Interspecific Recombination Research Articles

Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrus species: analysis of chromosome 2.

BackgroundThe most economically important Citrus species originated by natural interspecific hybridization between four ancestral taxa (Citrus reticulata, Citrus maxima, Citrus medica, and Citrus micrantha) and from limited subsequent interspecific recombination as a result of apomixis and vegetative propagation. Such reticulate evolution coupled with vegetative propagation results in mosaic genomes with large chromosome fragments from the basic taxa in frequent interspecific heterozygosity. Modern breeding of these species is hampered by their complex heterozygous genomic structures that determine species phenotype and are broken by sexual hybridisation. Nevertheless, a large amount of diversity is present in the citrus gene pool, and breeding to allow inclusion of desirable traits is of paramount importance. However, the efficient mobilization of citrus biodiversity in innovative breeding schemes requires previous understanding of Citrus origins and genomic structures. Haplotyping of multiple gene fragments along the whole genome is a powerful approach to reveal the admixture genomic structure of current species and to resolve the evolutionary history of the gene pools. In this study, the efficiency of parallel sequencing with 454 methodology to decipher the hybrid structure of modern citrus species was assessed by analysis of 16 gene fragments on chromosome 2.Results454 amplicon libraries were established using the Fluidigm array system for 48 genotypes and 16 gene fragments from chromosome 2. Haplotypes were established from the reads of each accession and phylogenetic analyses were performed using the haplotypic data for each gene fragment. The length of 454 reads and the level of differentiation between the ancestral taxa of modern citrus allowed efficient haplotype phylogenetic assignations for 12 of the 16 gene fragments. The analysis of the mixed genomic structure of modern species and cultivars (i) revealed C. maxima introgressions in modern mandarins, (ii) was consistent with previous hypotheses regarding the origin of secondary species, and (iii) provided a new picture of the evolution of chromosome 2.Conclusions454 sequencing was an efficient strategy to establish haplotypes with significant phylogenetic assignations in Citrus, providing a new picture of the mixed structure on chromosome 2 in 48 citrus genotypes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-014-0152-1) contains supplementary material, which is available to authorized users.

A recombinant Tobacco curly shoot virus causes leaf curl disease in tomato in a north-eastern state of India and has potentiality to trans-replicate a non-cognate betasatellite

Leaf curl disease is a serious constraint in tomato production throughout India. Several begomoviruses were reported from different parts of the country; however, identity of begomovirus associated with leaf curl disease in tomato in north-eastern states of India was obscured. In the present study, the complete genome of an isolate (To-Ag-1) of begomovirus was generated from a leaf curl sample collected from Tripura state. However, no DNA-B and betasatellite were detected in the field samples. The genome of To-Ag-1 isolate contained 2,755 nucleotides that shared 94.7 % sequence identity with Tobacco curly shoot virus (TbCSV) and 71.3-90.1 % sequence identity with the other tomato-infecting begomoviruses occurring in the Indian subcontinent. Several inter-specific recombination events among different tomato-infecting begomoviruses from India and intra-specific recombination among different isolates of TbCSV reported from China were observed in the genome of To-Ag-1 isolate. Agroinoculation of the virus alone produced leaf curl symptoms in tomato and Nicotiana benthamiana. However, co-inoculation with a non-cognate betasatellite, Croton yellow vein mosaic betasatellite (CroYVMB) with the TbCSV resulted in increased severity of the symptoms both in tomato and N. benthamiana. Systemic distribution of the TbCSV and CroYVMB was detected in the newly developed leaves of tobacco and tomato, which showed ability of TbCSV to trans-replicate CroYVMB. The present study for the first time provides evidence of occurrence of TbCSV in tomato in north-eastern region of India and showed increased virulence of TbCSV with a non-cognate betasatellite.

Recombination analysis of Maize dwarf mosaic virus (MDMV) in the Sugarcane mosaic virus (SCMV) subgroup of potyviruses

Recombination among RNA viruses is a natural phenomenon that appears to have played a significant role in the species development and the evolution of many strains. It also has particular significance for the risk assessment of plants which have been genetically modified for disease resistance by incorporating viral sequences into their genomes. However, the exact recombination events taking place in viral genomes are not investigated in detail for many virus groups. In this analysis, different single-stranded positive-sense RNA potyviruses were compared using various in silico recombination detection methods and new recombination events in the Sugarcane mosaic virus (SCMV) subgroup were detected. For an extended in silico recombination analysis, two of the analyzed Maize dwarf mosaic virus full-length genomes were sequenced additionally during this work. These results strengthen the evidence that recombination is a major driving force in virus evolution, and the emergence of new virus variants in the SCMV subgroup, paired with mutations, could generate viruses with altered biological properties. The intra- and interspecific homolog recombinations seem to be a general trait in this virus group, causing little or no changes to the amino acid of the progenies. However, we found a few breakpoints between the members of SCMV subgroup and the weed-infecting distant relatives, but only a few methods of the RDP3 package predicted these events with low significance level.

Abstract A06: Interspecific recombination between orthologous human and mouse BAC clones in E. coli: Exploring scalable humanization of cancer-relevant genes in the mouse genome

Abstract Our interests lie in humanizing specific regions of the mouse genome using large segments of human DNA with extents of 10s to 100s of kilobase pairs. To that end, we have undertaken a series of projects to transfer large segments of human DNA, from human BAC clones, into the orthologous region of corresponding mouse BAC clones using— (1), traditional recombineering methods; (2), recombinase-mediated cassette exchange (RCME); and (3), a novel technology that we call trans- or trimolecular-recombineering. In each instance the goal is to place human DNA within the larger context of homologous BAC-derived mouse arms in E. coli. Completed constructs will be used to drive homologous recombination in mouse embryonic stem (ES) cells with positive selection imparted at each end of the transferred human segment using dual, recombinase recognition site-flanked, selectable marker cassettes. Properly targeted ES cells will be used to develop viable mouse strains carrying the humanized segments. Selection cassettes will be removed by crossing to mouse strains with germline expression of the appropriate recombinases. All experiments have been designed to maintain a fixed genetic background from community-standard C57BL/6 strains. Our poster presentation details the specifics of our projects and describes progress to date. This research is supported by National Cancer Institute Grant Number 5P30CA034196-28. Citation Format: Tiffany Leidy-Davis, David E. Bergstrom. Interspecific recombination between orthologous human and mouse BAC clones in E. coli: Exploring scalable humanization of cancer-relevant genes in the mouse genome. [abstract]. In: Proceedings of the AACR Special Conference: The Translational Impact of Model Organisms in Cancer; Nov 5-8, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(11 Suppl):Abstract nr A06.

Phylogenetic relationships and the occurrence of interspecific recombination between beet chlorosis virus (BChV) and Beet mild yellowing virus (BMYV).

Samples containing two viruses belonging to the genus Polerovirus, beet chlorosis virus (BChV) and beet mild yellowing virus (BMYV), were collected from French and Polish sugar beet fields. The molecular properties of 24 isolates of BChV and BMYV were investigated, and their genetic diversity was examined in the coat protein (CP)- and P0-encoding genes. For the first time, we have demonstrated that beet polerovirus populations include recombinants between BChV and BMYV containing breakpoints within the CP gene. Moreover, a partial correlation between geographic origin and phylogenetic clustering was observed for BMYV isolates.

Phylogenetic and recombination analysis of the homing protein domain of grapevine fanleaf virus (GFLV) isolates associated with 'yellow mosaic' and 'infectious malformation' syndromes in grapevine.

The RNA2 of seven grapevine fanleaf virus (GFLV) isolates from vines with yellow mosaic (YM) symptoms from different origin were sequenced. These sequences showed a high variability in the homing protein (2A(HP)) and, in five of them, a putative recombination with arabis mosaic virus (ArMV) was detected. To investigate recombination frequency, the partial sequences of the 2A(HP) of 28 additional GFLV isolates from nine different countries, showing either YM or infectious malformations (MF) symptoms, were obtained and compared with those of GFLV isolates from GenBank. The analysis confirmed the high level of sequence variability (up to 41 % at the nucleotide level) among isolates. In phylogenetic trees constructed using different approaches, the sequenced isolates always clustered in four conserved groups, three of which comprised YM strains (groups 1, 2 and 3), and one (group 4) the MF strains. Potential interspecific recombination sites between GFLV and ArMV were predicted in the 2A(HP) gene of several isolates, all of which were associated with YM symptoms.

Complete genome sequence of a novel monopartite begomovirus infecting sweet potato in China

The complete genome sequence of a novel monopartite begomovirus, isolate G-YU-12-10, was obtained from sweet potato samples exhibiting severe leaf curl symptoms in Xinxiang, Henan Province, China. The genome sequence consisted of 2766 nucleotides and encoded two open reading frames (ORFs) (AV1 and AV2) in the viral-sense strand and four ORFs (AC1-AC4) in the complementary-sense strand. The genome of isolate G-YU-12-10 was closely related to other sweet-potato-infecting begomoviruses (sweepoviruses) and shared the highest nucleotide sequence identity (89.0 %) with sweet potato leaf curl China Sichuan virus (SPLCCSV, KC488316). Thus, the G-YU-12-10 isolate represents a novel species according to the demarcation criteria of species in the genus Begomovirus, for which the name Sweet potato leaf curl Henan virus (SPLCHnV) is proposed. Interspecific recombination analysis supported the recombination hypothesis, indicating that recombination with other begomoviruses had taken place within AC2 and AC3 ORFs of SPLCHnV and also in the non-coding intergenic region (IR).

Transmission Frequencies of Introgressed Festuca pratensis Chromosomes and Chromosome Segments in Lolium perenne

ABSTRACTThe introgression of genetic variation from related species into crops provides an important route by which superior plant varieties can be produced. The primary aim of introgression involves the transfer of a small chromosome segment from a related species into a chromosome of a crop species (via recombination at meiosis) to generate an interspecific recombinant chromosome. Very little is known about the selective pressures that act on the products of interspecific recombination. Seven monosomic substitution lines were developed between Lolium perenne and Festuca pratensis. When each line was backcrossed to L. perenne recombination occurred between the F. pratensis chromosome and its L. perenne homoeologue, resulting in backcross populations carrying L. perenne/F. pratensis recombinant chromosomes. This paper describes the relationship between the frequency of generation of interspecific recombinant chromosomes with the frequency of their transmission to the next generation. The results reveal the presence of neutral, negative, and positive selection pressures for the transmission of F. pratensis chromosomes and L. perenne/F. pratensis recombinant chromosomes through the gametes to the next generation. The type of selection pressure observed depended on which linkage group the F. pratensis chromosome under study was derived from. The implications of these results are discussed.

Genetic Structure and Evolution of the Leishmania Genus in Africa and Eurasia: What Does MLSA Tell Us

Leishmaniasis is a complex parasitic disease from a taxonomic, clinical and epidemiological point of view. The role of genetic exchanges has been questioned for over twenty years and their recent experimental demonstration along with the identification of interspecific hybrids in natura has revived this debate. After arguing that genetic exchanges were exceptional and did not contribute to Leishmania evolution, it is currently proposed that interspecific exchanges could be a major driving force for rapid adaptation to new reservoirs and vectors, expansion into new parasitic cycles and adaptation to new life conditions.To assess the existence of gene flows between species during evolution we used MLSA-based (MultiLocus Sequence Analysis) approach to analyze 222 Leishmania strains from Africa and Eurasia to accurately represent the genetic diversity of this genus. We observed a remarkable congruence of the phylogenetic signal and identified seven genetic clusters that include mainly independent lineages which are accumulating divergences without any sign of recent interspecific recombination. From a taxonomic point of view, the strong genetic structuration of the different species does not question the current classification, except for species that cause visceral forms of leishmaniasis (L. donovani, L. infantum and L. archibaldi). Although these taxa cause specific clinical forms of the disease and are maintained through different parasitic cycles, they are not clearly distinct and form a continuum, in line with the concept of species complex already suggested for this group thirty years ago. These results should have practical consequences concerning the molecular identification of parasites and the subsequent therapeutic management of the disease.

Complementation of a stable Met2-1 mutant of the zygomycete Absidia glauca by the corresponding wild-type allele of the mycoparasite Parasitella parasitica, transferred during infection

Compared with prokaryotes, where horizontal gene transfer events are frequently found and can be studied in the laboratory at the mechanistic level, few systems are known that allow direct experimental access to parasexual phenomena in eukaryotes. In zygomycetes, a basal lineage of fungi, several mycoparasitic fungi are known that inevitably form a cytoplasmic continuum with their hosts during infection. We provide evidence that, corresponding to the expectation suggested by the morphology of the infection process, gene transfer occurs from the parasite to the host. For analysing this parasexual system at the DNA level, we characterized interspecific recombinants obtained by infecting a stable methionine-auxotrophic Absidia glauca mutant with heavy rearrangements at the Met2-1 locus, which encodes homoserine acetyltransferase. Recipients were shown to be complemented by part of the corresponding gene from Parasitella parasitica. This foreign DNA is neither integrated at the putative Met2-2 locus in the recipient strain nor integrated at Met2-1, a locus encoding a hypothetical protein with amino acid similarity but with unknown function. Based on hybridization studies and on the phenotype of recipients that bear some mitotic instability of the acquired prototrophy, we propose that P. parasitica DNA is established in A. glauca recipients as extrachromosomally located replicons.

"A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids".

BackgroundModern banana cultivars are primarily interspecific triploid hybrids of two species, Musa acuminata and Musa balbisiana, which respectively contribute the A- and B-genomes. The M. balbisiana genome has been associated with improved vigour and tolerance to biotic and abiotic stresses and is thus a target for Musa breeding programs. However, while a reference M. acuminata genome has recently been released (Nature 488:213–217, 2012), little sequence data is available for the corresponding B-genome.To address these problems we carried out Next Generation gDNA sequencing of the wild diploid M. balbisiana variety ‘Pisang Klutuk Wulung’ (PKW). Our strategy was to align PKW gDNA reads against the published A-genome and to extract the mapped consensus sequences for subsequent rounds of evaluation and gene annotation.ResultsThe resulting B-genome is 79% the size of the A-genome, and contains 36,638 predicted functional gene sequences which is nearly identical to the 36,542 of the A-genome. There is substantial sequence divergence from the A-genome at a frequency of 1 homozygous SNP per 23.1 bp, and a high degree of heterozygosity corresponding to one heterozygous SNP per 55.9 bp. Using expressed small RNA data, a similar number of microRNA sequences were predicted in both A- and B-genomes, but additional novel miRNAs were detected, including some that are unique to each genome. The usefulness of this B-genome sequence was evaluated by mapping RNA-seq data from a set of triploid AAA and AAB hybrids simultaneously to both genomes. Results for the plantains demonstrated the expected 2:1 distribution of reads across the A- and B-genomes, but for the AAA genomes, results show they contain regions of significant homology to the B-genome supporting proposals that there has been a history of interspecific recombination between homeologous A and B chromosomes in Musa hybrids.ConclusionsWe have generated and annotated a draft reference Musa B-genome and demonstrate that this can be used for molecular genetic mapping of gene transcripts and small RNA expression data from several allopolyploid banana cultivars. This draft therefore represents a valuable resource to support the study of metabolism in inter- and intraspecific triploid Musa hybrids and to help direct breeding programs.

Genomic signatures of relaxed disruptive selection associated with speciation reversal in whitefish

BackgroundSpeciation reversal: the erosion of species differentiation via an increase in introgressive hybridization due to the weakening of previously divergent selection regimes, is thought to be an important, yet poorly understood, driver of biodiversity loss. Our study system, the Alpine whitefish (Coregonus spp.) species complex is a classic example of a recent postglacial adaptive radiation: forming an array of endemic lake flocks, with the independent origination of similar ecotypes among flocks. However, many of the lakes of the Alpine radiation have been seriously impacted by anthropogenic nutrient enrichment, resulting in a collapse in neutral genetic and phenotypic differentiation within the most polluted lakes. Here we investigate the effects of eutrophication on the selective forces that have shaped this radiation, using population genomics. We studied eight sympatric species assemblages belonging to five independent parallel adaptive radiations, and one species pair in secondary contact. We used AFLP markers, and applied FST outlier (BayeScan, Dfdist) and logistic regression analyses (MatSAM), to identify candidate regions for disruptive selection in the genome and their associations with adaptive traits within each lake flock. The number of outlier and adaptive trait associated loci identified per lake were then regressed against two variables (historical phosphorus concentration and contemporary oxygen concentration) representing the strength of eutrophication.ResultsWhilst we identify disruptive selection candidate regions in all lake flocks, we find similar trends, across analysis methods, towards fewer disruptive selection candidate regions and fewer adaptive trait/candidate loci associations in the more polluted lakes.ConclusionsWeakened disruptive selection and a concomitant breakdown in reproductive isolating mechanisms in more polluted lakes has lead to increased gene flow between coexisting Alpine whitefish species. We hypothesize that the resulting higher rates of interspecific recombination reduce either the number or extent of genomic islands of divergence surrounding loci evolving under disruptive natural selection. This produces the negative trend seen in the number of selection candidate loci recovered during genome scans of whitefish species flocks, with increasing levels of anthropogenic eutrophication: as the likelihood decreases that AFLP restriction sites will fall within regions of heightened genomic divergence and therefore be classified as FST outlier loci. This study explores for the first time the potential effects of human-mediated relaxation of disruptive selection on heterogeneous genomic divergence between coexisting species.

Evidence for inter-specific recombination among the mitochondrial genomes of Fusarium species in the Gibberella fujikuroi complex

BackgroundThe availability of mitochondrial genomes has allowed for the resolution of numerous questions regarding the evolutionary history of fungi and other eukaryotes. In the Gibberella fujikuroi species complex, the exact relationships among the so-called “African”, “Asian” and “American” Clades remain largely unresolved, irrespective of the markers employed. In this study, we considered the feasibility of using mitochondrial genes to infer the phylogenetic relationships among Fusarium species in this complex. The mitochondrial genomes of representatives of the three Clades (Fusarium circinatum, F. verticillioides and F. fujikuroi) were characterized and we determined whether or not the mitochondrial genomes of these fungi have value in resolving the higher level evolutionary relationships in the complex.ResultsOverall, the mitochondrial genomes of the three species displayed a high degree of synteny, with all the genes (protein coding genes, unique ORFs, ribosomal RNA and tRNA genes) in identical order and orientation, as well as introns that share similar positions within genes. The intergenic regions and introns generally contributed significantly to the size differences and diversity observed among these genomes. Phylogenetic analysis of the concatenated protein-coding dataset separated members of the Gibberella fujikuroi complex from other Fusarium species and suggested that F. fujikuroi (“Asian” Clade) is basal in the complex. However, individual mitochondrial gene trees were largely incongruent with one another and with the concatenated gene tree, because six distinct phylogenetic trees were recovered from the various single gene datasets.ConclusionThe mitochondrial genomes of Fusarium species in the Gibberella fujikuroi complex are remarkably similar to those of the previously characterized Fusarium species and Sordariomycetes. Despite apparently representing a single replicative unit, all of the genes encoded on the mitochondrial genomes of these fungi do not share the same evolutionary history. This incongruence could be due to biased selection on some genes or recombination among mitochondrial genomes. The results thus suggest that the use of individual mitochondrial genes for phylogenetic inference could mask the true relationships between species in this complex.

Effects of interspecific recombination on functional traits in trees revealed by metabolomics and genotyping-by-resequencing

Background : Understanding the potential and limits of recombination in adaptive evolution is of great interest to evolutionary biology. New (ultra-) high-throughput technologies in metabolomics and genomics hold great promise for addressing these questions, but their use in interspecific hybrids remains largely unexplored. Aims : Our goal was to test if recombination between the highly divergent genomes of Populus alba and P. tremula has the potential to contribute to the standing variation for functionally important chemical traits. Methods : We studied the metabolomes of interspecific hybrids by ultra-high-pressure liquid chromatography (UHPLC) coupled with quadrupole–time-of-flight (QTOF) mass spectrometry (MS) and initiated the characterisation of hybrid genomes by restriction site associated DNA (RAD) sequencing. Results : UHPLC-QTOF-MS indicated a complex ‘mosaic’ of chemical traits in recombinant hybrids and pointed to a heritable component for many of these. RAD sequencing confirmed the recombinant nature of natural hybrids previously characterised by microsatellites and suggested a complex history of recombination. Conclusions : It is likely that hybridisation has affected these species' genomes over several glacial cycles. Recombination holds great potential to create functionally relevant chemical variation in these trees. Nevertheless, correlations between chemical traits are not entirely broken up in recombinant hybrids, suggesting limits to adaptive evolution by genetic exchange.

Cytogenetic evidence of mixed disomic and polysomic inheritance in an allotetraploid (AABB) Musa genotype

Edible bananas originated mainly from two wild species, Musa acuminata Colla (AA) and Musa balbisiana Colla (BB), and triploid cultivars with an AAA, AAB or ABB genome are the most widely used. In the present study, chromosome pairing affinities are investigated in a sterile AB Indian variety and in its fertile colchicine-induced allotetraploid (AABB) derivative to determine the inheritance pattern of the tetraploid genotype. The potential implications of interspecific recombination and chromosomal composition of diploid gametes for Musa improvement are presented. The pairing of different chromosome sets at diploid and tetraploid levels was investigated through a combination of conventional cytogenetic and genomic in-situ hybridization (GISH) analyses of meiotic chromosomes, leading to a likelihood model of the pairing behaviour. GISH analysis of mitotic chromosomes was also conducted to reveal the chromosome constitution of hybrids derived from crosses involving the allotetraploid genotype. Analysis of chromosome associations at both ploidy levels suggested that the newly formed allotetraploid behaves as a 'segmental allotetraploid' with three chromosome sets in a tetrasomic pattern, three sets in a likely disomic pattern and the five remaining sets in an intermediate pattern. Balanced and unbalanced diploid gametes were detected in progenies, with the chromosome constitution appearing to be more homogenous in pollen than in ovules. Colchicine-induced allotetraploids in Musa provide access to the genetic background of natural AB varieties. The segmental inheritance pattern exhibited by the AABB allotetraploid genotype implies chromosome exchanges between M. acuminata and M. balbisiana species and opens new horizons for reciprocal transfer of valuable alleles.

Low Species Barriers in Halophilic Archaea and the Formation of Recombinant Hybrids

Speciation of sexually reproducing organisms requires reproductive barriers. Prokaryotes reproduce asexually butoften exchange DNA by lateral gene transfer mechanisms and recombination [1], yet distinct lineages are still observed. Thus, barriers to gene flow such as geographic isolation, genetic incompatibility or a physiological inability to transfer DNA represent potential underlying mechanisms behind preferred exchange groups observed in prokaryotes [2-6]. In Bacteria, experimental evidence showed that sequence divergence impedes homologous recombination between bacterial species [7-11]. Here we study interspecies gene exchange in halophilic archaea that possess a parasexual mechanism of genetic exchange that is functional between species [12, 13]. In this process, cells fuse forming a diploid state containing the full genetic repertoire of both parental cells, which facilitates genetic exchange and recombination. Later, cells separate, occasionally resulting in hybrids of the parental strains [14]. We show high recombination frequencies between Haloferax volcanii and Haloferax mediterranei, two species that have an average nucleotide sequence identity of 86.6%. Whole genome sequencing of Haloferax interspecies hybrids revealed the exchange of chromosomal fragments ranging from 310Kb to 530Kb. These results show that recombination barriers may be more permissive in halophilic archaea than they are in bacteria.

Fine‐scale genetic analysis of species‐specific female preference in Drosophila simulans

Behavioural differences are thought to be the first components to contribute to species isolation, yet the precise genetic basis of behavioural isolation remains poorly understood. Here, we used a combination of behaviour assays and genetic mapping to provide the first refined map locating candidate genes for interspecific female preference isolating Drosophila simulans from D.melanogaster. First, we tested whether two genes identified as affecting D.melanogaster female intraspecific mate choice also affect interspecific mate choice; neither of these genes was found to contribute to species-specific female preference. Next, we used deficiency mapping to locate genes on the right arm of the third chromosome for species-specific female preference and identified five small significant regions that contain candidate genes contributing to behavioural isolation. All five regions were located in areas that would have low interspecific recombination, which mirrors the results of other behavioural isolation studies that used quantitative trait locus (QTL) mapping, but without the potential concern of bias towards regions of low recombination that QTL mapping may have. As this model system may be refined to the individual gene level using the same methodology, this initial map we provide may potentially serve as a ready template for the identification and characterization of the first behavioural isolation genes.

Grapevine deformation virus: Completion of the sequence and evidence on its origin from recombination events between Grapevine fanleaf virus and Arabis mosaic virus

The complete nucleotide (nt) sequence of Grapevine deformation virus (GDefV) RNA-1 has been determined. It consists of 7386nt, excluding the poly(A) tail, and contains a single open reading frame (ORF) encoding a polyprotein (p1) of 252kDa. P1 comprises the 1APro-cof proteinase cofactor, the 1BHel NTP-binding protein, the 1CVPg viral protein genome-linked, the 1DProt proteinase and the 1EPol RNA-dependent RNA polymerase, all of which are conserved domains in polyproteins of different members of the order Picornavirales. The amino acid (aa) sequence of GDefV RNA1 p1 has the highest identity with the homologous products of Grapevine fanleaf virus (GFLV, 86–88%) and Arabis mosaic virus (ArMV, 73–74%), two nepoviruses of subgroup A. Four cleavage sites for proteins processing were predicted (C/A, C/S, G/E and R/G) and found similar to those of GFLV RNA1. Phylogenetic trees constructed with the complete aa sequences of protein p1 and the RNA2-encoded protein p2 of GDeFV, GFLV and ArMV, showed an incongruent allocation of GDefV in these trees. Pairwise alignment and prediction of recombination sites of both RNA segments showed that GDefV RNA2 has a mosaic structure resulting from recombination events between GFLV and ArMV at the level of the 2AHP (homing protein), 2BMP (movement protein), 2CCP (capsid protein) and the 3′NCR (non coding region). This strongly suggests that GDefV originated from the interspecific recombination between isolates of GFLV and ArMV.

Evolution of African cassava mosaic virus by recombination between bipartite and monopartite begomoviruses

BackgroundCassava mosaic disease (CMD) is a major constraint on cassava cultivation in Africa. The disease is endemic and is caused by seven distinct cassava mosaic geminiviruses (CMGs), some of them including several variants.FindingsFrom cassava leaf samples presenting CMD symptoms collected in Burkina Faso, four DNA-A begomovirus components were cloned and sequenced, showing 99.9% nucleotide identity among them. These isolates are most closely related to African cassava mosaic virus (ACMV) but share less than 89% nucleotide identity (taxonomic threshold) with any previously described begomovirus. A DNA-B genomic component, sharing 93% nucleotide identity with DNA-B of ACMV, was also characterized. Since all genomic components have a typical genome organization of Old World bipartite begomoviruses, this new species was provisionally named African cassava mosaic Burkina Faso virus (ACMBFV). Recombination analysis of the new virus demonstrated an interspecies recombinant origin, with major parents related to West African isolates of ACMV, and minor parents related to Tomato leaf curl Cameroon virus and Cotton leaf curl Gezira virus.ConclusionThis is the first report of an ACMV-like recombinant begomovirus arisen by interspecific recombination between bipartite and monopartite African begomoviruses.

DNA variation in the phenotypically-diverse brown alga Saccharina japonica.

BackgroundSaccharina japonica (Areschoug) Lane, Mayes, Druehl et Saunders is an economically important and highly morphologically variable brown alga inhabiting the northwest Pacific marine waters. On the basis of nuclear (ITS), plastid (rbcLS) and mitochondrial (COI) DNA sequence data, we have analyzed the genetic composition of typical Saccharina japonica (TYP) and its two common morphological varieties, known as the “longipes” (LON) and “shallow-water” (SHA) forms seeking to clarify their taxonomical status and to evaluate the possibility of cryptic species within S. japonica.ResultsThe data show that the TYP and LON forms are very similar genetically in spite of drastic differences in morphology, life history traits, and ecological preferences. Both, however, are genetically quite different from the SHA form. The two Saccharina lineages are distinguished by 109 fixed single nucleotide differences as well as by seven fixed length polymorphisms (based on a 4,286 bp concatenated dataset that includes three gene regions). The GenBank database reveals a close affinity of the TYP and LON forms to S. japonica and the SHA form to S. cichorioides. The three gene markers used in the present work have different sensitivity for the algal species identification. COI gene was the most discriminant gene marker. However, we have detected instances of interspecific COI recombination reflecting putative historical hybridization events between distantly related algal lineages. The recombinant sequences show highly contrasted level of divergence in the 5’- and 3’- regions of the gene, leading to significantly different tree topologies depending on the gene segment (5’- or 3’-) used for tree reconstruction. Consequently, the 5’-COI “barcoding” region (~ 650 bp) can be misleading for identification purposes, at least in the case of algal species that might have experienced historical hybridization events.ConclusionTaking into account the potential roles of phenotypic plasticity in evolution, we conclude that the TYP and LON forms represent examples of algae phenotypic diversification that enables successful adaptation to contrasting shallow- and deep-water marine environments, while the SHA form is very similar to S. cichorioides and should be considered a different species. Practical applications for algal management and conservation are briefly considered.