histone CENH3, which co-localizes with CRG hybridization on metaphase mitotic chromosomes. G. hirsutum is an allotetraploid composed of A and D genomes and CRG is also present in the centromere regions of other AD cotton species. Furthermore, FISH and genomic dot blot hybridization revealed that CRG is found in D-genome diploid cotton species, but not in A-genome diploid species, indicating that this retroelement may have invaded the A-genome centromeres during allopolyploid formation and amplified during evolutionary history. CRG is also found in other diploid Gossypium species, including B and E2 genome species, but not in the C, E1, F, and G genome species tested. Isolation of this centromere-specific retrotransposon from Gossypium provides a probe for further understanding of centromere structure, and a tool for future engineering of centromere mini-chromosomes in this important crop species.     

Application of Bacillus-antagonists for biocontrol of fungi degrading raw wood

Species composition of micromycete complexes colonizing aspen, birch, and pine wood was studied. Calculation of the Sorens-Tchekanovsky similarity coefficients showed that these complexes shared a high degree of similarity. They were dominated by the representatives of the genera Penicillium, Paecilomyces, Trichoderma, and Rhizopus. Some antagonistic bacilli inhibited growth and development of wood-decay fungi in vitro and led to the formation of spheroplasts on growing hyphae. A study of possible involvement of bacillary mycolytic enzymes in the inhibition of wood-decay fungi demonstrated selectivity of their lytic effect, which was determined by the genus and species of micromycetes and did not correlate with their relative resistance to antagonists.     

Detection of genome specific monomorphic loci in Bos taurus and Bubalus bubalis with oligodeoxyribonucleotide probe

A synthetic oligodeoxyribonucleotide probe (OAT36) comprising nine repeats of 5'GACA 3′ and several enzymes were used to analyse cow, (Bos taurus) and buffalo (Bubalus bubalis) genomes and a number of monomorphic loci were detected in both the species. Different animals from the same species showed an almost ‘similar’ monomorphic hybridization pattern but animals from two separate species showed a different ‘genome specific’ pattern. The overall hybridization with any enzyme and probe combination was found to be unique to one species. This forms the basis of genome specific hybridization which is substantiated by our zoo-blot hybridization studies. The evolutionary aspect of these loci in the context of sequence polymorphisms is discussed.     

An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes

One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of several groups of eukaryotic species has involved hybridization, and cases of adaptation through introgression have been already established. In this work, we report on PhyloNet-HMM—a new comparative genomic framework for detecting introgression in genomes. PhyloNet-HMM combines phylogenetic networks with hidden Markov models (HMMs) to simultaneously capture the (potentially reticulate) evolutionary history of the genomes and dependencies within genomes. A novel aspect of our work is that it also accounts for incomplete lineage sorting and dependence across loci. Application of our model to variation data from chromosome 7 in the mouse (Mus musculus domesticus) genome detected a recently reported adaptive introgression event involving the rodent poison resistance gene Vkorc1, in addition to other newly detected introgressed genomic regions. Based on our analysis, it is estimated that about 9% of all sites within chromosome 7 are of introgressive origin (these cover about 13 Mbp of chromosome 7, and over 300 genes). Further, our model detected no introgression in a negative control data set. We also found that our model accurately detected introgression and other evolutionary processes from synthetic data sets simulated under the coalescent model with recombination, isolation, and migration. Our work provides a powerful framework for systematic analysis of introgression while simultaneously accounting for dependence across sites, point mutations, recombination, and ancestral polymorphism.     

Testing hypotheses on egg number and size in black flies (Diptera: Simuliidae).

Field-collected gravid females were used to test a series of inter- and intraspecific hypotheses on egg size and number in 23 species of black flies. Qualitative differences between bird and mammal blood did not result in significant differences with respect to fecundity properties. The five species with overwintering larvae produced more eggs than did the 18 species with overwintering eggs. Contrary to prediction, egg size was correlated significantly with body size in only two of 17 examined species; indeed, in three species this relationship was negative. However, the association between female size and egg number within species was positive. Strong support was found for a tradeoff between egg size and number across species but not within species. The present study shows similarities with other dipterans but also substantial variability, probably reflecting a high degree of flexibility. The results are primarily discussed in an evolutionary context, but they also provide useful information for black fly management.     

Full-sized HERV-K (HML-2) human endogenous retroviral LTR sequences on human chromosome 21: map locations and evolutionary history

One of the evolutionary mechanisms for acquisition of novel functional sequences can be domestication of exogenous retroviruses that have been integrated into the germ line. The whole genome mapping of such elements in various species could reveal differences in positions of the retroviral integration and suggest possible roles of these differences in speciation. Here, we describe the number, locations and sequence features of the human endogenous retrovirus HERV-K (HML-2) long terminal repeat (LTR) sequences on human chromosome 21. We show that their distribution along the chromosome is not only non-random but also roughly correlated with the gene density. Amplification of orthologous LTR sites from a number of primate genomes produced patterns of presence and absence for each LTR sequence and allowed determination of the phylogenetic ages and evolutionary order of appearance of individual LTRs. The identity level and phylogenetic age of the LTRs did not correlate with their map locations. Thus, despite the non-random distribution of LTRs, they have apparently been inserted randomly into the chromosome relative to each other. As evidenced in previous studies of chromosomes 19 and 22, this is a characteristic of HERV-K integration.