Congfan Bu

The rapid advancement of sequencing technologies poses challenges in managing the large volume and exponential growth of sequence data efficiently and on time. To address this issue, we present GenBase (https://ngdc.cncb.ac.cn/genbase), an open-access data repository that follows the International Nucleotide Sequence Database Collaboration (INSDC) data standards and structures, for efficient nucleotide sequence archiving, searching, and sharing. As a core resource within the National Genomics Data Center (NGDC) of the China National Center for Bioinformation (CNCB; https://ngdc.cncb.ac.cn), GenBase offers bilingual submission pipeline and services, as well as local submission assistance in China. GenBase also provides a unique Excel format for metadata description and feature annotation of nucleotide sequences, along with a real-time data validation system to streamline sequence submissions. As of April 23, 2024, GenBase received 68,251 nucleotide sequences and 689,574 annotated protein sequences across 414 species from 2319 submissions. Out of these, 63,614 (93%) nucleotide sequences and 620,640 (90%) annotated protein sequences have been released and are publicly accessible through GenBase's web search system, File Transfer Protocol (FTP), and Application Programming Interface (API). Additionally, in collaboration with INSDC, GenBase has constructed an effective data exchange mechanism with GenBank and started sharing released nucleotide sequences. Furthermore, GenBase integrates all sequences from GenBank with daily updates, demonstrating its commitment to actively contributing to global sequence data management and sharing.

Pan-genome analysis is a crucial method for studying genomic dynamics. By creating pan-genome maps for prokaryotic organisms, we can gain valuable insights into their genetic diversity and ecological adaptability. However, current analytical methods often struggle to balance accuracy and computational efficiency, and they tend to provide primarily qualitative results. This study introduces PGAP2, an integrated software package that simplifies various processes, including data quality control, pan-genome analysis, and result visualization. PGAP2 facilitates the rapid and accurate identification of orthologous and paralogous genes by employing fine-grained feature analysis within constrained regions. Our systematic evaluation with simulated and gold-standard datasets demonstrates that PGAP2 is more precise, robust, and scalable than state-of-the-art tools for large-scale pan-genome data. Furthermore, PGAP2 introduces four quantitative parameters derived from the distances between or within clusters, enabling detailed characterization of homology clusters. Finally, we validate our quantitative findings by applying PGAP2 to construct a pan-genomic profile of 2794 zoonotic Streptococcus suis strains. This analysis offers new insights into the genetic diversity of S. suis, thereby enhancing our understanding of its genomic structure. PGAP2 is freely available at https://github.com/bucongfan/PGAP2 . Prokaryotic pan-genome analysis is crucial for understanding microbial diversity, however current analytical methods often struggle to balance accuracy and computational efficiency. Here the authors present a more precise, robust and scalable toolkit for large-scale pan genome analysis.

Many studies have evaluated the correlation between peptidylarginine deiminase 4 (PADI4) -92C/G polymorphism and rheumatoid arthritis (RA), but the results remain inconclusive. Therefore, we performed a meta-analysis in the Chinese population to provide comprehensive data on the association between PADI4 -92C/G polymorphism and RA. Eligible studies published before May 2016 were identified in PubMed and Chinese databases. The strengths of these associations were assessed by pooled odds ratios (OR) and 95% confidence interval (CI). Eight studies documenting a total of 1351 RA cases and 1585 controls were included in this meta-analysis. In the overall analysis, a significant association between the PADI4 -92C/G polymorphism and RA was found in the Chinese population (G vs C: OR=1.32, 95%CI=1.02-1.71; GG+CG vs CC: OR=1.75, 95%CI=1.20-2.53). The subgroup analyses stratified by geographic area(s) and source of controls revealed significant results in South China, in hospital-based studies and population-based studies. In summary, this meta-analysis suggested that PADI4 -92C/G polymorphism may be associated with the RA incidence in the Chinese population, especially for South China. Further studies conducted on other ethnic groups are required for definite conclusions.

BACKGROUND: TNRC6B encodes a protein crucial for RNA silencing, and heterozygous variants of TNRC6B have been associated with developmental delay/intellectual disability, speech and language delay, fine and motor delay, and a range of neurobehavioral phenotypes, including autism and attention deficit and hyperactivity disorder (ADHD). Rett syndrome (RTT) is a neurodevelopmental disorder primarily affecting girls, characterized by loss of acquired speech and motor skills, repetitive hand movements, breathing irregularities, seizures, and is a prevalent cause of intellectual disability in females. Most RTT cases are due to pathogenic variants in the MECP2 gene located at Xq28, encoding methyl-CpG binding protein 2 (MeCP2). The phenotypic spectrum of heterozygous TNRC6B variants combined with MECP2 gene deletion has not been well described. CASE PRESENTATION: A 17-month-old Chinese female patient with severe malnutrition and global developmental delay (GDD) was enrolled in this study. Whole-exome sequencing was conducted, and clinical data were obtained retrospectively from medical history and formal neuropsychological evaluation. The heterozygous TNRC6B variants (c.1409A > G; p.Asp470Ser) and a 4.066 Kb intragenic deletion of Xq28 encompassing the MECP2 gene were found. This expands the genetic spectrum of TNRC6B variants. The patient exhibited GDD, behavioral abnormalities, stunting, underweight, microcephaly and facial dysmorphism, including low-set ears, wide-set eyes, upslanting lateral canthi, underbite and hypertonia. The patient has received feeding guidance and rehabilitation training, and is currently under regular follow-up. This case broadens the phenotypic spectrum associated with TNRC6B variants and MECP2 gene deletion. CONCLUSION: This is the first report of a Xq28 microdeletion encompassing the MECP2 gene combined with heterozygous variants in TNRC6B. Our study expands the genotypic and phenotypic spectrum of TNRC6B deficiency syndrome and Rett syndrome. Our findings suggest that patients with TNRC6B and MECP2 gene deficiencies may experience more severe developmental delay and malnutrition.

<p indent="0mm">The dataset of morphological traits of pierid based on Fauna Sinica is extracted by a self-developed special tool used for biological morphological features marking after digitizing Fauna Sinicna (INSECTA Vol. 52 Lepidoptera Pieridae). This dataset contains 24 genera, 155 species of Pierididae (177 subspecies), Lepidoptera, Insecta. Each record in this dataset is the extraction of a single morphological characteristic from morphology, measurement, and other morphological description data of different species/subspecies in different genders and various developmental stages, mainly in shape, color, and texture. This dataset provides basic data for the biological research of these pierid groups, such as biogeography and phylogeny, and also provides valuable corpus resources for natural language processing and understanding research.