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Oiltea-camellia ( C. oleifera ) is a widely cultivated woody oil crop in Southern China and Southeast Asia. The genome of oiltea-camellia was very complex and not well explored. Recently, genomes of three oiltea-camellia species were sequenced and assembled, multi-omic studies of oiltea-camellia were carried out and provided a better understanding of this important woody oil crop. In this review, we summarized the recent assembly of the reference genomes of oiltea-camellia, genes related to economic traits (flowering, photosynthesis, yield and oil component), disease resistance (anthracnose) and environmental stress tolerances (drought, cold, heat and nutrient deficiency). We also discussed future directions of integrating multiple omics for evaluating genetic resources and mining key genes of important traits, and the application of new molecular breeding and gene editing technologies to accelerate the breeding process of oiltea-camellia.

Background Hard ticks act as arthropod vectors in the transmission of human and animal pathogens and are widely distributed in northern China. The aim of this study is to screen the important tick-borne pathogens (TBPs) carried by hard ticks in Inner Mongolia using metagenomic next-generation sequencing (mNGS) and to estimate the risk of human infection imposed by tick bites. Methods The adult Dermacentor nuttalli ( n  = 203) and Ixodes persulcatus ( n  = 36) ticks feeding on cattle were collected. The pooled DNA samples prepared from these ticks were sequenced as the templates for mNGS to survey the presence of TBPs at the genus level. Individual tick DNA samples were detected by genus--specific or group-specific nested polymerase chain reaction (PCR) of these TBPs and combined with DNA sequencing assay to confirm the results of mNGS. Results R. raoultii (45.32%, 92/203), Candidatus R. tarasevichiae (5.42%, 11/203), Anaplasma sp. Mongolia (26.60%, 54/203), Coxiella- like endosymbiont (CLE) (53.69%, 109/203), and Babesia venatorum (7.88%, 16/203) were detected in D. nuttalli , while R. raoultii (30.56%, 11/36), Anaplasma sp. Mongolia (27.80%, 10/36), and CLE (27.80%, 10/36) were detected in I. persulcatus . The double- and triple-pathogen/endosymbiont co-infections were detected in 40.39% of D. nuttalli and 13.89% of I. persulcatus , respectively. The dual co-infection with R. raoultii and CLE (14.29%, 29/203) and triple co-infection with R. raoultii , Anaplasma sp. Mongolia, and CLE (13.79%, 28/203) were most frequent in D. nuttalli . Conclusions This study provides insight into the microbial diversity of D. nuttalli and I. persulcatus in Inner Mongolia, China, reporting for the first time that Candidatus R. tarasevichiae had been found in D. nuttalli in China, and for the first time in the world that Anaplasma sp. Mongolia has been detected in I. persulcatus . This study proves that various vertically transmitted pathogens co-inhabit D. nuttalli and I. persulcatus , and indicates that cattle in Inner Mongolia are exposed to several TBPs. Graphical Abstract

Coxiella burnetii is the etiological agent of the zoonotic disease Q fever, which is featured by its ability to replicate in acid vacuoles resembling the lysosomal network. One key virulence determinant of C . burnetii is the Dot/Icm system that transfers more than 150 effector proteins into host cells. These effectors function to construct the lysosome-like compartment permissive for bacterial replication, but the functions of most of these effectors remain elusive. In this study, we used an affinity tag purification mass spectrometry (AP-MS) approach to generate a C . burnetii -human protein-protein interaction (PPI) map involving 53 C . burnetii effectors and 3480 host proteins. This PPI map revealed that the C . burnetii effector CBU0425 (designated CirB) interacts with most subunits of the 20S core proteasome. We found that ectopically expressed CirB inhibits hydrolytic activity of the proteasome. In addition, overexpression of CirB in C . burnetii caused dramatic inhibition of proteasome activity in host cells, while knocking down CirB expression alleviated such inhibitory effects. Moreover, we showed that a region of CirB that spans residues 91–120 binds to the proteasome subunit PSMB5 (beta 5). Finally, PSMB5 knockdown promotes C . burnetii virulence, highlighting the importance of proteasome activity modulation during the course of C . burnetii infection.

Q fever is a worldwide zoonosis caused by Coxiella burnetii (Cb). From January 2018 to November 2019, plasma samples from 2,382 patients with acute fever of unknown cause at a hospital in Zhuhai city of China were tested using metagenomic next-generation sequencing (mNGS). Of those tested, 138 patients (5.8%) were diagnosed with Q fever based on the presence of Cb genomic DNA detected by mNGS. Among these, 78 cases (56.5%) presented from Nov 2018 to Mar 2019, suggesting an outbreak of Q fever. 55 cases with detailed clinical information that occurred during the outbreak period were used for further analysis. The vast majority of plasma samples from those Cb-mNGS-positive patients were positive in a Cb-specific quantitative polymerase chain reaction (n = 38) and/or indirect immunofluorescence assay (n = 26). Mobile phone tracing data was used to define the area of infection during the outbreak. This suggested the probable infection source was Cb-infected goats and cattle at the only official authorized slaughterhouse in Zhuhai city. Phylogenic analysis based on genomic sequences indicated Cb strains identified in the patients, goat and cattle were formed a single branch, most closely related to the genomic group of Cb dominated by strains isolated from goats. Our study demonstrates Q fever was epidemic in 2018–2019 in Zhuhai city, and this is the first confirmed epidemic of Q fever in a contemporary city in China.

ABSTRACT Introduction Previous studies have reported inconsistent findings regarding the associationbetween ALK and ROS1 rearrangements in lung cancer and thromboembolic risk. This retrospective study aimed to investigate this association in advanced lung adenocarcinoma patients with ALK, ROS1, RET rearrangements, and EGFR mutations. Materials and Methods We retrospectively collected information on patients with advanced lung adenocarcinoma in the First Affiliated Hospital of Zhejiang University School of Medicine from January 2013 to March 2021. All patients with confirmed ALK, ROS1, or RET rearrangements, as well as a comparison cohort of those with EGFR mutation, were included. Clinical characteristics were analyzed, and the association between driver genes and TE risks was analyzed using competing risk and logistic regression. Results A total of 546 patients were included in the study. Among them, those with ROS1 rearrangements exhibited the highest cumulative incidence of thromboembolic events (TEs), reaching 17.5% ± 0.2% during the peri‐diagnostic period (within 6 months following diagnosis). Regardless of the entire follow‐up or the peri‐diagnostic period, ROS1 rearrangements were significantly associated with an increased risk of TEs. Multivariate analysis revealed ROS1 rearrangements, the number of comorbidities, the size of mediastinal lymph nodes, and elevated C‐reactive protein (CRP) levels as TE risk factors during the peri‐diagnostic period. Throughout the follow‐up period, ROS1 rearrangements and hypertension were independent TE risk factors. In addition, the development of TE significantly affected the overall survival of patients with EGFR mutations. Conclusion ROS1 rearrangements were significantly associated with an increased risk of TE. In this retrospective study of 546 lung adenocarcinoma patients with four different driver genes, ROS1 rearrangements were associated with the increased risk of thromboembolic events (TEs), particularly during the peri‐diagnostic period (6 months before and after diagnosis). Risk factors of TEs during the peri‐diagnostic period included ROS1 rearrangements, multiple comorbidities, enlarged mediastinal lymph nodes, and elevated CRP levels.

Infectious bursal disease (IBD) is an acute, highly contagious, and immunosuppressive avian disease caused by IBD virus (IBDV). MicroRNAs (miRNAs) are involved in host-pathogen interactions and innate immune response to viral infection. However, the role of miRNAs in host response to IBDV infection is not clear. We report here that gga-miR-155 acts as an anti-virus host factor inhibiting IBDV replication. We found that transfection of DF-1 cells with gga-miR-155 suppressed IBDV replication, while blockage of the endogenous gga-miR-155 by inhibitors enhanced IBDV replication. Furthermore, our data showed that gga-miR-155 enhanced the expression of type I interferon in DF-1 cells post IBDV infection. Importantly, we found that gga-miR-155 enhanced type I interferon expression via targeting SOCS1 and TANK, two negative regulators of type I IFN signaling. These results indicate that gga-miR-155 plays a critical role in cell response to IBDV infection.

Sinocyclocheilus jii , a cavefish species endemic to China, belongs to the genus Sinocyclocheilus within the family Cyprinidae. Species within this genus exhibit significant morphological differentiation, making it not only the most species-rich genus within Cyprinidae in China but also the most diverse group of cavefishes worldwide. However, the limited availability of genomic resources has limited investigations into the genetic basis of trait variations, phylogenetic relationships, and adaptive evolution in this genus. In this study, we assembled a chromosome-level reference genome for S. jii by integrating PacBio HiFi long reads, Illumina short reads, and Hi-C sequencing data. Flow cytometry was used to estimate the genome size prior to assembly, providing a key step in technical validation. The final genome assembly spans 1.75 Gb with a contig N50 of 35.0 Mb. Using Hi-C sequencing data, the assembled scaffolds were successfully anchored to 50 chromosomes. The completeness of the chromosome-level assembly was estimated at 98.9% by BUSCO analysis. Genome annotation identified 855.5 Mb of repetitive sequences and predicted a total of 52,867 protein-coding genes, of which 51,932 genes were functionally annotated. This study presents a high-quality chromosome-level genome assembly and annotation of S. jii , providing a fundamental genomic resource for future phylogenetic and evolutionary studies.

Avian reoviruses (ARV) are a group of poultry pathogens that cause runting and stunting syndrome (RSS), a condition otherwise known as “frozen chicken”, which are characterized by dramatically delayed growth in broilers. It has been known that p17, a nonstructural protein encoded by ARV, prohibits cellular proliferation by halting the cell cycle at the G2/M phase, the result of which is directly associated with the typical clinical sign of RSS. Nevertheless, the mechanism by which p17 modulates cell-cycle progression remains largely unknown. Here, we screened the interactome of ectopically expressed p17 through a yeast two-hybrid assay and identified Bub3, a cellular mitotic checkpoint protein, as a binding partner of p17. The infection of the Vero cells by ARV downregulated the Bub3 expression, while the knockdown of Bub3 alleviated the p17-modulated cell-cycle arrest during ARV infection. Remarkably, the suppression of Bub3 by RNAi in the Vero cells significantly reduced the viral mRNA and protein abundance, which eventually led to diminished virus replication. Altogether, our findings reveal that ARV p17 impedes host cell proliferation through a Bub3-dependent cell-cycle arrest, which eventually contributes to efficient virus replication. These results also unveil a hitherto unknown therapeutic target for RSS.

Background Coxiella burnetii (Cb) is the causative agent of the zoonotic disease Q fever which is distributed worldwide. Molecular typing of Cb strains is essential to find out the infectious source and prevent Q fever outbreaks, but there has been a lack of typing data for Cb strains in China. The aim of this study was to investigate the genotypes of Cb strains in wild rats in Yunnan Province, China. Results Eighty-six wild rats ( Rattus flavipectus ) were collected in Yunnan Province and 8 of the 86 liver samples from the wild rats were positive in Cb-specific quantitative PCR (qPCR). The Cb strains from the 8 rats were then typed into 3 genotypes using 10-spacer multispacer sequence typing (MST), and 2 of the 3 genotypes were recognized as novel ones. Moreover, the Cb strains in the wild rats were all identified as genotype 1 using 6-loci multilocus variable number of tandem repeat analysis (MLVA). Conclusions This is the first report of genotypic diversity of Cb strains from wild rats in China. Further studies are needed to explore the presence of more genotypes and to associate the genotypes circulating in the wildlife-livestock interaction with those causing human disease to further expand on the epidemiological aspects of the pathogen.

Q fever is a worldwide zoonosis caused by Coxiella burnetii. Human Q fever is typically acquired through inhalation of contaminated aerosols, resulting in an initial pulmonary infection. In this study, BALB/c mice were infected with C. burnetii via an intratracheal (IT) route using a non-invasive aerosol pulmonary delivery device to directly place the living C. burnetii organisms into the lungs of the mice. The bacterial loads, pathological lesions, and antibody and cellular responses were analyzed and compared with those of mice infected via an intraperitoneal (IP) route. Compared with mice infected via an IP route, mice infected via an IT route exhibited a higher bacterial load and more severe pathological lesions in the heart and lungs at days 3 and 7 post-infection (pi). The levels of interferon-γ and IL-12p70 in the serum of mice infected via the IT route were significantly higher than those of mice infected via the IP route at day 3 pi. In conclusion, this murine model of acute C. burnetii infection via IT inoculation closely resembles the natural route of C. burnetii infection than that of IP injection. Thus, this newly developed model will be useful for investigating the pathogenesis and immunity of C. burnetii aerosol infection, as well as for the evaluation of therapeutic drugs and preventive vaccines of Q fever.