Xinyue Cheng

Fast economic development accelerates biological invasions in China.

Increasing levels of global trade and intercontinental travel have been cited as the major causes of biological invasion. However, indirect factors such as economic development that affect the intensity of invasion have not been quantitatively explored. Herein, using principal factor analysis, we investigated the relationship between biological invasion and economic development together with climatic information for China from the 1970s to present. We demonstrate that the increase in biological invasion is coincident with the rapid economic development that has occurred in China over the past three decades. The results indicate that the geographic prevalence of invasive species varies substantially on the provincial scale, but can be surprisingly well predicted using the combination of economic development (R2 = 0.378) and climatic factors (R2 = 0.347). Economic factors are proven to be at least equal to if not more determinant of the occurrence of invasive species than climatic factors. International travel and trade are shown to have played a less significant role in accounting for the intensity of biological invasion in China. Our results demonstrate that more attention should be paid to economic factors to improve the understanding, prediction and management of biological invasions.

Metagenomic analysis of the pinewood nematode microbiome reveals a symbiotic relationship critical for xenobiotics degradation

Our recent research revealed that pinewood nematode (PWN) possesses few genes encoding enzymes for degrading α-pinene, which is the main compound in pine resin. In this study, we examined the role of PWN microbiome in xenobiotics detoxification by metagenomic and bacteria culture analyses. Functional annotation of metagenomes illustrated that benzoate degradation and its related metabolisms may provide the main metabolic pathways for xenobiotics detoxification in the microbiome, which is obviously different from that in PWN that uses cytochrome P450 metabolism as the main pathway for detoxification. The metabolic pathway of degrading α-pinene is complete in microbiome, but incomplete in PWN genome. Experimental analysis demonstrated that most of tested cultivable bacteria can not only survive the stress of 0.4% α-pinene, but also utilize α-pinene as carbon source for their growth. Our results indicate that PWN and its microbiome have established a potentially mutualistic symbiotic relationship with complementary pathways in detoxification metabolism.

MicroRNA Discovery and Analysis of Pinewood Nematode Bursaphelenchus xylophilus by Deep Sequencing

BACKGROUND MicroRNAs (miRNAs) are considered to be very important in regulating the growth, development, behavior and stress response in animals and plants in post-transcriptional gene regulation. Pinewood nematode, Bursaphelenchus xylophilus, is an important invasive plant parasitic nematode in Asia. To have a comprehensive knowledge about miRNAs of the nematode is necessary for further in-depth study on roles of miRNAs in the ecological adaptation of the invasive species. METHODS AND FINDINGS Five small RNA libraries were constructed and sequenced by Illumina/Solexa deep-sequencing technology. A total of 810 miRNA candidates (49 conserved and 761 novel) were predicted by a computational pipeline, of which 57 miRNAs (20 conserved and 37 novel) encoded by 53 miRNA precursors were identified by experimental methods. Ten novel miRNAs were considered to be species-specific miRNAs of B. xylophilus. Comparison of expression profiles of miRNAs in the five small RNA libraries showed that many miRNAs exhibited obviously different expression levels in the third-stage dispersal juvenile and at a cold-stressed status. Most of the miRNAs exhibited obviously down-regulated expression in the dispersal stage. But differences among the three geographic libraries were not prominent. A total of 979 genes were predicted to be targets of these authentic miRNAs. Among them, seven heat shock protein genes were targeted by 14 miRNAs, and six FMRFamide-like neuropeptides genes were targeted by 17 miRNAs. A real-time quantitative polymerase chain reaction was used to quantify the mRNA expression levels of target genes. CONCLUSIONS Basing on the fact that a negative correlation existed between the expression profiles of miRNAs and the mRNA expression profiles of their target genes (hsp, flp) by comparing those of the nematodes at a cold stressed status and a normal status, we suggested that miRNAs might participate in ecological adaptation and behavior regulation of the nematode. This is the first description of miRNAs in plant parasitic nematodes. The results provide a useful resource for further in-depth study on molecular regulation and evolution of miRNAs in plant parasitic nematodes.

Competitive displacement of the native species Bursaphelenchus mucronatus by an alien species Bursaphelenchus xylophilus (Nematoda: Aphelenchida: Aphelenchoididae): a case of successful invasion

The presence of alien invasive species has serious negative impact on endemic biodiversity, especially on native species that occupy the same niche in the ecosystem. To study the influence of the alien invasive species Bursaphelenchus xylophilus on its native sister species B. mucronatus, the two nematode species were mix-cultured in a fungal mat and mix-inoculated into a susceptible host. By comparing the propagation parameters of both species under competitive and noncompetitive conditions it was shown that the propagation level of B. xylophilus was clearly higher than that of B. mucronatus under laboratory culture. Furthermore, the propagation capacity of B. xylophilus under competitive conditions was much higher than that under noncompetitive conditions, both in laboratory culture and with host inoculation. Bursaphelenchus xylophilus also excluded B. mucronatus when the two species were cultured as a mixture for a longer time. The relative abundance ratios of the two species in natural pinewoods were also determined by random sampling of dying pine trees from regions with different invasion histories. It was noted that with an increase in invasion years the distribution frequency of B. xylophilus increased while that of B. mucronatus decreased. Experimental tests verified our hypothesis that because of its high fecundity and strong competitive ability, the invasive species B. xylophilus out-competed the native species B. mucronatus and displaced it in natural ecosystems. The successful invasion of B. xylophilus is attributed to competitive displacement, which may be one of the ecological invasive mechanisms.

Analysis of the complete mitochondrial genome of Pochonia chlamydosporia suggests a close relationship to the invertebrate-pathogenic fungi in Hypocreales

BackgroundThe fungus Pochonia chlamydosporia parasitizes nematode eggs and has become one of the most promising biological control agents (BCAs) for plant-parasitic nematodes, which are major agricultural pests that cause tremendous economic losses worldwide. The complete mitochondrial (mt) genome is expected to open new avenues for understanding the phylogenetic relationships and evolution of the invertebrate-pathogenic fungi in Hypocreales.ResultsThe complete mitogenome sequence of P. chlamydosporia is 25,615 bp in size, containing the 14 typical protein-coding genes, two ribosomal RNA genes, an intronic ORF coding for a putative ribosomal protein (rps3) and a set of 23 transfer RNA genes (trn) which recognize codons for all amino acids. Sequence similarity studies and syntenic gene analyses show that 87.02% and 58.72% of P. chlamydosporia mitogenome sequences match 90.50% of Metarhizium anisopliae sequences and 61.33% of Lecanicillium muscarium sequences with 92.38% and 86.04% identities, respectively. A phylogenetic tree inferred from 14 mt proteins in Pezizomycotina fungi supports that P. chlamydosporia is most closely related to the entomopathogenic fungus M. anisopliae. The invertebrate-pathogenic fungi in Hypocreales cluster together and clearly separate from a cluster comprising plant-pathogenic fungi (Fusarium spp.) and Hypocrea jecorina. A comparison of mitogenome sizes shows that the length of the intergenic regions or the intronic regions is the major size contributor in most of mitogenomes in Sordariomycetes. Evolutionary analysis shows that rps3 is under positive selection, leading to the display of unique evolutionary characteristics in Hypocreales. Moreover, the variability of trn distribution has a clear impact on gene order in mitogenomes. Gene rearrangement analysis shows that operation of transposition drives the rearrangement events in Pezizomycotina, and most events involve in trn position changes, but no rearrangement was found in Clavicipitaceae.ConclusionsWe present the complete annotated mitogenome sequence of P. chlamydosporia. Based on evolutionary and phylogenetic analyses, we have determined the relationships between the invertebrate-pathogenic fungi in Hypocreales. The invertebrate-pathogenic fungi in Hypocreales referred to in this paper form a monophyletic group sharing a most recent common ancestor. Our rps3 and trn gene order results also establish a foundation for further exploration of the evolutionary trajectory of the fungi in Hypocreales.

Composition of bacterial communities associated with a plant-parasitic nematode Bursaphelenchus mucronatus.

Bursaphelenchus mucronatus is a plant–parasitic nematode widely existing in Eurasian pine forests. To analyze the diversity and role of bacteria associated with the nematode, culture-dependent and culture-independent methods were used to identify and characterize the composition of bacterial community. A total of 13 bacterial isolates were obtained from B. mucronatus by the culture-dependent method. Sixty-four species of bacteria were identified from two 16S rDNA clone libraries constructed from the nematodes of a Chinese and a Japanese population. These bacteria were clustered into four groups: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Comparison of the two libraries showed that the Chinese library had a higher diversity than that of the Japanese library, and the dominant group and species in each library were also different. In the Japanese library, Alphaproteobacteria group was obviously dominant (60.3%), and Rhizobium sp. was the most dominant species. Whereas in the Chinese library the proportion of each group was similar (from 19.4 to 23.6%), and Pedobacter sp. was a slightly dominant species. Moreover, 18 operational taxonomic units (OTUs) were obtained from each of the two libraries according to a 97% sequence similarity. Metabolic analysis showed that 61.5 and 38.5% of the bacterial isolates could have protease and lipase activities, respectively. But only one had cellulase activity. Testing of reproductive parameter showed that the wild-type nematodes (bacteria carried) could produce more progeny than the bacterium-free nematodes did. So, we speculated that bacteria could promote the propagation and development of the nematode B. mucronatus.

Comparative transcriptomics of two pathogenic pinewood nematodes yields insights into parasitic adaptation to life on pine hosts

Bursaphelenchus xylophilus and Bursaphelenchus mucronatus are migratory endoparasitic nematodes that live in pine trees. To gain insight into their molecular similarities and differences, transcriptomes of the two nematodes were analysed. A total of 23,765 and 21,782 contigs (>300 bp) were obtained from B. xylophilus and B. mucronatus, respectively. More than 80% of the contigs could map to each others transcriptome reciprocally. A total of 23,467 and 21,370 Open Reading Frames were predicted, respectively. Besides those known parasitism-related proteins, six new venom allergen-like proteins (VAPs) were found, which were not homologous to known VAPs. Enzymes involved in xenobiotic biodegradation were abundant in the two transcriptomes based on KEGG functional annotation. Metabolism of xenobiotics by cytochrome P450 comprised the main detoxification pathways. The mRNA expression levels of detoxification genes in nematodes living in the host were higher than those in nematodes feeding on fungus. However, there were fewer enzymes involved in the α-pinene degradation. Our results indicate that the two pinewood nematodes have evolved similar molecular mechanisms to adapt to life on pine hosts.

Impact of Different Economic Factors on Biological Invasions on the Global Scale

Social-economic factors are considered as the key to understand processes contributing to biological invasions. However, there has been few quantified, statistical evidence on the relationship between economic development and biological invasion on a worldwide scale. Herein, using principal factor analysis, we investigated the relationship between biological invasion and economic development together with biodiversity for 91 economies throughout the world. Our result indicates that the prevalence of invasive species in the economies can be well predicted by economic factors (R2 = 0.733). The impact of economic factors on the occurrence of invasive species for low, lower-middle, upper-middle and high income economies are 0%, 34.3%, 46.3% and 80.8% respectively. Greenhouse gas emissions (CO2, Nitrous oxide, Methane and Other greenhouse gases) and also biodiversity have positive relationships with the global occurrence of invasive species in the economies on the global scale. The major social-economic factors that are correlated to biological invasions are different for various economies, and therefore the strategies for biological invasion prevention and control should be different.

Identification of MicroRNAs in Meloidogyne incognita Using Deep Sequencing

MicroRNAs play important regulatory roles in eukaryotic lineages. In this paper, we employed deep sequencing technology to sequence and identify microRNAs in M. incognita genome, which is one of the important plant parasitic nematodes. We identified 102 M. incognita microRNA genes, which can be grouped into 71 nonredundant miRNAs based on mature sequences. Among the 71 miRANs, 27 are known miRNAs and 44 are novel miRNAs. We identified seven miRNA clusters in M. incognita genome. Four of the seven clusters, miR-100/let-7, miR-71-1/miR-2a-1, miR-71-2/miR-2a-2 and miR-279/miR-2b are conserved in other species. We validated the expressions of 5 M. incognita microRNAs, including 3 known microRNAs (miR-71, miR-100b and let-7) and 2 novel microRNAs (NOVEL-1 and NOVEL-2), using RT-PCR. We can detect all 5 microRNAs. The expression levels of four microRNAs obtained using RT-PCR were consistent with those obtained by high-throughput sequencing except for those of let-7. We also examined how M. incognita miRNAs are conserved in four other nematodes species: C. elegans, A. suum, B. malayi and P. pacificus. We found that four microRNAs, miR-100, miR-92, miR-279 and miR-137, exist only in genomes of parasitic nematodes, but do not exist in the genomes of the free living nematode C. elegans. Our research created a unique resource for the research of plant parasitic nematodes. The candidate microRNAs could help elucidate the genomic structure, gene regulation, evolutionary processes, and developmental features of plant parasitic nematodes and nematode-plant interaction.

SSR data mined from expressed sequence tags of phytoparasitic nematodes

SummarySSR markers have become the most popular resource for studying population genetic variation in eukaryotes. However, few studies with SSR markers have been carried out with phytoparasitic nematodes. In this study a primary survey on EST-SSRs was made utilizing bioinformatics methods to derive SSRs from expressed sequence tags (ESTs) of 16 species of PPN, which belong to 7 genera and 5 families. The results showed that trinucleotide repeats were the most abundant SSRs in coding ESTs, while tetranucleotide SSRs were predominant in non-coding ESTs and genome sequences. AG/CT, AAC/GTT and (AAAN)n motifs were predominant, and CG/GC, ACT/AGT motifs were scanty in the ESTs of most genera and species. SSRs were more abundant in non-coding ESTs than in coding ESTs. The distribution frequencies of SSR motifs in coding ESTs, non-coding ESTs and genomes are different. Our results will provide useful information for screening SSRs from each genus and species for further genetic study of phytoparastic nematodes.