Genetic diversity of root-knot nematodes from Brazil and development of SCAR markers specific for the coffee-damaging species

Development of sequence characterized amplified genomic regions (SCAR) for fungal systematics: proof of principle using Alternaria, Ascochyta and Tilletia

SCARs were developed by cloning RAPD-PCR amplicons into commercially available vectors, sequencing them and designing specific primers for PCR, direct sequencing and phylogenetic analysis. Eighteen to seventy percent of cloned RAPD-PCR amplicons were phylogenetically informative among closely related small-spored Alternaria spp., Ascochyta spp. and Tilletia spp., taxa that have been resistant to phylogenetic analysis with universally primed, protein-coding sequence data. Selected SCARs were sequenced for larger, population-scale samples of each taxon and demonstrated to be useful for phylogenetic inference. Variation observed in the cloned SCARs generally was higher than variation in nuclear ribosomal internal transcribed spacer (ITS) and several protein-coding sequences commonly used in lower level fungal systematics. Sequence data derived from SCARs will provide sufficient resolution to address lower level phylogenetic hypotheses in Alternaria, Ascochyta, Tilletia and possibly many other fungal groups and organisms.

The map-1 gene family in root-knot nematodes, Meloidogyne spp.: a set of taxonomically restricted genes specific to clonal species

Taxonomically restricted genes (TRGs), i.e., genes that are restricted to a limited subset of phylogenetically related organisms, may be important in adaptation. In parasitic organisms, TRG-encoded proteins are possible determinants of the specificity of host-parasite interactions. In the root-knot nematode (RKN) Meloidogyne incognita, the map-1 gene family encodes expansin-like proteins that are secreted into plant tissues during parasitism, thought to act as effectors to promote successful root infection. MAP-1 proteins exhibit a modular architecture, with variable number and arrangement of 58 and 13-aa domains in their central part. Here, we address the evolutionary origins of this gene family using a combination of bioinformatics and molecular biology approaches. Map-1 genes were solely identified in one single member of the phylum Nematoda, i.e., the genus Meloidogyne, and not detected in any other nematode, thus indicating that the map-1 gene family is indeed a TRG family. A phylogenetic analysis of the distribution of map-1 genes in RKNs further showed that these genes are specifically present in species that reproduce by mitotic parthenogenesis, with the exception of M. floridensis, and could not be detected in RKNs reproducing by either meiotic parthenogenesis or amphimixis. These results highlight the divergence between mitotic and meiotic RKN species as a critical transition in the evolutionary history of these parasites. Analysis of the sequence conservation and organization of repeated domains in map-1 genes suggests that gene duplication(s) together with domain loss/duplication have contributed to the evolution of the map-1 family, and that some strong selection mechanism may be acting upon these genes to maintain their functional role(s) in the specificity of the plant-RKN interactions.

Biometrical, Biochemical, and Molecular Diagnosis of Portuguese Meloidogyne hispanica Isolates

Meloidogyne hispanica infects many economically important crops worldwide. The accurate identification of this pathogen is essential for the establishment of efficient and sustainable integrated pest management programs. Portuguese M. hispanica isolates were studied by biometrical, biochemical, and molecular characteristics. Biometrical characteristics of M. hispanica females, males, and second-stage juveniles were similar to the original description. Biochemical studies revealed a unique enzyme pattern (Hi4) for M. hispanica esterases that allowed for species differentiation. Molecular analysis of the mtDNA region from COII and 16S rRNA genes resulted in amplification products (1,800 bp) similar to M. hispanica, M. ethiopica, and M. javanica, and the described HinfI was unable to discriminate M. hispanica from the other two species. Analysis of the mtDNA sequences revealed altered nucleotides among the isolates that created new restriction sites for AluI and DraIII. The resulting restriction patterns successfully discriminated between the three species, providing a new tool for Meloidogyne identification. Finally, the phylogenetic relationship between M. hispanica and several Meloidogyne spp. sequences was analyzed using mtDNA, confirming the divergence between meiotic and mitotic species and revealing the proximity of M. hispanica to closely related species. Based on the studies conducted, the application of isozyme or polymerase chain reaction restriction fragment length polymorphism analysis would be a useful and efficient methodology for M. hispanica identification.

Multiplex PCR for the simultaneous identification and detection of Meloidogyne incognita, M. enterolobii, and M. javanica using DNA extracted directly from individual galls

Meloidogyne incognita, M. enterolobii, and M. javanica are the most widespread species of root-knot nematodes in South China, affecting many economically important crops, ornamental plants, and fruit trees. In this study, one pair of Meloidogyne universal primers was designed and three pairs of species-specific primers were employed successfully to rapidly detect and identify M. incognita, M. enterolobii, and M. javanica by multiplex polymerase chain reaction (PCR) using DNA extracted from individual galls. Multiplex PCR from all M. incognita, M. enterolobii, and M. javanica isolates generated two fragments of ≈500 and 1,000, 500 and 200, and 500 and 700 bp, respectively. The 500-bp fragment is the internal positive control fragment of rDNA 28S D2/D3 resulting from the use of the universal primers. Other Meloidogyne spp. included in this study generated only one fragment of ≈500 bp in size. Using this approach, M. incognita, M. enterolobii, and M. javanica were identified and detected using DNA extracted directly from individual galls containing the Meloidogyne spp. at various stages of their life cycle. Moreover, the percentage of positive PCR amplification increased with nematode development and detection was usually easy after the late stage of the second-stage juvenile. The protocol was applied to galls from naturally infested roots and the results were found to be fast, sensitive, robust, and accurate. This present study is the first to provide a definitive diagnostic tool for M. incognita, M. enterolobii, and M. javanica using DNA extracted directly from individual galls using a one-step multiplex PCR technique.

Respostas de genótipos de Coffea spp. a diferentes populações de Meloidogyne exigua

Em Meloidogyne exigua, um dos principais patógenos do cafeeiro no Brasil, já foram observadas variabilidade bioquímica, molecular, morfológica e fisiológica. No entanto, a expressão desta variabilidade quanto à virulência a genótipos de cafeeiro não é bem conhecida. O objetivo deste trabalho foi estudar o efeito de populações de M. exigua, as quais exibiam diferentes fenótipos de esterase e preferências por hospedeiros, em 25 genótipos de cafeeiro, com o propósito de se conhecer melhor a interação de biótipos desse nematóide com o gênero Coffea. Seis mudas de cafeeiro por tratamento foram inoculadas no estádio de 3 a 4 pares de folhas definitivas com 5.000 ovos de cada população de M. exigua por planta. O número de galhas e ovos por sistema radicular e a biomassa da matéria fresca das raízes foram avaliados aos 110 dias após a inoculação. Em função da reação frente às populações de M. exigua, os genótipos de Coffea spp. foram classificados em 14 suscetíveis, 5 imunes e 6 segregantes. Estes últimos segregaram de maneira diferenciada conforme a população do patógeno, evidenciando a existência de variabilidade intraespecífica em relação à virulência ao cafeeiro. Assim, o uso de diferentes populações desse patógeno, que englobem essa variabilidade é fundamental no desenvolvimento de cultivares resistentes.

Challenges in tropical plant nematology

A major challenge facing agricultural scientists today is the need to secure food for an increasing world population. This growth occurs predominantly in developing, mostly tropical countries, where the majority of hungry people live. Reducing yield losses caused by pathogens of tropical agricultural crops is one measure that can contribute to increased food production. Although plant-parasitic nematodes are often not as important as some other biotic and nonbiotic constraints on crop production in the tropics, they can nevertheless cause extensive damage and substantial yield losses. The effects of agricultural, environmental, socioeconomic, and policy changes on the occurrence of plant-parasitic nematodes in the tropics and the losses these pathogens cause are largely undocumented. Recent developments pose new challenges to tropical nematology. The increased application of molecular diagnostics may widen the knowledge gap between nematologists working in developed countries and in the tropics. Uncertainties concerning the validity of nematode species will lead to practical problems related to quarantine measures and nematode management. The study of interactions between nematodes and other pathogens in disease complexes provide opportunities for multidisciplinary research with scientists from other disciplines but remain underexploited. Difficulties in recognizing emerging nematode threats prevent the timely implementation of management strategies, thus increasing yield losses. Research is needed to address these challenges. Examples are presented mainly but not exclusively from banana, peanut, and rice nematology.

Characterization of a new β-1,4-endoglucanase gene from the root-knot nematode Meloidogyne incognita and evolutionary scheme for phytonematode family 5 glycosyl hydrolases

Cellulases from plant parasitic nematodes are encoded by multiple gene families and are thought to originate from horizontal gene transfer. Unraveling the evolution of these genes in the phylum will help understanding the evolution of plant parasitism in nematodes. Here we describe a new gene, named MI-eng-2, that encodes a family 5 glycosyl hydrolase (GHF5) with a predicted signal peptide and devoid of linker domain and cellulose-binding domain. The beta-1,4-endoglucanase activity of the protein MI-ENG-2 was confirmed in vitro and the transcription of the gene was localized in the secretory oesophageal glands of infective juveniles, suggesting that MI-ENG-2 is involved in plant cell wall degradation during parasitism. Phylogenetic and exon/intron structure analyses of beta-1,4-endoglucanase genes in the order Tylenchida strengthen the hypothesis that nematode GHF5 genes result from horizontal gene transfer of a bacterial gene with a cellulose-binding domain. GHF5 gene families in Tylenchida result from gene duplications associated with occasional loss of the cellulose-binding domain and the linker domain during their evolution.

Interplay of selective pressure and stochastic events directs evolution of the MEL172 satellite DNA library in root-knot nematodes

According to the library model, related species can have in common satellite DNA (satDNA) families amplified in differing abundances, but reasons for persistence of particular sequences in the library during long periods of time are poorly understood. In this paper, we characterize 3 related satDNAs coexisting in the form of a library in mitotic parthenogenetic root-knot nematodes of the genus Meloidogyne. Due to sequence similarity and conserved monomer length of 172 bp, this group of satDNAs is named MEL172. Analysis of sequence variability patterns among monomers of the 3 MEL172 satellites revealed 2 low-variable (LV) domains highly reluctant to sequence changes, 2 moderately variable (MV) domains characterized by limited number of mutations, and 1 highly variable (HV) domain. The latter domain is prone to rapid spread and homogenization of changes. Comparison of the 3 MEL172 consensus sequences shows that the LV domains have 6% changed nucleotide positions, the MV domains have 48%, whereas 78% divergence is concentrated in the HV domain. Conserved distribution of intersatellite variability might indicate a complex pattern of interactions in heterochromatin, which limits the range and phasing of allowed changes, implying a possible selection imposed on monomer sequences. The lack of fixed species-diagnostic mutations in each of the examined MEL172 satellites suggests that they existed in unaltered form in a common ancestor of extant species. Consequently, the evolution of these satellites seems to be driven by interplay of selective constraints and stochastic events. We propose that new satellites were derived from an ancestral progenitor sequence by nonrandom accumulation of mutations due to selective pressure on particular sequence segments. In the library of particular taxa, established satellites might be subject to differential amplification at chance due to stochastic mechanisms of concerted evolution.

High conservation of the differentially amplified MPA2 satellite DNA family in parthenogenetic root-knot nematodes

Sequence variability and distribution of a newly characterized MPA2 satellite DNA family are described in five root-knot nematode species of the genus Meloidogyne, the mitotic parthenogens M. paranaensis, M. incognita, M. arenaria and M. javanica, and the meiotic/mitotic M. hapla (isolates A and B, respectively). The lack of distinctive mutations and the considerable contribution (40.8%) of ancestral changes disclose an ancient satellite DNA which existed in the common ancestor of extant parthenogenetic species in the same or similar form and remained preserved for a period of at least 43 My. Nonuniformly distributed polymorphic sites along the satellite monomer suggest differences in constraints acting on particular sequence segments. Sequence diversity is clearly unaffected by significant differences in genomic abundance of the MPA2 satellite DNA in the examined species. Observed results suggest that the dynamics of this satellite DNA family might be in the first instance a consequence of characteristics of its nucleotide sequence and possible constraints imposed on it. Under conditions of mitotic and meiotic parthenogenesis, slow accumulation of mutations and slow replacement of old MPA2 sequence variants with new ones may be equivalent to the dynamics of some satellite DNA sequences conserved for extremely long evolutionary periods in sexual species.

Sequence characterized amplified region markers tightly linked to the mating factors of Lentinula edodes

Detecting the mating types in shiitake, Lentinula edodes (Berk.) Pegler, is important for making progress in the breeding of this mushroom and determining the compatibility of the pair to cross. Shiitake is a tetrapolar fungus with two unlinking mating factors, A factor and B factor. We screened molecular markers linked to the mating factors using the randomly amplified polymorphic DNA (RAPD) method to develop the mating type identification procedure. Using 147 oligonucleotide primers, a total of 6 linkage markers for the shiitake mating factors, 4 markers for the A factor and 2 markers for the B factor, were discovered with a logarithm of the odds threshold of 3.0 for linkage. Two RAPDs that perfectly segregated with each mating factor among 72 basidiospore strains were detected. Both of these RAPDs were cloned and sequenced to convert them to the sequence characterized amplified region (SCAR) markers. Four primers, two sets of primers, were designed according to the internal sequences of two RAPDs tightly linking to the A factor or B factor. Consequently, we determined the polymerase chain reaction condition for multiplex analyses of these SCAR markers.