Baylisascaris schroederi,a roundworm(ascaridoid)parasite specific to the bamboo-feeding giant panda(Ailuropoda melanoleuca),represents a leading cause of mortality in wild giant panda populations.Here,we present a 293-megabase chromosome-level genome assembly of B.schroederi to infer its biology,including host adaptations.Comparative genomics revealed an evolutionary trajectory accompanied by host-shift events in ascaridoid parasite lineages after host separations,suggesting their potential for transmission and rapid adaptation to new hosts.Genomic and anatomical lines of evidence,including expansion and positive selection of genes related to the cuticle and basal metabolisms,indicate that B.schroederi undergoes specific adaptations to survive in the sharp-edged bamboo-enriched gut of giant pandas by structurally increasing its cuticle thickness and efficiently utilizing host nutrients through gut parasitism.Additionally,we characterized the secretome of B.schroederi and predicted potential drug and vaccine targets for new control strategies.Overall,this genome resource provides new insights into the host adaptation of B.schroederi to the giant panda as well as the host-shift events in ascaridoid parasite lineages.Our findings on the unique biology of B.schroederi will also aid in the development of prevention and treatment measures to protect giant panda populations from roundworm parasitism.

COVID-19/virology* ; China/epidemiology* ; Disease Outbreaks ; Genetic Linkage ; Humans ; Phylogeny ; Polymorphism, Single Nucleotide ; SARS-CoV-2/isolation & purification*

In the past ten years, the research and application of microbiome has continued to increase. The microbiome has gradually become the research focus in the fields of life science, environmental science, and medicine. Meanwhile, many countries and organizations around the world are launching their own microbiome projects and conducting a multi-faceted layout, striving to gain a strategic position in this promising field. In addition, whether it is scientific research or industrial applications, there has been a climax of research and a wave of investment and financing, accordingly, products and services related to the microbiome are constantly emerging. However, due to the rapid development of microbiome sequencing and analysis related technologies and methods, the research and application from various countries have not yet unified on the standards of technology, programs, and data. Domestic industry participants also have insufficient understanding of the microbiome. New methods, technologies, and theories have not yet been fully accepted and used. In addition, some of the existing standards and guidelines are too general with poor practicality. This not only causes obstacles in the integration of scientific research data and waste of resources, but also gives related companies unfair competition opportunity. More importantly, China still lacks national standards related to the microbiome, and the national microbiome project is still in the process of preparation. In this context, the experts and practitioners of the microbiome worked together and developed the consensus of experts. It can not only guide domestic scientific research and industrial institutions to regulate the production, learning and research of the microbiome, the application can also provide reference technical basis for the relevant national functional departments, protect the scale and standardized corporate company's interests, strengthen industry self-discipline, avoid unregulated enterprises from disrupting the market, and ultimately promote the benign development of microbiome-related industries.
China ; Consensus ; Humans ; Industry ; Microbiota

Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function. Although the availability of massive RNA-seq data provides great opportunities for gene model refinement, few efforts have been made to adopt these precious data in rice genome reannotation. Here we reannotate the rice (Oryza sativa L. ssp. japonica) genome based on integration of large-scale RNA-seq data and release a new annotation system IC4R-2.0. In general, IC4R-2.0 significantly improves the completeness of gene structure, identifies a number of novel genes, and integrates a variety of functional annota-tions. Furthermore, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are system-atically characterized in the rice genome. Performance evaluation shows that compared to previous annotation systems, IC4R-2.0 achieves higher integrity and quality, primarily attributable to mas-sive RNA-seq data applied in genome annotation. Consequently, we incorporate the improvedannotations into the Information Commons for Rice (IC4R), a database integrating multiple omics data of rice, and accordingly update IC4R by providing more user-friendly web interfaces and implementing a series of practical online tools. Together, the updated IC4R, which is equipped with the improved annotations, bears great promise for comparative and functional genomic studies in rice and other monocotyledonous species. The IC4R-2.0 annotation system and related resources are freely accessible at http://ic4r.org/.

Objective To construct the UAS-Hey transgenic fly strains to provide a tool for researching the function of Hey gene in the fly development.Methods The Hey gene coding sequence was amplified by reverse transcription PCR and subcloned into pUAST expression vector.The pUAS-Hey recombinant plasmid was constructed and microinjected into the embryos of wild type flies.The UAS-Hey transgenic flies with red eyes were screened out with mini-white marker,then the balancing and mapping of these transgenic strains were performed.The identification was performed by using the PCR amplification method.Results The pUAS-Hey recombinant plasmid was successfully constructed,and seven independent transgenic strains were obtained by microinjection and transgenic fly screening and balance.PCR analysis confirmed that the P[mini-white,UAS-Hey] was integrated into genomes of transgenic strains and was in expressible region.Conclusion The UAS-Hey transgenic flies are successfully constructed,which lays the foundation for further studies of the function and regulation of Hey gene with GAL4/UAS system.

The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of version-dependent annotation files and other compatible public dataset for downstream analysis. To handle these tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool (RGAAT), a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNA-seq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool (RATT), RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification, genome comparison, and coordinate conversion. RGAAT is available at https://sourceforge.net/projects/rgaat/ and https://github.com/wushyer/RGAAT_v2 at no cost.
Genome ; Genomics ; High-Throughput Nucleotide Sequencing ; methods ; standards ; Humans ; Reference Standards ; Sequence Analysis, DNA ; methods ; standards ; Software

Objective To observe the value of virtual tough tissue imaging quantification (VTIQ) in differential diagnosis of thyroid imaging reporting and data system(TI-RADS) 4 thyroid nodules.Methods A total of 185 patients with 192 TI-RADS 4 nodules were included in this study.The nodules were divided into three groups according to the maximum size as follows:Group Ⅰ,the maximum size≤0.6 cm;Group Ⅱ,0.6 cm＜ the maximum size≤ 1.0 cm;Group Ⅲ,the maximum size ＞ 1.0 cm.Shear wave velocities (SWV) of nodules were measured by means of VTIQ technique.With pathological diagnosis as the gold standard,SWV value of benign and malignant nodules were analyzed and ROC curve was drawn to assess the diagnostic efficiency.Results By the ROC curve test,at SWV cut-off values of 2.44 m/s for group Ⅰ and group Ⅱ,2.49 m/s for group Ⅲ,the sensitivity were 79.0 ％,76.0 ％,88.6％,specificity were 88.6％,89.5 ％,93.7 ％,accuracy were 83.5 ％,81.8 ％,90.1％,Youden index were 0.68,0.66,0.82,respectively.Conclusions VTIQ can reflect the hardness of TI-RADS 4 nodules,the value of the differential diagnosis of such nodules is high,convenient,noninvasive and not limited by the size of nodules.

Objective To explore the ultrasonographic features and diagnostic value of the axillary masses. Methods Ultrasonographic findings of 275 cases confirmed suffering from axillary mass by operation or puncture biopsy and pathology were analyzed retrospectively. Results All cases were classified as follows, 86 cases of accessory, 158 cases of lesions of lymph node, 23 cases of benign tumor, 2 cases of abscess, 6 cases of radical mastectomy of breast cancer axillary effusion. Diagnosis sensitivity rate of ultrasound was 98.2%, diagnosis coincide rate of ultrasound was 97.1%. Conclusion Axillary masses have certain ultrasonographic features, Ultrasonic examination can be used as an important means of the diagnosis of axillary mass.

Objective To explore the ultrasonographic features and diagnostic value of the appendix diseases. Methods Ultrasonographic findings of 6 093 cases confirmed suffering from appendix disease by surgery, pathology or clinical were analyzed retrospectively. Results All cases were classified as follows, 1 073 cases of acute simple appendicitis, 2 810 cases of acute suppurative appendicitis, 521 cases of acute gangrene appendicitis, 679 cases of appendix ab-scess, 976 cases of chronic appendicitis, 2 cases of appendix diverticulitis, 15 cases of appendix mucous cyst, 9 cases of appendix bursae adenoma, 3 cases of appendix mucous cyst-adenocarcinoma, 2 cases of adenocarcinoma of the ap-pendix, 3 cases of carcinoid appendix. All of which had certain ultrasonographic features and those features in ultra-sonographic findings played a decisive role in the differential diagnosis. Diagnosis coincide rate of ultrasound was 86.9%(5 295/6 093). Conclusion Ultrasonic examination is valuable in diagnosis of the appendix diseases.

Ribonucleic acid (RNA) deserves not only a dedicated field of biological research -- a discipline or branch of knowledge -- but also explicit definitions of its roles in cellular processes and molecular mechanisms. Ribogenomics is to study the biology of cellular RNAs, including their origin, biogenesis, structure and function. On the informational track, messenger RNAs (mRNAs) are the major component of ribogenomes, which encode proteins and serve as one of the four major components of the translation machinery and whose expression is regulated at multiple levels by other operational RNAs. On the operational track, there are several diverse types of RNAs--their length distribution is perhaps the most simplistic stratification--involving in major cellular activ-ities, such as chromosomal structure and organization, DNA replication and repair, transcriptional/post-transcriptional regulation, RNA processing and routing, translation and cellular energy/metabolism regulation. An all-out effort exceeding the magnitude of the Human Genome Project is of essence to construct just mammalian transcriptomes in multiple contexts including embryonic development, circadian and seasonal rhythms, defined life-span stages, pathological conditions and anatomy-driven tissue/organ/cell types.