Bursaphelenchus xylophilus is the causative agent of pine wilt disease which has caused huge economic losses in many countries. It has been reported that two forms of pine wood nematodes existed in its native region, i.e., with strong virulence and weak virulence. However, little is known about the molecular differences between the two forms. To better understand their molecular variations, transcriptome and genome sequences of three strongly virulent and one weakly virulent strains were analyzed. We found 238 transcripts and 84 exons which showed notable changes between the two virulent forms. Functional analyses of both differentially expressed transcripts and exons indicated that different virulence strains showed dissimilar nematode growth, reproduction, and oxidoreductase activities. In addition, we also detected a small number of exon-skipping events in B. xylophilus. Meanwhile, 117 SNPs were identified as potential genetic markers in distinguishing the two forms. Four of them were further proved to have undergone allele specific expressions and possibly interrupted the target site of evolutionary conserved B. xylophilus miR-47. These particular SNPs were experimentally verified by including eight additional strains to ensure the validity of our sequencing results. These results could help researchers to better diagnose nematode species with different virulence and facilitate the control of pine wilt disease.

BACKGROUND: Bursaphelenchus xylophilus, the pinewood nematode, kills millions of pine trees worldwide every year, and causes enormous economic and ecological losses. Despite extensive research on population variation, there is little understanding of the population-wide variation spectrum in China.RESULTS: We sequenced an inbred B. xylophilus strain using Pacbio+Illumina+Bionano+Hi-C and generated a chromosomelevel assembly (AH1) with six chromosomes of 77.1 Mb (chromosome N50: 12 Mb). The AH1 assembly shows very high continuity and completeness, and contains novel genes with potentially important functions compared with previous assemblies. Subsequently, we sequenced 181 strains from China and the USA and found ∼7.8 million single nucleotide polymorphisms (SNPs). Analysis shows that the B. xylophilus population in China can be divided into geographically bounded subpopulations with severe cross-infection and potential migrations. In addition, distribution of B. xylophilus is dominated by temperature zones while geographically associated SNPs are mainly located on adaptation related GPCR gene families, suggesting the nematode has been evolving to adapt to different temperatures. A machine-learning based epidemic tracking method has been established to predict their geographical origins, which can be applied to any other species.CONCLUSION: Our study provides the community with the first high-quality chromosome-level assembly which includes a comprehensive catalogue of genetic variations. It provides insights into population structure and effective tracking method for this invasive species, which facilitates future studies to address a variety of applied, genomic and evolutionary questions in B. xylophilus as well as related species.

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The pine wood nematode Bursaphelenchus xylophilus parasitizes millions of pine trees worldwide each year, causing severe wilt and the death of host trees. Glycoside hydrolase 45 genes of B. xylophilus are reported to have been acquired by horizontal gene transfer from fungi and are responsible for cell wall degradation during nematode infection. Previous studies ignored the possibility of copy number variations of such genes. In this study, we determined that two of the glycoside hydrolase 45 genes evolved to maintain multiple copies with distinct expression levels, enabling the nematode to infect a variety of pine hosts. Additionally, tandem repeat variations within coding regions were also detected between different copies of glycoside hydrolase 45 genes that could result in changes in protein sequences and serve as an effective biological marker to detect copy number variations among different B. xylophilus populations. Consequently, we were able to further identify the copy number variations of glycoside hydrolase 45 genes among B. xylophilus strains with different virulence. Our results provide new insights into the pathogenicity of B. xylophilus, provide a practical marker to genotype copy number variations and may aid in population classification.

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Pinus thunbergii Parl. (Japanese black pine), an evergreen species, is distributed along the seacoasts of China. In addition, this species has been planted along seacoasts as a windbreak to prevent soil erosion due to its resistance to salt and various environmental stresses. It can also be found in public parks and gardens due to its exquisite appearance and toughness. In August 2020, needle blight symptoms were found on several black pine trees in Sichuan Province, China. Further surveys showed that these symptoms are common. The disease incidence is less than 30% while severity of the disease is high. The tips of old needles first turn grayish green that developed into brown bands ranging from 1 to 2 mm. To determine the pathogen, small needle pieces (3-4 mm2 long) from the margin of fresh lesions were surface-sterilized for 30 s in 75% ethanol, follow by 1% NaOCl for 90 s, then washed three times with sterile water, and then were placed on potato dextrose agar (PDA) with 0.1 mg/mL ampicillin and incubated at 25°C. Pure cultures of 8 isolates were obtained by monosporic isolation, and a representative isolate (SC03) was deposited in the Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University. When cultured on Spezieller Nährstoffarmer Agar medium (Leslie and Summerell, 2006), the SC03 colony was beige-white, cottony from top view and pale orange near the center on the reverse side. The daily growth rate was 11.8 mm/day at 25°C in the dark. Microscopic observations showed hyaline and septate hyphae, slightly curved macroconidia with two to three septa measuring 17.5 - 30 × 3.7 - 7.5 μm (23.2 × 5.7 on average), and aseptate microconidia measuring 7.5 - 12.5 × 2.5 - 5.0 μm, (9.7 × 4.3 on average). The morphological characteristics of conidia and other structures of SC03 matched those of the Fusarium fujikuroi species complex (FFSC) (Abdalla et al. 2000). For accurate identification, translation elongation factor 1-alpha（TEF-1α） , and the second largest RNA polymerase subunit (RPB2) were amplified and sequenced using the primer pairs EF1 and EF2, RPB5f2 and RPB7cr. The sequences were deposited in GenBank [Accession TEF-1α: ON049647, RBP2: ON049648]. A Blast search of GenBank showed that TEF-1α and RPB2 sequences of SC03 matched Fusarium proliferatum (Matsush) Nirenberg at a high level (>99%). Phylogenetic analysis using neighbor joining and concatenated sequences (TEF-1α and RPB2) with MEGA X placed SC03 in F. proliferatum. For the pathogenicity test, a conidial suspension was prepared with a concentration of 2.0 × 107 conidia/ml. The suspension was sprayed onto 3 annual seedlings’ needles, and the control was sprayed with sterile water. Inoculated and uninoculated plants were kept in humid chambers in a glasshouse where the average humidity was 60% and the average temperature was 27℃. After 10 days, typical symptoms appeared on inoculated needles, whereas control needles remained symptomless. These symptoms were similar to those observed in field. The fungus, F. proliferatum, was reisolated from those lesions, confirming Koch's postulates. No symptoms were observed on control plants. Fusarium proliferatum is a ubiquitous saprophytic fungus on cankers and very rarely reported to cause disease on pine needles. It has been reported to cause leaf blight of Polygonatum cyrtonema (Zhou et al. 2021) and Majesty palm (Polizzi and Vitale 2003). To our knowledge, this is the first report of needle blight on P. thunbergii caused by F. proliferatum in China. The disease represents a threat to producers and more research on the biology and management is needed.

Pinus thunbergii Parl., known as black pine, is widely distributed all over China. This pine variety can prevent soil desertification and promote soil conservation and is excellent for constructing fast-growing forests and shelter belts. The timber of this species can be used for infrastructure construction and furniture production. In August 2020, needle blight symptoms were found on several trees of black pine in Sichuan Province, China. Further surveys showed that these symptoms are common while the disease incidence is less than 30% which indicated the severity of the disease is mild. The tips of old needles first turn grayish green and developed into brown bands ranging from 1 to 2 mm. To determine the pathogen, 20 needle samples with typical symptoms were disinfected with 75% alcohol, and sections of the tissue were cut from joints of diseased and healthy tissues (visually healthy) with a sterilized scalpel, surface sterilized for 45 seconds in 75% alcohol, soaked for 90 seconds in 1.5% NaCIO, rinsed in sterilized water and dried. Small cut tissues were placed on potato dextrose agar (PDA) at 25℃ for 10 days. Pure cultures were obtained by monosporic isolation. The colonies initially appeared white to cream, yeast-like, and later turned to pink and remained at least 10 days. Conidia were hyaline, smooth-walled, single-celled, and ellipsoidal with variable shape and size, 7.5 to 16 × 3.5 to 7 µm (Zalar et al. 2008). DNA was extracted from the mycelium of the isolate by the cetyltriethylammonium bromide (CTAB) method and amplified through polymerase chain reaction (PCR) with the internal transcribed spacer (ITS) region of rDNA and partial β-tubulin genes of a representative isolate (SC05) were amplified using the ITS1/ITS4 and Bt2a/Bt2b primer pairs, respectively(Wu et al. 2017). The sequences submitted to GenBank (Accession Nos. MW228368 for ITS and MW256762 for β-tubulin) showed high similarity with BLAST sequences of Aureobasidium pullulans (ITS, KR704881 [100%]; β-tubulin, MT671934 [99.49%]). For the pathogenicity test, a conidial suspension was prepared with a concentration of 2.0 × 107 conidia/ml. The suspension was sprayed onto 3 annual seedlings’ needles, and the control was sprayed with sterile water. Inoculated and non-inoculated plants were kept in humid chambers in a glasshouse. After 10 days, typical symptoms appeared on inoculated needles, whereas control needles remained symptomless. The fungus, A. pullulans, was reisolated from those lesions, confirming Koch's postulates. No symptoms were observed on control plants. Aureobasidium pullulans, a ubiquitous saprophytic fungus on many fruits and very rarely reported to cause disease on pine needles. Only reported invasion of Ozone‐injured needles in P. strobus (Costonis and Sinclair 1972) and needles damaged by acid rain in P. sylvestris (Ranta 1990). To our knowledge, this is the first report of brown spot needle blight on P. thunbergii caused by A. pullulans in China. The disease represents a threat to pine manufactures and more research on the pathogenesis and management is needed.

Bursaphelenchus xylophilus is considered the most dangerous quarantine pest in China. It causes enormous economic and ecological losses in many countries from Asia and Europe. The glycoside hydrolase 45 gene family has been demonstrated in early studies to contribute to the cell wall degradation ability of B. xylophilus during its infection. However, the copy number variation (CNV) of the GH45 gene and its association with B. xylophilus pathogenicity were not fully elucidated. In this study, we found that the GH45 gene with two copies is the most predominant type among 259 B. xylophilus strains collected from China and Japan. Additionally, 18 strains are identified as GH45 genes with a single copy, and only two strains are verified to have three copies. Subsequent expression analysis and inoculation test suggest that the copy numbers of the GH45 gene are correlated with gene expression as well as the B. xylophilus pathogenicity. B. xylophilus strains with more copies of the GH45 gene usually exhibit more abundant expression and cause more severe wilt symptoms on pine trees. The aforementioned results indicated the potential regulatory effects of CNV in B. xylophilus and provided novel information to better understand the molecular pathogenesis of this devastating pest.