Sequence characterized amplified polymorphic markers for the pitch canker pathogen,Fusarium circinatum

Fusarium circinatum is the causal agent of pitch canker disease of pines. This pathogen is thought to have originated in Central America and currently poses a serious threat to commercial pine plantations in many areas of the world. In this study, polymorphic molecular markers were developed for F. circinatum using the internal short sequence repeats‐polymerase chain reaction (ISSR‐PCR) technique. Nine sequence characterized amplified polymorphic markers were developed. Thirty‐two putative alleles were observed among 103 F. circinatum isolates from different geographical areas using the nine polymorphic markers. These sequence characterized amplified polymorphic markers can be used as genetic tools in populations studies of F. circinatum.     

Detection and Quantification of Airborne Conidia of Fusarium circinatum, the Causal Agent of Pine Pitch Canker, from Two California Sites by Using a Real-Time PCR Approach Combined with a Simple Spore Trapping Method

Pinus radiata (Monterey pine), a tree native to coastal California and Mexico, is widely planted worldwide for timber production. A major threat to Monterey pine plantations is the fungal disease pine pitch canker, caused by Fusarium circinatum (Hypocreales). We present a novel trapping approach using filter paper in combination with a rapid molecular method to detect the presence of inoculum in the air. The assay is also useful for diagnosing the presence of the pathogen on plants. The test is based on the F. circinatum specific primer pair CIRC1A-CIRC4A, which amplifies a 360-bp DNA fragment in the intergenic spacer region of the nuclear ribosomal operon. Real-time PCR was used to calculate the number of fungal spores present in each reaction mixture by comparing the threshold cycle (Ct) of unknown spore samples to the Ct values of standards with known amounts of F. circinatum spores. The filter paper method allows prolonged and more sensitive spore sampling in the field compared to traditional traps using petri dishes filled with selective medium. A field test at two sites in coastal California infested with pine pitch canker was carried out during the summer and fall of 2002. Spore counts were in the range of ca. 1 × 10³ to ca. 7 × 10⁵/m², with the highest spore counts in the fall, suggesting a seasonal fluctuation.     

Characterization of Fusarium circinatum from Pinus spp. in northern Spain

Pitch canker caused by Fusarium circinatum was recently reported on Pinus spp. in Spain. In this study, a collection of 157 isolates of F. circinatum obtained from different geographical origins and hosts in northern Spain were identified and characterized by cultural and morphological features, PCR-RFLPs of the histone H3 gene, IGS region, and the translation elongation factor 1-alpha gene (TEF). Mating types were determined by multiplex PCR and sexual compatibility was performed under laboratory conditions. Both mating types were present in Spain and were able to form the teleomorph Gibberella circinata. Morphological differences between mating types, not previously reported, were observed: MAT-1 isolates showed clear, coiled, sterile hyphae characteristic of F. circinatum, whereas MAT-2 isolates presented sterile hyphae but not coiled. Virulence of representative isolates was tested on seven to eight-month-old P. nigra, P. pinaster and P. sylvestris seedlings. All isolates tested were pathogenic to these pine species, MAT-1 isolates being more virulent than MAT-2 isolates.     

Genome-Wide Macrosynteny among Fusarium Species in the Gibberella fujikuroi Complex Revealed by Amplified Fragment Length Polymorphisms

The Gibberella fujikuroi complex includes many Fusarium species that cause significant losses in yield and quality of agricultural and forestry crops. Due to their economic importance, whole-genome sequence information has rapidly become available for species including Fusarium circinatum, Fusarium fujikuroi and Fusarium verticillioides, each of which represent one of the three main clades known in this complex. However, no previous studies have explored the genomic commonalities and differences among these fungi. In this study, a previously completed genetic linkage map for an interspecific cross between Fusarium temperatum and F. circinatum, together with genomic sequence data, was utilized to consider the level of synteny between the three Fusarium genomes. Regions that are homologous amongst the Fusarium genomes examined were identified using in silico and pyrosequenced amplified fragment length polymorphism (AFLP) fragment analyses. Homology was determined using BLAST analysis of the sequences, with 777 homologous regions aligned to F. fujikuroi and F. verticillioides. This also made it possible to assign the linkage groups from the interspecific cross to their corresponding chromosomes in F. verticillioides and F. fujikuroi, as well as to assign two previously unmapped supercontigs of F. verticillioides to probable chromosomal locations. We further found evidence of a reciprocal translocation between the distal ends of chromosome 8 and 11, which apparently originated before the divergence of F. circinatum and F. temperatum. Overall, a remarkable level of macrosynteny was observed among the three Fusarium genomes, when comparing AFLP fragments. This study not only demonstrates how in silico AFLPs can aid in the integration of a genetic linkage map to the physical genome, but it also highlights the benefits of using this tool to study genomic synteny and architecture.     

Homologous recombination and allele replacement in transformants of Fusarium fujikuroi

The ascomycete Fusarium fujikuroi could be transformed stably to hygromycin resistance only when the transforming plasmid contained a fragment of DNA from the fungus. The transformation frequencies were roughly independent of the sequence of the particular fungal DNA fragment used, of its size (1.8 or 6 kb), and of whether this DNA was present only once in the fungal genome or about forty times (the genes for ribosomal RNA). The plasmid was integrated into the fungal genome by homologous recombination in the eighteen transformants tested; ectopic integration was never observed. The carB gene of F. fujikuroi was cloned and shown to complement unpigmented mutants deficient in phytoene dehydrogenase. A mutant carB allele was prepared in vitro and used to transform wild-type protoplasts; the transformants contained a genomic duplication and were heterozygous for carB; the mutant allele replaced the original wild-type allele when this was spontaneously lost in the transformants. This loss was due to gene conversion in some cases and to recombination between repeated sequences in others. Received: 5 November 1999 / Accepted: 16 March 2000     

Differentiation of Fusarium subglutinans f. sp. pini by Histone Gene Sequence Data

Fusarium subglutinans f. sp. pini (= F. circinatum) is a pathogen of pine and is one of eight mating populations (i.e., biological species) in the Gibberella fujikuroi species complex. This species complex includes F. thapsinum, F. moniliforme (= F. verticillioides), F. nygamai, and F. proliferatum, as well as F. subglutinans associated with sugarcane, maize, mango, and pineapple. Differentiating these forms of F. subglutinans usually requires pathogenicity tests, which are often time-consuming and inconclusive. Our objective was to develop a technique to differentiate isolates of F. subglutinans f. sp. pini from other isolates identified as F. subglutinans. We sequenced the histone H3 gene from a representative set of Fusarium isolates. The H3 gene sequence was conserved and contained two introns in all the isolates studied. From both the intron and the exon sequence data, we developed a PCR-restriction fragment length polymorphism technique that reliably distinguishes F. subglutinans f. sp. pini from the other biological species in the G. fujikuroi species complex.     

Role of insect vectors in epidemiology and invasion risk of <Emphasis Type="Italic">Fusarium circinatum</Emphasis>, and risk assessment of biological control of invasive <Emphasis Type="Italic">Pinus contorta</Emphasis>

Pitch canker, caused by the pathogen Fusarium circinatum, is a serious disease of pines, Pinus species. It is a threat to natural and planted pine forests, and to date it has invaded countries across five continents. Pine-feeding insects can play a key role in the epidemiology of the disease, as wounding agents allowing pathogen access or as vectors transmitting the pathogen from infected to healthy trees. We reviewed the role of insects in the epidemiology of pitch canker worldwide and assessed which insects are present in New Zealand that may act as wounding agents or vectors to determine whether pathogen invasion could adversely affect Pinus radiata plantation forests and urban trees. We also evaluated whether cone or seed insects of pines could be introduced as biological control agents of invasive Pinus contorta and how this may affect the impact of a potential F. circinatum invasion. As there are no native pines or other Pinaceae in New Zealand, there are only a few pine insects, mainly accidental introductions. None of the insects recorded on pines in New Zealand is likely to be a vector, suggesting low disease risk. Of six potentially suitable biocontrol candidates, the European pine cone weevil Pissodes validirostris is the most promising regarding host specificity and impact on seed production, but there is uncertainty about its ability to act as a vector of F. circinatum. Our methodology to review and evaluate the vector potential of pine associates can be used as a generic framework to assess the potential impacts of F. circinatum invasion.     

Fusarium fractiflexum sp. nov. and two other species within theGibberella fujikuroi species complex recently discovered in Japan that form aerial conidia in false heads

Morphological and molecular phylogenetic analyses were conducted on 12 strains ofFusarium, deposited in MAFF asF. subglutinans (≡F. moniliforme var.subglutinans≡F. sacchari var.subglutinans) orFusarium sp. because they formed aerial conidia in false heads in the dark. These strains were resolved as three distinct species within theGibberella fujikuroi species complex. A new species,F. fractiflexum, and two species new to Japan,F. circinatum andF. concentricum, are described and illustrated and their morphological features are discussed.Fusarium fractiflexum, isolated from diseased yellow leaf spots ofCymbidium spp., is differentiated from other fusaria based on its yellowish colonies and aerial conidia formed in false heads in the dark and in zigzag-like conidial chains under black light. Japanese strains ofF. circinatum also formed elongate, coiled sterile hyphae. Phialidic aerial conidia with a pointed apex and a wedgeshaped base were found inF. concentricum cultured under black light and represent a new diagnostic character of the species, in addition to colonies with alternating concentric rings when cultured on PDA. Based on DNA sequences of the β-tubulin gene and two other loci, strains ofF. fractiflexum were resolved phylogenetically as members of the Asian clade of theG. fujikuroi species complex. In addition, Japanese strains ofF. circinatum andF. concentricum were phylogenetically identical to the ex-type strains.     

In vitro Evaluation of Wood Preservatives to Prevent Dispersal of Pitch Canker Pathogen,Fusarium circinatum

Fusarium circinatum, the causal agent of pitch canker disease on pines, can be disseminated by wood produced in infested areas. The purpose of the study was to evaluate the effect of wood preservatives, commonly used against sapstain and wood‐decay fungi, on growth and sporulation of Fusarium circinatum. Seven active ingredients of antisapstain and anti‐wood‐decay preservatives were evaluated by their inhibition of mycelial growth. Propiconazole, tebuconazole, and 3‐iodo‐2‐propinyl butyl carbamate (IPBC) were effective against F. circinatum, whereas hydroxycarbonate of cooper was not. An assay was also conducted to evaluate the efficacy of three commercial antisapstain and two anti‐wood‐decay preservatives on Pinus radiata sapwood blocks that were previously inoculated with Fusarium circinatum. The product with the best efficacy was an antidecay preservative composed of tebuconazole, propiconazole, and dichlofluanid. None of the antisapstain preservatives tested was effective even though they contained fungicidal ingredients. Effects of dosage, product application, and formulation on the efficacy of these preservatives are discussed.     

Pine genes regulated by the necrotrophic pathogen <Emphasis Type="Italic">Fusarium circinatum</Emphasis>

A targeted genomics approach was used to construct a cDNA array of potential pathogen-regulated genes for investigating host–pathogen interactions in pine trees (Pinus species). This array, containing a nonredundant set of 311 cDNAs, was assembled by combining smaller sets of cDNAs generated by differential display or suppression subtraction hybridization using a variety of pathogen treatments and elicitors. The array was probed to identify host genes regulated by Fusarium circinatum, a necrotrophic fungus that incites pitch canker disease on pine stems. A set of 29 cDNAs were induced during the disease state. Notably, cDNAs on the array that were derived from experiments with fusiform rust, incited by Cronartium quercuum f. sp. fusiforme (a biotrophic fungus) were unregulated by Fusarium. The results imply distinct genetic responses in pine to diseases incited by necrotrophs and biotrophs. This cDNA collection expands the genomics toolkit for understanding interactions between conifers and their microbial associates in forest ecosystems.     

The role of olfactory stimuli in the location of weakened hosts by twig‐infesting Pityophthorus spp.

1. Senescing, shade‐suppressed, or broken branches of Monterey pine Pinus radiata are infested by twig beetles in the genus Pityophthorus (Coleoptera: Scolytidae). The studies reported here tested whether twig beetles can discriminate between healthy and pitch canker‐diseased branches, whether diseased branch tips produce more ethylene than undamaged controls, and whether ethylene and other volatiles, produced by the plant in response to tissue damage, are utilised by twig beetles in host location. 2. Significantly greater numbers of twig beetles were reared from pitch canker‐symptomatic than from pitch canker‐asymptomatic branches of Monterey pine collected in the field. 3. Needles of Monterey pine branches inoculated with the pitch canker fungal pathogen Fusarium circinatum produced significantly higher levels of ethylene than needles of control branches, and this was evident just prior to, and during, symptom expression. 4. In trapping studies in which pheromone production was prevented, there was no evidence of attraction of twig beetles to a source of ethylene alone, to cut host branches, or to cut branches treated with the ethylene‐releasing compound, ethephon. The results suggest that twig beetles identify weakened branches after landing.     

Fusarium chlamydosporum,causing wilt disease of guava (Psidium guajava L.) in India

Wilt is a serious disease of guava crop in India. Fusarium oxysporum f. sp. psidii and F. solani have been reported as the main causative agents of this disease. Most recently a survey on guava plants affected with wilt disease was conducted in severely affected areas of India, and two new species of Fusarium viz. Fusarium proliferatum and Fusarium chlamydosporum were found to be associated with this disease. However, pathogenecity of Fusarium chlamydosporum was successfully conducted in the field trials. The culture of F. chlamydosporum was processed for DNA sequencing and DNA sequence was submitted to NCBI with GenBank accession no. HM102506. The submitted DNA sequence of F. chlamydosporum was compared for the genetic position in Fusarium spp. evolutionary phylogenic tree.     

Genetic mapping of expressed sequence tag polymorphism (ESTP) markers in loblolly pine (Pinus taeda L.)

The development and mapping of genetic markers based upon expressed sequence tag polymorphisms (ESTPs) in loblolly pine (Pinus taeda L.) are reported. The new markers were generated by PCR-amplification of loblolly pine genomic DNAs with primers designed from sequenced cDNAs. The cDNA libraries were constructed from RNAs expressed in the needles of loblolly pine seedlings or in the xylem from young trees. DNA polymorphisms were identified by analyzing the amplified products for differences in fragment size or restriction sites, or by examining mobility differences using denaturing gradient gel electrophoresis (DGGE). DGGE revealed more DNA polymorphisms than the other two methods. Fifty six ESTPs were mapped using either of two mapping populations and positioned onto a loblolly pine consensus genetic map. Unlike many other markers commonly used in forestry, ESTPs can be used as orthologous markers for comparative mapping, to map genes of known function, or to identify candidate genes affecting important traits in loblolly pine. Received: 10 April 2000 / Accepted: 13 July 2000     

Primers designed to amplify a mitochondrial nad1 intron in ponderosa pine, Pinus ponderosa, limber pine, P. flexilis, and Scots pine, P. sylvestris

The b/c intron of the mitochondrial nad1 gene, was sequenced to characterize the indel region of ponderosa pine, Pinus ponderosa. The sequence in ponderosa pine was aligned with the sequence in Scots pine, Pinus sylvestris, to design seven primers that are useful for sequencing and for revealing size variation in amplified fragments in ponderosa pine, Scots pine, and limber pine, Pinus flexilis. These primers reveal variability in all three species, and the pattern of variability within ponderosa pine is described by a preliminary survey. The indel region of ponderosa pine contains three distinct elements with lengths of 31, 32, and 34 bp. Received: 1 March 2000 / Accepted: 14 April 2000<@head-com-p1a.lf>Communicated by P.M.A. Tigerstedt     

Restriction Fragment Length Polymorphism Analysis of the Mitochondrial DNA of Fusarium oxysporum f. sp. ciceris

Seven isolates of Fusarium oxysporum f. sp. ciceris, representing pathogenic races 1 , 2, 3, and 4 from India and 0, 5, and 6 from Spain, were assayed for restriction fragment length polymorphisms (RFLPs) in the mitochondrial DNA,(mt DNA). The mt DNA fraction of total fungal DNA was purified and digested with the restriction endonucleases Bam HI, Bgl II, Eco RI. Kpn I, Sac I, Sal I, Sma I, and Xho I. The mt DNA is a circular molecule of 40.5 kb. No RFLP in the mt DNA was detected among the seven races of F. o. ciceris. The identical restriction patterns of mt DNA indicates an extensive conservation in the gene composition of mt DNA without sequence variation, and suggests that mt DNA of F. o. ciceris may not be responsible for pathogenic diversity. The restriction map of mt DNA from the race 6 isolate Fo 8272 was constructed by digestion of the mt DNA with five restriction enzymes: Eco RI, Kpn I, Sac I, Sal I, and Xho I, either singly or in selected pairs.     

Whole‐exome targeted sequencing of the uncharacterized pine genome

The large genome size of many species hinders the development and application of genomic tools to study them. For instance, loblolly pine (Pinus taeda L.), an ecologically and economically important conifer, has a large and yet uncharacterized genome of 21.7 Gbp. To characterize the pine genome, we performed exome capture and sequencing of 14 729 genes derived from an assembly of expressed sequence tags. Efficiency of sequence capture was evaluated and shown to be similar across samples with increasing levels of complexity, including haploid cDNA, haploid genomic DNA and diploid genomic DNA. However, this efficiency was severely reduced for probes that overlapped multiple exons, presumably because intron sequences hindered probe:exon hybridizations. Such regions could not be entirely avoided during probe design, because of the lack of a reference sequence. To improve the throughput and reduce the cost of sequence capture, a method to multiplex the analysis of up to eight samples was developed. Sequence data showed that multiplexed capture was reproducible among 24 haploid samples, and can be applied for high‐throughput analysis of targeted genes in large populations. Captured sequences were de novo assembled, resulting in 11 396 expanded and annotated gene models, significantly improving the knowledge about the pine gene space. Interspecific capture was also evaluated with over 98% of all probes designed from P. taeda that were efficient in sequence capture, were also suitable for analysis of the related species Pinus elliottii Engelm.     

High levels of population differentiation for mitochondrial DNA haplotypes inPinus radiata,muricata, andattenuata

We analyzed mitochondrial (mt) DNA restriction fragment length polymorphisms (RFLPs) associated with cytochrome oxidase, subunit I (coxI)-related gene sequences in 268 trees derived from 19 natural populations of three species of pines from California (USA): Monterey pine (Pinus radiata D. Don), bishop pine (P. Muricata D. Don), and knobcone pine (P. attenuata Lemm.). Total genomic DNA was digested with four restriction endonucleases and probed with a 750-bp fragment of the mitochondrialcoxI gene amplified fromP. attenuata via the polymerase chain reaction (PCR). ThecoxI gene is repeated at least 4 times in some populations, and all variants that we observed resulted from complex rearrangements rather than from point mutations. There was limited intrapopulation variation, but strong differentiation among populations. When applied to haplotype frequencies, Nei's gene diversity within populations (H_s) averaged 7% (±3), and G_st varied from 75% forP. Radiata to 96% forP. muricata. The high degree of population differentiation for mtDNA suggests that it can be a powerful marker of population differences, but its rapid rate of structural evolution appears to result from recombination among a limited number of repetitive elements-giving frequent homoplasious fragment phenotypes. The phylogenetic trees disagreed with results from chloroplast DNA, nuclear gene, and morphological studies.