Detection of viral genes in Metarhizium anisopliae JEF-290-infected longhorned tick, Haemaphysalis longicornis using transcriptome analysis.

Ticks are carriers of viruses that can cause disease in humans and animals. The longhorned ticks (Haemaphysalis longicornis; LHT), for example, mediates the severe fever with thrombocytopenia syndrome virus (SFTSV) in humans, and the population of ticks is growing due to increases in temperature caused by climate change. As ticks carry primarily RNA viruses, there is a need to study the possibility of detecting new viruses through tick virome analysis. In this study, viruses in LHTs collected in Korea were investigated and virus titers in ticks exposed to the entomopathogenic fungus Metarhizium anisopliae JEF-290 were analyzed. Total RNA was extracted from the collected ticks, and short reads were obtained from Illumina sequencing. A total of 50,024 contigs with coding capacity were obtained after de novo assembly of the reads in the metaSPAdes genome assembler. A series of BLAST-based analyses using the GenBank database was performed to screen viral contigs, and three putative virus species were identified from the tick meta-transcriptome, such as Alongshan virus (ALSV), Denso virus and Taggert virus. Measurements of virus-expression levels of infected and non-infected LHTs failed to detect substantial differences in expression levels. However, we suggest that LHT can spread not only SFTSV, but also various other disease-causing viruses over large areas of the world. From the phylogenetic analysis of ALSV glycoproteins, genetic differences in the ALSV could be due to host differences as well as regional differences. Viral metagenome analysis can be used as a tool to manage future outbreaks of disease caused by ticks by detecting unknown viruses.

Pathogenesis and defense mechanism while Beauveria bassiana JEF-410 infects poultry red mite, Dermanyssus gallinae.

The poultry red mite, Dermanyssus gallinae (Mesostigmata: Dermanyssidae), is a major pest that causes great damage to chicken egg production. In one of our previous studies, the management of red mites using entomopathogenic fungi was evaluated, and the acaricidal fungus Beauveria bassiana JEF-410 was selected for further research. In this study, we tried to elucidate the pathogenesis of B. bassiana JEF-410 and the defense mechanisms of red mites at a transcriptome level. Red mites collected from a chicken farm were treated with B. bassiana JEF-410. When the mortality of infected red mites reached 50%, transcriptome analyses were performed to determine the interaction between B. bassiana JEF-410 and red mites. Uninfected red mites and non-infecting fungus served as controls. In B. bassiana JEF-410, up-regulated gene expression was observed in tryptophan metabolism and secondary metabolite biosynthesis pathways. Genes related to acetyl-CoA synthesis were up-regulated in tryptophan metabolism, suggesting that energy metabolism and stress management were strongly activated. Secondary metabolites associated with fungal up-regulated DEGs were related to the production of substances toxic to insects such as beauvericin and beauveriolide, efflux pump of metabolites, energy production, and resistance to stress. In red mites, physical and immune responses that strengthen the cuticle against fungal infection were highly up-regulated. From these gene expression analyses, we identified essential factors for fungal infection and subsequent defenses of red mites. These results will serve as a strong platform for explaining the interaction between B. bassiana JEF-410 and red mites in the stage of active infection.

Management of overwintering pine sawyer beetle, Monochamus alternatus with colonized Beauveria bassiana ERL836.

Monochamus alternatus is a major forest pest that spreads pine wilt disease in pine trees as a vector of pine wilt nematodes. Chemical insecticides used as fumigants to control overwintering M. alternatus in forests are highly toxic to the environment, so we investigated entomopathogenic fungus Beauveria bassiana ERL836 as an eco-friendly and alternative material to control overwintering M. alternatus. In this work, we evaluated the insecticidal activity of B. bassiana ERL836 against M. alternatus adults, the possibility of fungal colonization on pine tree bark, and finally the control efficacy of fungal pre-treatment on pine tree logs against emerging M. alternatus adults in semi-field and field conditions. M. alternatus adults were killed on the pine tree logs pre-treated with the B. bassiana ERL836. White conidia were observed not only on the surface of the dead adults but also on the pine tree logs, suggesting that the adults were killed by the fungus on the pine. A formulated ERL836 powder treatment on larvae-infested pine logs showed high insecticidal activity against adults, similar to that with the fungal powder suspension treatment, but we demonstrated that using the fungal powder was simpler than using the suspension in field conditions. Even in the field condition, the fungal powder treatment showed high insecticidal activity against M. alternatus adults, which we attribute to its ability to maintain fungal activity for a long time in field conditions by covering the pine tree logs with a film during overwintering. We confirmed that the risk that fungus-infected M. alternatus adults would spread the fungus to other non-target forest insects was low. Thus, even a high-concentration treatment in a specific area is unlikely to transmit the fungus outside that area, so it can be safely used to control this pine wilt nematode vector in forest ecosystems.

Whole-Genome Sequence of Beauveria bassiana JEF-350, a Strain with High Insecticidal Activity against Melon Thrips (Thrips palmi).

The entomopathogenic fungus Beauveria bassiana JEF-350 was isolated from forest soil in South Korea. Here, we report the whole-genome sequence of JEF-350, along with the analyzed genetic information, which can be used to study insecticidal mechanisms and fungal diversity.

General circulation and global heat transport in a quadrupling CO2 pulse experiment.

To investigate the response of the general circulation and global transport of heat through both atmosphere and ocean to two-types of carbon dioxide removal scenario, we performed an earth system model experiment in which we imposed a pulse-type quadrupling of CO2 forcing for 50 years and a gradual peak-and-decline of four-time CO2 forcing. We found that the results from two experiments are qualitatively similar to each other. During the forcing-on period, a dominant warming in the upper troposphere over the tropics and on the surface at high latitudes led to a slowdown in the Hadley circulation, but the poleward atmospheric energy transport was enhanced due to an increase in specific humidity. This counteracted the reduction in poleward oceanic energy transport owing to the suppression of the meridional overturning circulation in both Hemispheres. After returning the original CO2 level, the hemispheric thermal contrast was reversed, causing a southward shift of the intertropical convergence zone. To reduce the hemispheric thermal contrast, the northward energy transports in the atmosphere and ocean surface were enhanced while further weakening of the global-scale Atlantic meridional overturning circulation led to southward energy transport in the deep ocean.

Early-Stage Defense Mechanism of the Cotton Aphid Aphis gossypii Against Infection With the Insect-Killing Fungus Beauveria bassiana JEF-544.

Aphis gossypii, commonly known as the cotton aphid, is a widely distributed pest of agricultural crops and acts as a vector for many serious plant viruses. Cotton aphid shows high resistance to chemical insecticides due to rapid rates of genetic diversity as a result of its short life cycle, seasonal migration, and host alteration. As an alternative, entomopathogenic fungi can be used to control cotton aphids in an environmentally sound manner. However, little is known about how cotton aphids respond to fungal infection. In this work, a new Beauveria bassiana strain JEF-544 (Bb JEF-544) was selected and isolated through bioassays with high virulence against cotton aphid. Early response of cotton aphid to Bb JEF-544 infection was analyzed at the transcriptome level. Infected aphids were collected two days after treatment at 25% lethal time (LT25), and total RNA of non-infected and Bb JEF-544-infected aphids was independently subjected to sequencing. Infected aphids showed significant up-regulation of the insect hormone biosynthesis pathway. Bursicon (Burs) and crustacean cardioactive peptide (CCAP) receptors involved in molting along with ecdysone synthesis were also strongly up-regulated in the aphid response to the fungal infection. In the immune response, melanization in the hemocoel was significantly up-regulated, while phagocytosis was less actively transcribed. In conclusion, cotton aphids protect themselves from Bb JEF-544 infection by activating the immune response including melanization and insect molting hormones to shed infected cuticles. In addition to describing the initial stages of Bb JEF-544 infection at the transcriptome level, this work provides potential treatment targets and insight into how fungal isolates can effectively be used to control this serious aphid species.

Distinctive Roles of Two Acinetobactin Isomers in Challenging Host Nutritional Immunity.

The human pathogen Acinetobacter baumannii produces and utilizes acinetobactin for iron assimilation. Although two isomeric structures of acinetobactin, one featuring an oxazoline (Oxa) and the other with an isoxazolidinone (Isox) at the core, have been identified, their differential roles as virulence factors for successful infection have yet to be established. This study provides direct evidence that Oxa supplies iron more efficiently than Isox, primarily owing to its specific recognition by the cognate outer membrane receptor, BauA. The other components in the acinetobactin uptake machinery appear not to discriminate these isomers. Interestingly, Oxa was found to form a stable iron complex that is resistant to release of the chelated iron upon competition by Isox, despite their comparable apparent affinities to Fe(III). In addition, both Oxa and Isox were found to be competent iron chelators successfully scavenging iron from host metal sequestering proteins responsible for nutritional immunity. These observations collectively led us to propose a new model for acinetobactin-based iron assimilation at infection sites. Namely, Oxa is the principal siderophore mediating the core Fe(III) supply chain for A. baumannii, whereas Isox plays a minor role in the iron delivery and, alternatively, functions as an auxiliary iron collector that channels the iron pool toward Oxa. The unique siderophore utilization mechanism proposed here represents an intriguing strategy for pathogen adaptation under the various nutritional stresses encountered at infection sites. IMPORTANCE Acinetobacter baumannii has acquired antibiotic resistance at an alarming rate, and it is becoming a serious threat to society, particularly due to the paucity of effective treatment options. Acinetobactin is a siderophore of Acinetobacter baumannii, responsible for active iron supply, and it serves as a key virulence factor to counter host nutritional immunity during infection. While two acinetobactin isomers were identified, their distinctive roles for successful infection of Acinetobacter baumannii remained unsettled. This study clearly identified the isomer containing an oxazoline core as the principal siderophore based on comparative analysis of the specificity of the acinetobactin uptake machinery, the stability of the corresponding iron complexes, and the iron scavenging activity against the host iron sequestering proteins. Our findings are anticipated to stimulate efforts to discover a potent antivirulence agent against Acinetobacter baumannii that exploits the acinetobactin-based iron assimilation mechanism.

Interactive Gene Expression Between Metarhizium anisopliae JEF-290 and Longhorned Tick Haemaphysalis longicornis at Early Stage of Infection.

The longhorned tick, Haemaphysalis longicornis (Acari: Ixodidae), is a hard tick and a vector for severe fever with thrombocytopenia syndrome (SFTS) virus. The number of patients infected with SFTS is rapidly increasing. Recently, the invertebrate pathogen Metarhizium anisopliae JEF-290 was reported to be useful to control the tick as an alternative to chemical acaricides, which are not easily applicable in human living areas where the tick is widely spread. In this study, we analyzed how the tick and the fungal pathogen interact at the transcriptional level. Field-collected tick nymphs were treated with JEF-290 conidia at 1 × 108 conidia/ml. In the early stage of infection with 2.5% mortality, the infected ticks were subjected to RNA sequencing, and non-infected ticks and fungal masses served as controls. Fungus and tick genes were mostly up-regulated at the early stage of infection. In the gene set enrichment analysis of the infecting fungus, catabolic processes that included lipids, phospholipids, and detoxification processes, the response to oxidative stress, and toxic substances were significantly up-regulated. In this fungal up-regulation, various lipase, antioxidant enzyme, and hydrolase genes were highly transcribed. The gene set enrichment analysis of the infected tick showed that many peptide synthesis processes including translation, peptide metabolism, ribonucleotide metabolism, and energy production processes that included ATP generation and ADP metabolism were significantly up-regulated. Structurally, mitochondria and ribosome subunit genes in ticks were highly transcribed to upregulate these processes. Together these results indicate that JEF-290 initiates process that infects the tick while the tick actively defends against the fungal attack. This work provides background to improve our understanding of the early stage of fungal infection in longhorned tick.

Transcriptome Analysis of the Japanese Pine Sawyer Beetle, Monochamus alternatus, Infected with the Entomopathogenic Fungus Metarhizium anisopliae JEF-197.

The Japanese pine sawyer (JPS) beetle, Monochamus alternatus Hope (Coleoptera: Cerambycidae), damages pine trees and transmits the pine wilt nematode, Bursaphelenchus xylophilus Nickle. Chemical agents have been used to control JPS beetle, but due to various issues, efforts are being made to replace these chemical agents with entomopathogenic fungi. We investigated the expression of immune-related genes in JPS beetle in response to infection with JEF-197, a Metarhizium anisopliae isolate, using RNA-seq. RNA samples were obtained from JEF-197, JPS adults treated with JEF-197, and non-treated JPS adults on the 8th day after fungal treatment, and RNA-seq was performed using Illumina sequencing. JPS beetle transcriptome was assembled de novo and differentially expressed gene (DEG) analysis was performed. There were 719 and 1953 up- and downregulated unigenes upon JEF-197 infection, respectively. Upregulated contigs included genes involved in RNA transport, ribosome biogenesis in eukaryotes, spliceosome-related genes, and genes involved in immune-related signaling pathways such as the Toll and Imd pathways. Forty-two fungal DEGs related to energy and protein metabolism were upregulated, and genes involved in the stress response were also upregulated in the infected JPS beetles. Together, our results indicate that infection of JPS beetles by JEF-197 induces the expression of immune-related genes.

Gene-disruption of the entomopathogenic fungus Beauveria bassiana incubated with dsRNA.

The species of Beauveria bassiana is widely used for the management of agricultural insect pests. In this study, we integrated egfp-double-stranded RNA (dsRNA) to a previously generated egfp-expressing B. bassiana transformant (Bb-egfp#3) using a protoplast integration method. The Bb-egfp#3 protoplast was mixed with the dsRNA under PEG/CaCl2 conditions and liquid-cultured in Sabouraud dextrose broth for 5 days. A control culture followed the same procedure without dsRNA. Bb-egfp#3/egfp-dsRNA cultures showed very low fungal growth (OD630 = 0.2) compared to the control culture, Bb-egfp#3 only (OD630 = 1.1). Screening of possible transformants on Sabouraud dextrose agar revealed a transformant T3, without egfp signal. T3 was confirmed as B. bassiana through sequencing of conserved genes and insect bioassays. Interestingly, the genomic egfp fragment of T3 was disrupted, and the egfp signal was not detected over four subcultures, which was also confirmed by RNA-seq of Bb-egfp#3 and T3. This study provides an interesting observation that protoplast integration with dsRNA could possibly generate significantly reduced gene expression in B. bassiana and it is stable across several generations.

Gene diversity explains variation in biological features of insect killing fungus, Beauveria bassiana.

Beauveria bassiana is a species complex whose isolates show considerable natural genetic variability. However, little is known about how this genetic diversity affects the fungus performance. Herein, we characterized the diversity of genes involved in various mechanisms of the infective cycle of 42 isolates that have different growth rates, thermotolerance and virulence. The analysed genes showed general genetic diversity measured as non-synonymous changes (NSC) and copy number variation (CNV), with most of them being subjected to positive episodic diversifying selection. Correlation analyses between NSC or CNV and the isolate virulence, thermotolerance and growth rate revealed that various genes shaped the biological features of the fungus. Lectin-like, mucin signalling, Biotrophy associated and chitinase genes NSCs correlated with the three biological features of B. bassiana. In addition, other genes (i.e. DNA photolyase and cyclophilin B) that had relatively conserved sequences, had variable CNs across the isolates which were correlated with the variability of either virulence or thermotolerance of B. bassiana isolates. The data obtained is important for a better understanding of population structure, ecological and potential impact when isolates are used as mycoinsecticides and can justify industrialization of new isolates.

Beauveria bassiana ERL836 and JEF-007 with similar virulence show different gene expression when interacting with cuticles of western flower thrips, Frankniella occidentalis.

BACKGROUND: Insect-killing fungal species, Beauveria bassiana, is as an environment-friendly pest management tool, and many isolates are on the track of industrialization. However, some of B. bassiana isolates show similar morphology and virulence against insect pests, and so it is hard to differentiate them. Herein we used two patented isolates, ERL836 and JEF-007, and investigated their virulence against western flower thrips, Frankliniella occidentalis, and further analyzed genome structures and transcriptional responses when interacting with cuticles of thrips to see possible differences on the initial step of fungal infection. RESULTS: The two isolates showed no significant differences in fungal growth, conidial production, and virulence against thrips, and they were structurally similar in genome. But, in transcription level, ERL836 appeared to infect thrips easily, while JEF-007 appeared to have more difficulty. In the GO analysis of ERL836 DEGs (differentially expressed genes), the number of up-regulated genes was much larger than that of down-regulated genes, when compared to JEF-007 DEGs (more genes down-regulated). Interestingly, in the enrichment analysis using shared DEGs between two infecting isolates, plasma membrane-mediated transporter activity and fatty acid degradation pathway including cytochrome P450 were more active in infecting ERL836. CONCLUSION: The two B. bassiana isolates had similar morphology and virulence as well as genome structure, but in transcription level they differently interacted with the cuticle of western flower thrips. This comparative approach using shared DEG analysis could be easily applied to characterize the difference of the two B. bassiana isolates, JEF-007 and ERL836.

Pathogenesis-related genes of entomopathogenic fungi.

All living things on Earth experience various diseases such as those caused by viruses, bacteria, and fungi. Insects are no exception to this rule, and fungi that cause disease in insects are called entomopathogenic fungi. These fungi have been developed as microbial insecticides and are used to control various pests. Generally, the mode of action of entomopathogenic fungi is divided into the attachment of conidia, germination, penetration, growth, and generation of secondary infectious conidia. In each of these steps, that entomopathogenic fungi use genes in a complex manner (specific or diverse) has been shown by gene knock-out and RNA-sequencing analysis. In this review, the information mechanism of entomopathogenic fungi was divided into six steps: (1) attachment of conidia to host, (2) germination and appressorium, (3) penetration, (4) fungal growth in hemolymph, (5) conidia production on host, and (6) transmission and dispersal. The strategy used by the fungi in each step was described at the genetic level. In addition, an approach for studying the mode of action of the fungi is presented.

Soil Application of Metarhizium anisopliae JEF-314 Granules to Control, Flower Chafer Beetle, Protaetia brevitarsis seulensis.

Root-feeding Scarabaeidae, particularly white grubs are considered among the most harmful coleopteran insect pests in turfgrass. In this work, sixteen entomopathogenic fungal species were assayed against flower chafer beetle, Protaetia brevitarsis (Coleoptera: Scarabaeidae) and Metarhizium anisopliae JEF-314 showed high virulence. The control ability of the isolate JEF-314 has been in detail tested for a model insect flower chafer beetle. Further analyses showed insect stage-dependent virulence where the fungal virulence was the highest against smaller instar larvae. Additionally, we confirmed that millet-based solid cultured granule was effective against the soil-dwelling larval stage. The isolate also showed a similar ability for a representative pest (Popillia spp.) in laboratory conditions. Our results clearly suggest a high potential of M. anisopliae JEF-314 to control the flower chafer beetle, possibly resulting in controlling of root-feeding white grubs in turfgrass. Based on the insect life cycle and susceptibility to the fungus, late spring and summer time would be the optimum time to apply JEF-314 granules for an effective control. Further characterization of the efficacy of the fungus under field conditions against the Scarabaeidae beetles might provide an efficient tool to control this beetle in an environment-friendly way.

Colonization of Metarhizium anisopliae on the surface of pine tree logs: A promising biocontrol strategy for the Japanese pine sawyer, Monochamus alternatus.

We investigated the colonization potential of five Metarhizium anisopliae isolates on pine tree surfaces under laboratory conditions, determined the influence of the pine bark extract on fungal growth and evaluated the insecticidal activity following colonization on the Japanese pine sawyer. Finally, the effect of colonization on adults pine sawyer was evaluated using the top three performing isolates (JEF-197, JEF-271 and JEF-279) under laboratory and field conditions. As a result, isolate JEF-197 showed the highest conidial production on the pine surfaces, and five isolates, including JEF-197, showed higher hyphal growth on autoclaved pine bark extract agar, compared to a water agar. Pine bark treated with the isolates showed 40-70 % mortality of adults pine sawyer. Under mimicked overwintering conditions, in the JEF-197 treatment group, 40 % of the inserted larvae became adults and all were dead after 59 d. In a field test, colonized isolate JEF-197 also showed 37 % insecticidal activity against emerged adults from the pine logs as overwintering sites. This work suggests that M. anisopliae isolate JEF-197 possibly colonized the pine surface and application of a conidial suspension on the pine logs as overwintering sites could be an effective strategy to control the pine sawyer.

High A20 expression negatively impacts survival in patients with breast cancer.

BACKGROUND: A20 protein has ubiquitin-editing activities and acts as a key regulator of inflammation and immunity. Previously, our group showed that A20 promotes tumor metastasis through multi-monoubiquitylation of SNAIL1 in basal-like breast cancer. Here, we investigated survival outcomes in patients with breast cancer according to A20 expression. PATIENTS AND METHODS: We retrospectively collected tumor samples from patients with breast cancer. Immunohistochemistry (IHC) with an A20-specific antibody was performed, and survival outcomes were analyzed. RESULTS: A20 expression was evaluated in 442 patients. High A20 expression was associated with advanced anatomical stage and young age. High A20 expression showed significantly inferior recurrence-free-survival and overall-survival (P<0.001 and P<0.001, respectively). Multivariate analysis showed that A20 was an independent prognostic marker for RFS (HRs: 2.324, 95% CIs: 1.446-3.736) and OS (HRs: 2.629, 95% CIs: 1.585-4.361). In human epidermal growth factor receptor 2 (HER2)-positive and triple negative breast cancer (TNBC) subtypes, high A20 levels were associated with poor OS. CONCLUSION: We found that A20 expression is a poor prognostic marker in breast cancer. The prognostic impact of A20 was pronounced in aggressive tumors, such as HER2-positive and TNBC subtypes. Our findings suggested that A20 may be a valuable target in patients with aggressive breast cancer.

Use of Metarhizum aniopliae s.l. to control soil-dwelling longhorned tick, Haemaphysalis longicornis.

The longhorned tick (bush tick),Haemaphysalis longicornis (Ixodida: Ixodidae), is a serious pest; it transmits the severe fever with thrombocytopenia syndrome (SFTS) virus to humans and has a wide distribution. The use of chemical control is not favored for environmental and health reasons, so more environmentally sound management methods need to be developed. Herein, we describe the use of an entomopathogenic fungal library to develop a fungus-mediated tick management system. Field-collected nymphs were assayed for their susceptibility to entomopathogenic fungi belonging to genera Beauveria, Metarhizium, Cordyceps, and Akanthomyces. Three M. anisopliae s.l. isolates, JEF-214, -279, and -290 showed high virulence in a dose-dependent manner. One Cordyceps isolate was pathogenic but virulence was much lower than the M. anisopliae isolates. Beauveria isolates were not pathogenic to the tick. Because the longhorned tick dwells on the soil surface except for blood-feeding periods, the soil surface was sprayed with conidial suspensions of the isolates after the release of longhorned ticks. The treatments resulted in 60-90% mortality after 30 days. M. anisopliae s.l. isolates were highly virulent against longhorned tick, and the application of fungus-based biopesticides on the soil surface could be an effective control strategy to reduce the tick population for long-term tick management.

Immediate Breast Reconstruction Does Not Have a Clinically Significant Impact on Adjuvant Treatment Delay and Subsequent Survival Outcomes.

PURPOSE: The use of immediate breast reconstruction (IBR) has been debated because it may be a causative factor in adjuvant treatment delay and may subsequently increase the probability of recurrence. We investigated whether IBR was related to adjuvant treatment delay and survival outcomes. METHODS: We retrospectively analyzed the duration from operation to adjuvant treatment administration and survival outcomes according to IBR status among patients with breast cancer who underwent mastectomy followed by adjuvant chemotherapy from January 2005 to December 2014. Propensity score matching was performed to balance the clinicopathologic baseline characteristics between patients who did and did not undergo IBR. RESULTS: Of 646 patients, 107 (16.6%) underwent IBR, and the median follow-up was 72 months. The median duration from surgery to adjuvant chemotherapy was significantly longer in patients who underwent IBR than in those who did not (14 vs. 12 days, respectively, p = 0.008). Based on propensity score matching, patients who underwent IBR received adjuvant therapy 3 days later than those who did not (14 vs. 11 days, respectively, p = 0.044). The duration from surgery to post-mastectomy radiation therapy (PMRT) did not significantly differ between the 2 groups. Local recurrence-free survival, regional recurrence-free survival, systemic recurrence-free survival, and overall survival were also not significantly different between the 2 groups (p = 0.427, p = 0.445, p = 0.269, and p = 0.250, respectively). In the case-matched cohort, survival outcomes did not change. CONCLUSION: IBR was associated with a modest increase in the duration from surgery to chemotherapy that was statistically but not clinically significant. Moreover, IBR had no influence on PMRT delay or survival outcomes, suggesting that it is an acceptable option for patients with non-metastatic breast cancer undergoing mastectomy.

SEQprocess: a modularized and customizable pipeline framework for NGS processing in R package.

BACKGROUNDS: Next-Generation Sequencing (NGS) is now widely used in biomedical research for various applications. Processing of NGS data requires multiple programs and customization of the processing pipelines according to the data platforms. However, rapid progress of the NGS applications and processing methods urgently require prompt update of the pipelines. Recent clinical applications of NGS technology such as cell-free DNA, cancer panel, or exosomal RNA sequencing data also require appropriate customization of the processing pipelines. Here, we developed SEQprocess, a highly extendable framework that can provide standard as well as customized pipelines for NGS data processing. RESULTS: SEQprocess was implemented in an R package with fully modularized steps for data processing that can be easily customized. Currently, six pre-customized pipelines are provided that can be easily executed by non-experts such as biomedical scientists, including the National Cancer Institute's (NCI) Genomic Data Commons (GDC) pipelines as well as the popularly used pipelines for variant calling (e.g., GATK) and estimation of allele frequency, RNA abundance (e.g., TopHat2/Cufflink), or DNA copy numbers (e.g., Sequenza). In addition, optimized pipelines for the clinical sequencing from cell-free DNA or miR-Seq are also provided. The processed data were transformed into R package-compatible data type 'ExpressionSet' or 'SummarizedExperiment', which could facilitate subsequent data analysis within R environment. Finally, an automated report summarizing the processing steps are also provided to ensure reproducibility of the NGS data analysis. CONCLUSION: SEQprocess provides a highly extendable and R compatible framework that can manage customized and reproducible pipelines for handling multiple legacy NGS processing tools.