Novel introner-like elements in fungi are involved in parallel gains of spliceosomal introns
Collemare, J. ; Beenen, H.G. ; Crous, P.W. ; Wit, P.J.G.M. de; Burgt, A. van der - \ 2015
PLoS ONE 10 (2015)6. - ISSN 1932-6203 - 12 p.
daphnia populations - maximum-likelihood - evolution - gene - positions - conservation - selection - sequence - genomes
Spliceosomal introns are key components of the eukaryotic gene structure. Although they contributed to the emergence of eukaryotes, their origin remains elusive. In fungi, they might originate from the multiplication of invasive introns named Introner-Like Elements (ILEs). However, so far ILEs have been observed in six fungal species only, including Fulvia fulva and Dothistroma septosporum (Dothideomycetes), arguing against ILE insertion as a general mechanism for intron gain. Here, we identified novel ILEs in eight additional fungal species that are phylogenetically related to F. fulva and D. septosporum using PCR amplification with primers derived from previously identified ILEs. The ILE content appeared unique to each species, suggesting independent multiplication events. Interestingly, we identified four genes each containing two gained ILEs. By analysing intron positions in orthologues of these four genes in Ascomycota, we found that three ILEs had inserted within a 15 bp window that contains regular spliceosomal introns in other fungal species. These three positions are not the result of intron sliding because ILEs are newly gained introns. Furthermore, the alternative hypothesis of an inferred ancestral gain followed by independent losses contradicts the observed degeneration of ILEs. These observations clearly indicate three parallel intron gains in four genes that were randomly identified. Our findings suggest that parallel intron gain is a phenomenon that has been highly underestimated in ILE-containing fungi, and likely in the whole fungal kingdom.
Small Homologous Blocks in Phytophthora Genomes Do Not Point to an Ancient Whole-Genome Duplication
Hooff, J.J.E. van; Snel, B. ; Seidl, M.F. - \ 2014
Genome Biology and Evolution 6 (2014)5. - ISSN 1759-6653 - p. 1079 - 1085.
pathogen phytophthora - maximum-likelihood - evolution - genes - consequences - mechanisms - adaptation - repertoire - sequences - infestans
Genomes of the plant-pathogenic genus Phytophthora are characterized by small duplicated blocks consisting of two consecutive genes (2HOM blocks) and by an elevated abundance of similarly aged gene duplicates. Both properties, in particular the presence of 2HOM blocks, have been attributed to a whole-genome duplication (WGD) at the last common ancestor of Phytophthora. However, large intraspecies synteny-compelling evidence for a WGD-has not been detected. Here, we revisited the WGD hypothesis by deducing the age of 2HOM blocks. Two independent timing methods reveal that the majority of 2HOM blocks arose after divergence of the Phytophthora lineages. In addition, a large proportion of the 2HOM block copies colocalize on the same scaffold. Therefore, the presence of 2HOM blocks does not support a WGD at the last common ancestor of Phytophthora. Thus, genome evolution of Phytophthora is likely driven by alternative mechanisms, such as bursts of transposon activity.
Diaporthe species associated with Vaccinium, with specific reference to Europe
Lombard, L. ; Leeuwen, G.C.M. van; Guarnaccia, V. ; Polizzi, G. ; Rijswick, P.C.J. van; Rosendahl, K.C.H.M. ; Gabler, J. ; Crous, P.W. - \ 2014
Phytopathologia Mediterranea 53 (2014)2. - ISSN 0031-9465 - p. 287 - 299.
phomopsis-vaccinii - maximum-likelihood - south-africa - stem canker - blueberry - grapevines - cranberry - australafricana - inference - diseases
Species of the genus Vaccinium are commercially cultivated in Europe for their berries, which are highly valued for dietary and pharmaceutical properties. Cultivation is severely limited due to a range of fungal diseases, especially those caused by species of Diaporthe. A number of Diaporthe isolates have been collected from Vaccinium growing regions in Europe, and initially identified as D. vaccinii based on host association. Using DNA sequence inference of the combined ß-tubulin, calmodulin, translation elongation factor 1-alpha and the internal transcribed spacer region of the nuclear rDNA, along with morphological characteristics, six species were characterised. Diaporthe eres, D. vaccinii and D. viticola are known species and three novel taxa are described here as D. asheicola, D. baccae and D. sterilis. This study is the first confirmed report of D. vaccinii in Latvia and the Netherlands.
The evolution of the placenta drives a shift in sexual selection in livebearing fish
Pollux, B.J.A. ; Meredith, R.W. ; Springer, M.S. ; Garland, T. ; Reznick, D.N. - \ 2014
Nature 513 (2014). - ISSN 0028-0836 - p. 233 - 236.
parent-offspring conflict - molecular phylogenetic-relationships - mosquitofish gambusia-holbrooki - reproductive mode - size dimorphism - poeciliidae cyprinodontiformes - maximum-likelihood - viviparity - hypothesis - gene
The evolution of the placenta from a non-placental ancestor causes a shift of maternal investment from pre- to post-fertilization, creating a venue for parent–offspring conflicts during pregnancy1, 2, 3, 4. Theory predicts that the rise of these conflicts should drive a shift from a reliance on pre-copulatory female mate choice to polyandry in conjunction with post-zygotic mechanisms of sexual selection2. This hypothesis has not yet been empirically tested. Here we apply comparative methods to test a key prediction of this hypothesis, which is that the evolution of placentation is associated with reduced pre-copulatory female mate choice. We exploit a unique quality of the livebearing fish family Poeciliidae: placentas have repeatedly evolved or been lost, creating diversity among closely related lineages in the presence or absence of placentation5, 6. We show that post-zygotic maternal provisioning by means of a placenta is associated with the absence of bright coloration, courtship behaviour and exaggerated ornamental display traits in males. Furthermore, we found that males of placental species have smaller bodies and longer genitalia, which facilitate sneak or coercive mating and, hence, circumvents female choice. Moreover, we demonstrate that post-zygotic maternal provisioning correlates with superfetation, a female reproductive adaptation that may result in polyandry through the formation of temporally overlapping, mixed-paternity litters. Our results suggest that the emergence of prenatal conflict during the evolution of the placenta correlates with a suite of phenotypic and behavioural male traits that is associated with a reduced reliance on pre-copulatory female mate choice.
Annonaceae substitution rates - a codon model perspective
Chatrou, L.W. ; Pirie, M.D. ; Velzen, R. van; Bakker, F.T. - \ 2014
Revista Brasileira de Fruticultura 36 (2014)edição especial, e.. - ISSN 0100-2945 - p. 108 - 117.
molecular evolution - flowering plants - phylogeny reconstruction - historical biogeography - nucleotide substitution - maximum-likelihood - genera - diversification - characters - patterns
The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.
Evolution of a symbiotic receptor through gene duplications in the legume-rhizobium mutualism
Mita, S. De; Streng, A. ; Bisseling, T. ; Geurts, R. - \ 2014
New Phytologist 201 (2014)3. - ISSN 0028-646X - p. 961 - 972.
amino-acid sites - medicago-truncatula - phylogenetic perspectives - mycorrhizal symbiosis - arbuscular mycorrhiza - populus-trichocarpa - maximum-likelihood - draft genome - land plants - nodulation
•The symbiosis between legumes and nitrogen-fixing rhizobia co-opted pre-existing endomycorrhizal features. In particular, both symbionts release lipo-chitooligosaccharides (LCOs) that are recognized by LysM-type receptor kinases. We investigated the evolutionary history of rhizobial LCO receptor genes MtLYK3-LjNFR1 to gain insight into the evolutionary origin of the rhizobial symbiosis. •We performed a phylogenetic analysis integrating gene copies from nonlegumes and legumes, including the non-nodulating, phylogenetically basal legume Cercis chinensis. Signatures of differentiation between copies were investigated through patterns of molecular evolution. •We show that two rounds of duplication preceded the evolution of the rhizobial symbiosis in legumes. Molecular evolution patterns indicate that the resulting three paralogous gene copies experienced different selective constraints. In particular, one copy maintained the ancestral function, and another specialized into perception of rhizobial LCOs. It has been suggested that legume LCO receptors evolved from a putative ancestral defense-related chitin receptor through the acquisition of two kinase motifs. However, the phylogenetic analysis shows that these domains are actually ancestral, suggesting that this scenario is unlikely. •Our study underlines the evolutionary significance of gene duplication and subsequent neofunctionalization in MtLYK3-LjNFR1 genes. We hypothesize that their ancestor was more likely a mycorrhizal LCO receptor, than a defense-related receptor kinase.
Positive selection and intragenic recombination contribute to high allelic diversity in effector genes of Mycosphaerella fijiensis, causal agent of the black leaf streak disease of banana
Stergiopoulos, I. ; Cordovez da Cunha, V. ; Okmen, B. ; Beenen, H.G. ; Kema, G.H.J. ; Wit, P.J.G.M. de - \ 2014
Molecular Plant Pathology 15 (2014)5. - ISSN 1464-6722 - p. 447 - 460.
pathogen cladosporium-fulvum - phylogenetic analysis - musa-acuminata - cf-4-mediated resistance - population-genetics - maximum-likelihood - evolution - proteins - fungal - tomato
Previously, we have determined the nonhost-mediated recognition of the MfAvr4 and MfEcp2 effector proteins from the banana pathogen Mycosphaerella fijiensis in tomato, by the cognate Cf-4 and Cf-Ecp2 resistance proteins, respectively. These two resistance proteins could thus mediate resistance against M.¿fijiensis if genetically transformed into banana (Musa spp.). However, disease resistance controlled by single dominant genes can be overcome by mutated effector alleles, whose products are not recognized by the cognate resistance proteins. Here, we surveyed the allelic variation within the MfAvr4, MfEcp2, MfEcp2-2 and MfEcp2-3 effector genes of M.¿fijiensis in a global population of the pathogen, and assayed its impact on recognition by the tomato Cf-4 and Cf-Ecp2 resistance proteins, respectively. We identified a large number of polymorphisms that could reflect a co-evolutionary arms race between host and pathogen. The analysis of nucleotide substitution patterns suggests that both positive selection and intragenic recombination have shaped the evolution of M.¿fijiensis effectors. Clear differences in allelic diversity were observed between strains originating from South-East Asia relative to strains from other banana-producing continents, consistent with the hypothesis that M.¿fijiensis originated in the Asian-Pacific region. Furthermore, transient co-expression of the MfAvr4 effector alleles and the tomato Cf-4 resistance gene, as well as of MfEcp2, MfEcp2-2 and MfEcp2-3 and the putative Cf-Ecp2 resistance gene, indicated that effector alleles able to overcome these resistance genes are already present in natural populations of the pathogen, thus questioning the durability of resistance that can be provided by these genes in the field.
Species delimitation and DNA barcoding of Atlantic Ensis (Bivalvia, Pharidae)
Vierna, J. ; Cuperus, J. ; Martinez-lage, A. ; Jansen, J.M. ; Perina, A. ; Pelt-Heerschap, H.M.L. van; Gonzalez-Tizon, A.M. - \ 2014
Zoologica Scripta 43 (2014)2. - ISSN 0300-3256 - p. 161 - 171.
pcr-rflp analysis - phylogenetic networks - maximum-likelihood - mollusca-bivalvia - 5s rdna - siliqua - directus - macha - population - taxonomy
Ensis Schumacher, 1817 razor shells occur at both sides of the Atlantic and along the Pacific coasts of tropical west America, Peru, and Chile. Many of them are marketed in various regions. However, the absence of clear autapomorphies in the shell and the sympatric distributions of some species often prevent a correct identification of specimens. As a consequence, populations cannot be properly managed, and edible species are almost always mislabelled along the production chain. In this work, we studied whether the currently accepted Atlantic Ensis morphospecies are different evolutionary lineages, to clarify their taxonomic status and enable molecular identifications through DNA barcoding. For this, we studied 109 specimens sampled at 27 sites, which were identified as belonging to nine of those morphospecies. We analysed nucleotide variation at four nuclear (18S, 5.8S, ITS1, and ITS2) and two mitochondrial (COI and 16S) regions, although the 18S and 5.8S regions were not informative at the species level and were not further considered. The phylogenetic trees and networks obtained supported all morphospecies as separately evolving lineages. Phylogenetic trees recovered Ensis at each side of the Atlantic as reciprocally monophyletic. Remarkably, we confirm the co-occurrence of the morphologically similar E. minor (Chenu, 1843) and E. siliqua (Linné, 1758) along the NW Iberian coast, a fact that has been often overlooked. In South America, a relevant divergence between E. macha (Molina, 1792) individuals from Chile and Argentina was unveiled and suggests incipient speciation. We also confirm the occurrence of the North American species E. directus (Conrad, 1843) as far south as north-eastern Florida. Among the genomic regions analysed, we suggest COI as the most suitable DNA barcode for Atlantic Ensis. Our results will contribute to the conservation and management of Ensis populations and will enable reliable identifications of the edible species, even in the absence of the valves. The name Ensis coseli Vierna nom. nov. is proposed to replace E. minor Dall, 1899 non (Chenu, 1843).
Birth, death and horizontal transfer of the fumonisin biosynthetic gene cluster during the evolutionary diversification of Fusarium
Proctor, R.H. ; Hove, F. van; Susca, A. ; Stea, G. ; Busman, M. ; Lee, T.A.J. van der; Waalwijk, C. ; Moretti, A. ; Ward, T.J. - \ 2013
Molecular Microbiology 90 (2013)2. - ISSN 0950-382X - p. 290 - 306.
fujikuroi species complex - maximum-likelihood - gibberella-moniliformis - aspergillus-parasiticus - secondary metabolism - comparative genomics - adaptive evolution - multigene family - section liseola - mixed models
Fumonisins are a family of carcinogenic secondary metabolites produced by members of the Fusarium fujikuroi species complex (FFSC) and rare strains of Fusarium oxysporum. In Fusarium, fumonisin biosynthetic genes (FUM) are clustered, and the cluster is uniform in gene organization. Here, sequence analyses indicated that the cluster exists in five different genomic contexts, defining five cluster types. In FUM gene genealogies, evolutionary relationships between fusaria with different cluster types were largely incongruent with species relationships inferred from primary-metabolism (PM) gene genealogies, and FUM cluster types are not trans-specific. In addition, synonymous site divergence analyses indicated that three FUM cluster types predate diversification of FFSC. The data are not consistent with balancing selection or interspecific hybridization, but they are consistent with two competing hypotheses: (i) multiple horizontal transfers of the cluster from unknown donors to FFSC recipients and (ii) cluster duplication and loss (birth and death). Furthermore, low levels of FUM gene divergence in F.¿bulbicola, an FFSC species, and F.¿oxysporum provide evidence for horizontal transfer of the cluster from the former, or a closely related species, to the latter. Thus, uniform gene organization within the FUM cluster belies a complex evolutionary history that has not always paralleled the evolution of Fusarium
Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus
Frantz, L.A.F. ; Madsen, O. ; Megens, H.J.W.C. ; Paudel, Y. ; Bosse, M. ; Crooijmans, R.P.M.A. ; Groenen, M. ; Schraiber, J.G. - \ 2013
Genome Biology 14 (2013)9. - ISSN 1474-7596 - 12 p.
last glacial period - southeast-asia - recombination rates - complex speciation - maximum-likelihood - genetic-evidence - se asia - evolution - inference - reconstructions
Background Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal. Conclusions Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.
Metagenomic species profiling using universal phylogenetic marker genes
Sunagawa, S. ; Mende, D.R. ; Zeller, G. ; Izquierdo-Carrasco, F. ; Berger, S.A. ; Kultima, J.R. ; Coelho, L.P. ; Arumugam, M. ; Tap, J. ; Nielsen, H.B. ; Rasmussen, S. ; Brunak, S. ; Pedersen, O. ; Guarner, F. ; Vos, W.M. de; Wang, J. ; Li, J. ; Doré, J. ; Ehrlich, S.D. ; Stamatakis, A. ; Bork, P. - \ 2013
Nature Methods : techniques for life scientists and chemists 10 (2013)12. - ISSN 1548-7091 - p. 1196 - 1199.
maximum-likelihood - human microbiome - gut microbiome - alignments - accurate - catalog - reads - life - tree - ibd
To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/
The Bemisia tabaci species complex: Additions from different parts of the world
Firdaus, S. ; Vosman, B. ; Hidayati, N. ; Supena, E.D.J. ; Visser, R.G.F. ; Heusden, A.W. van - \ 2013
Insect Science 20 (2013)6. - ISSN 1672-9609 - p. 723 - 733.
mitochondrial-dna markers - hemiptera aleyrodidae - q-biotype - genetic differentiation - maximum-likelihood - b-biotype - populations - china - sternorrhyncha - geminiviruses
Bemisia tabaci is one of the most threatening pests in many crops. We sequenced part of the mitochondrial cytochrome oxidase I gene from fifty whitefly populations collected in Indonesia, Thailand, India and China. Nineteen unique sequences (haplotypes) of the cytochrome oxidase I were identified in these populations. They were combined with sequences available in databases, resulting in a total of 407 haplotypes and analyzed together with nine outgroup accessions. A phylogenetic tree was calculated using the maximum likelihood method. The tree showed that all groups that were found in previous studies were also present in our study. Additionally, seven new groups were identified based on the new haplotypes. Most B. tabaci haplotypes grouped based on their geographical origin. Two groups were found to have a worldwide distribution. Our results indicate that our knowledge on the species complex around B. tabaci is still far from complete.
Repeated loss of an anciently horizontally transferred gene cluster in Botrytis
Campbell, M.A. ; Staats, M. ; Kan, J.A.L. van; Rokas, A. ; Slot, J.C. - \ 2013
Mycologia 105 (2013)5. - ISSN 0027-5514 - p. 1126 - 1134.
fusaric acid - phylogenetic analysis - maximum-likelihood - fungi - bikaverin - eukaryotes - metabolism - oxysporum - evolution - models
At least five of the six genes of the bikaverin secondary metabolic gene cluster were shown to have undergone horizontal transfer (HGT) from a Fusarium donor to the Botrytis lineage. Of these five, two enzyme-encoding genes are found as pseudogenes in B. cinerea whereas two regulatory genes and the transporter remain intact. To reconstruct the evolutionary events leading to decay of this gene cluster and infer a more precise timing of its transfer, we examined the genomes of nine additional broadly sampled Botrytis species. We found evidence that a Botrytis ancestor acquired the entire gene cluster through an ancient HGT that occurred before the diversification of the genus. During the subsequent evolution and diversification of the genus, four of the 10 genomes appear to have lost the gene cluster, while in the other six the cluster is in various stages of degeneration. Across the Botrytis genomes, the modes of gene decay in the cluster differed between enzyme-encoding genes, which had higher rates of transition to or retention of pseudogenes and were universally inactivated, and regulatory genes (particularly the non-pathway-specific regulator bik4), which more frequently appeared intact. Consistent with these results, the regulatory genes bik4 and bik5 showed stronger evidence of transcriptional expression than other bikaverin genes under multiple conditions in B. cinerea. These results could be explained by pleiotropy in the bikaverin regulatory genes either through rewiring or their interaction with more central pathways or by constraints on the order of gene loss driven by the intrinsic toxicity of the pathway. Our finding that most of the bikaverin pathway genes have been lost or pseudogenized in these Botrytis genomes suggests that the incidence of HGT of gene cluster-encoded metabolic pathways might be higher than what is possible to be inferred from isolated genome analyses.
The duck genome and transcriptome provide insight into an avian influenza virus reservoir species
Huang, Y. ; Li, Y. ; Burt, D.W. ; Chen, H. ; Groenen, M.A.M. ; Crooijmans, R.P.M.A. ; Kraus, R.H.S. - \ 2013
Nature Genetics 45 (2013). - ISSN 1061-4036 - p. 776 - 783.
gene family evolution - positive selection - a virus - maximum-likelihood - phylogenetic trees - protein - transmission - duplication - expression - defensins
The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A viruses. We present the duck genome sequence and perform deep transcriptome analyses to investigate immune-related genes. Our data indicate that the duck possesses a contractive immune gene repertoire, as in chicken and zebra finch, and this repertoire has been shaped through lineage-specific duplications. We identify genes that are responsive to influenza A viruses using the lung transcriptomes of control ducks and ones that were infected with either a highly pathogenic (A/duck/Hubei/49/05) or a weakly pathogenic (A/goose/Hubei/65/05) H5N1 1 virus. Further, we show how the duck’s defense mechanisms against influenza infection have been optimized through the diversification of its b-defensin and butyrophilin-like repertoires. These analyses, in combination with the genomic and transcriptomic data, provide a resource for characterizing the interaction between host and influenza viruses.
The banana (Musa acuminata) genome and the evolution of monocotyledonous plants
Hont, A. D'; Denoeud, F. ; Aury, J.M. ; Kema, G.H.J. ; Dita Rodriguez, M.A. ; Waalwijk, C. - \ 2012
Nature 488 (2012). - ISSN 0028-0836 - p. 213 - 217.
in-situ hybridization - sequence count data - dna-sequences - differential expression - maximum-likelihood - gene - rice - diversification - identification - resource
Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries1. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations2, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish)1. Pests and diseases have gradually become adapted, representing an imminent danger for global banana production3, 4. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon–eudicotyledon divergence
In silico characterization and molecular evolutionary analysis of a novel superfamily of fungal effector proteins
Stergiopoulos, I. ; Kourmpetis, Y.A. ; Slot, J.C. ; Bakker, F.T. ; Wit, P.J.G.M. de; Rokas, A. - \ 2012
Molecular Biology and Evolution 29 (2012)11. - ISSN 0737-4038 - p. 3371 - 3384.
amino-acid sites - functional divergence - kluyveromyces-lactis - maximum-likelihood - cladosporium-fulvum - multigene families - gene duplication - death process - mixed models - phylogeny
Most fungal plant pathogens secrete effector proteins during pathogenesis to manipulate their host’s defense and promote disease. These are so highly diverse in sequence and distribution, they are essentially considered as species-specific. However, we have recently shown the presence of homologous effectors in fungal species of the Dothideomycetes class. One such example is Ecp2, an effector originally described in the tomato pathogen Cladosporium fulvum but later detected in the plant pathogenic fungi Mycosphaerella fijiensis and Mycosphaerella graminicola as well. Here, using in silico sequence-similarity searches against a database of 135 fungal genomes and GenBank, we extend our queries for homologs of Ecp2 to the fungal kingdom and beyond, and further study their history of diversification. Our analyses show that Ecp2 homologs are members of an ancient and widely distributed superfamily of putative fungal effectors, which we term Hce2 for Homologs of C. fulvum Ecp2. Molecular evolutionary analyses show that the superfamily originated and diversified within the fungal kingdom, experiencing multiple lineage-specific expansions and losses that are consistent with the birth-and- death model of gene family evolution. Newly formed paralogs appear to be subject to diversification early after gene duplication events, whereas at later stages purifying selection acts to preserve diversity and the newly evolved putative functions. Some members of the Hce2 superfamily are fused to fungal Glycoside Hydrolase family 18 chitinases that show high similarity to the Zymocin killer toxin from the dairy yeast Kluyveromyces lactis, suggesting an analogous role in antagonistic interactions. The observed high rates of gene duplication and loss in the Hce2 superfamily, combined with diversification in both sequence and possibly functions within and between species suggest that Hce2s are involved in adaptation to stresses and new ecological niches. Such findings address the need to rationalize effector biology and evolution beyond the perspective of solely host-microbe interactions
Qualitative and quantitative late blight resistance in the potato cultivar Sarpo Mira is determined by the perception of five distinct RXLR effectors
Rietman, H. ; Visser, R.G.F. ; Vossen, J.H. ; Bijsterbosch, G. ; Cano, L.M. ; Jacobsen, E. ; Kamoun, S. ; Lee, H.R. ; Vleeshouwers, V.G.A.A. - \ 2012
Molecular Plant-Microbe Interactions 25 (2012)7. - ISSN 0894-0282 - p. 910 - 919.
phytophthora-infestans - disease resistance - solanum-tuberosum - hypersensitive response - maximum-likelihood - general resistance - field-resistance - genome sequence - central mexico - toluca valley
Potato defends against Phytophthora infestans infection by resistance (R)-gene-based qualitative resistance as well as a quantitative field resistance. R genes are renowned to be rapidly overcome by this oomycete, and potato cultivars with a decent and durable resistance to current P. infestans populations are hardly available. However, potato cultivar Sarpo Mira has retained resistance in the field over several years. We dissected the resistance of 'Sarpo Mira' in a segregating population by matching the responses to P. infestans RXLR effectors with race-specific resistance to differential strains. The resistance is based on the combination of four pyramided qualitative R genes and a quantitative R gene that was associated with field resistance. The qualitative R genes include R3a, R3b, R4, and the newly identified Rpi-Smira1. The qualitative resistances matched responses to avirulence (AVR)3a, AVR3b, AVR4, and AVRSmira1 RXLR effectors and were overcome by particular P. infestans strains. The quantitative resistance was determined to be conferred by a novel gene, Rpi-Smira2. It was only detected under field conditions and was associated with responses to the RXLR effector AvrSmira2. We foresee that effector-based resistance breeding will facilitate selecting and combining qualitative and quantitative resistances that may lead to a more durable resistance to late blight.
A new subfamilial and tribal classification of the pantropical flowering plant family Annonaceae informed by molecular phylogenetics
Chatrou, L.W. ; Pirie, M.D. ; Erkens, R.H.J. ; Couvreur, T.L.P. ; Neubig, K.M. ; Abbott, J.R. ; Mols, J.B. - \ 2012
Botanical Journal of the Linnean Society 169 (2012)1. - ISSN 0024-4074 - p. 5 - 40.
historical biogeography - anaxagorea annonaceae - maximum-likelihood - uvaria annonaceae - character evolution - taxonomic revision - neotropical genera - sequence data - mixed models - missing data
The pantropical flowering plant family Annonaceae is the most species-rich family of Magnoliales. Despite long-standing interest in the systematics of Annonaceae, no authoritative classification has yet been published in the light of recent molecular phylogenetic analyses. Here, using the largest, most representative, molecular dataset compiled on Annonaceae to date, we present, for the first time, a robust family-wide phylogenetic tree and subsequent classification. We used a supermatrix of up to eight plastid markers sequenced from 193 ingroup and seven outgroup species. Some of the relationships at lower taxonomic levels are poorly resolved, but deeper nodes generally receive high support. Annonaceae comprises four major clades, which are here given the taxonomic rank of subfamily. The description of Annonoideae is amended, and three new subfamilies are described: Anaxagoreoideae, Ambavioideae and Malmeoideae. In Annonoideae, seven tribes are recognized, one of which, Duguetieae, is described as new. In Malmeoideae, seven tribes are recognized, six of which are newly described: Dendrokingstonieae, Fenerivieae, Maasieae, Malmeeae, Monocarpieae and Piptostigmateae. This new subfamilial and tribal classification is discussed against the background of previous classifications and characters to recognize subfamilies are reviewed
Evolutionary Analysis of Inter-Farm Transmission Dynamics in a Highly Pathogenic Avian Influenza Epidemic
Bataille, A. ; Meer, F. van der; Stegeman, A. ; Koch, G. - \ 2011
PLoS Pathogens 7 (2011)6. - ISSN 1553-7366
amino-acid sites - virus h7n7 - a virus - phylogenetic analysis - maximum-likelihood - poultry farms - netherlands - selection - h5n1 - recombination
Phylogenetic studies have largely contributed to better understand the emergence, spread and evolution of highly pathogenic avian influenza during epidemics, but sampling of genetic data has never been detailed enough to allow mapping of the spatiotemporal spread of avian influenza viruses during a single epidemic. Here, we present genetic data of H7N7 viruses produced from 72% of the poultry farms infected during the 2003 epidemic in the Netherlands. We use phylogenetic analyses to unravel the pathways of virus transmission between farms and between infected areas. In addition, we investigated the evolutionary processes shaping viral genetic diversity, and assess how they could have affected our phylogenetic analyses. Our results show that the H7N7 virus was characterized by a high level of genetic diversity driven mainly by a high neutral substitution rate, purifying selection and limited positive selection. We also identified potential reassortment in the three genes that we have tested, but they had only a limited effect on the resolution of the inter-farm transmission network. Clonal sequencing analyses performed on six farm samples showed that at least one farm sample presented very complex virus diversity and was probably at the origin of chronological anomalies in the transmission network. However, most virus sequences could be grouped within clearly defined and chronologically sound clusters of infection and some likely transmission events between farms located 0.8-13 Km apart were identified. In addition, three farms were found as most likely source of virus introduction in distantly located new areas. These long distance transmission events were likely facilitated by human-mediated transport, underlining the need for strict enforcement of biosafety measures during outbreaks. This study shows that in-depth genetic analysis of virus outbreaks at multiple scales can provide critical information on virus transmission dynamics and can be used to increase our capacity to efficiently control epidemics.
Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens
Klosterman, S.J. ; Subbarao, K.V. ; Kang, S. ; Veronese, P. ; Gold, S.E. ; Thomma, B.P.H.J. ; Chen, Z.J. ; Henrissat, B. ; Lee, Y.H. ; Park, J. ; Garcia-Pedrajas, M.D. ; Barbara, D.J. ; Anchieta, A. ; Jonge, R. de; Santhanam, P. ; Maruthachalam, K. ; Atallah, Z. ; Amyotte, S.G. ; Paz, Z. ; Inderbitzin, P. ; Hayes, R.J. ; Heiman, D.I. ; Young, S. ; Zeng, Q. ; Engels, R. ; Galagan, J. ; Cuomo, C. ; Dobinson, K.F. ; Ma, L.J. - \ 2011
PLoS Pathogens 7 (2011)7. - ISSN 1553-7366 - 19 p.
induced point mutation - cladosporium-fulvum - verticillium wilt - fusarium-oxysporum - nep1-like proteins - maximum-likelihood - transcription factor - neurospora-crassa - virulence factor - effector ecp6
The vascular wilt fungi Verticillium dahliae and V. albo-atrum infect over 200 plant species, causing billions of dollars in annual crop losses. The characteristic wilt symptoms are a result of colonization and proliferation of the pathogens in the xylem vessels, which undergo fluctuations in osmolarity. To gain insights into the mechanisms that confer the organisms' pathogenicity and enable them to proliferate in the unique ecological niche of the plant vascular system, we sequenced the genomes of V. dahliae and V. albo-atrum and compared them to each other, and to the genome of Fusarium oxysporum, another fungal wilt pathogen. Our analyses identified a set of proteins that are shared among all three wilt pathogens, and present in few other fungal species. One of these is a homolog of a bacterial glucosyltransferase that synthesizes virulence-related osmoregulated periplasmic glucans in bacteria. Pathogenicity tests of the corresponding V. dahliae glucosyltransferase gene deletion mutants indicate that the gene is required for full virulence in the Australian tobacco species Nicotiana benthamiana. Compared to other fungi, the two sequenced Verticillium genomes encode more pectin-degrading enzymes and other carbohydrate-active enzymes, suggesting an extraordinary capacity to degrade plant pectin barricades. The high level of synteny between the two Verticillium assemblies highlighted four flexible genomic islands in V. dahliae that are enriched for transposable elements, and contain duplicated genes and genes that are important in signaling/transcriptional regulation and iron/lipid metabolism. Coupled with an enhanced capacity to degrade plant materials, these genomic islands may contribute to the expanded genetic diversity and virulence of V. dahliae, the primary causal agent of Verticillium wilts. Significantly, our study reveals insights into the genetic mechanisms of niche adaptation of fungal wilt pathogens, advances our understanding of the evolution and development of their pathogenesis, and sheds light on potential avenues for the development of novel disease management strategies to combat destructive wilt diseases.