A novel strain of Shigella isolated from the gut of Lepidocephalichthys guntea has in its genome a complete gene package for Type ll secretion system, and elaborate repertoire of genes responsible for multiple antibiotic-resistance and metal resistance via specific efflux channels.

The bacterial strain GCP5 was isolated from the gut of a bottom-dwelling fish Lepidocephalichthys guntea, that lives in the Magurmari River near North Bengal University in Siliguri, India. GCP5 was phylogenetically assigned to the Shigella genus using whole genome-based trees, k-mer analysis, the multilocus species tree (MLST), and single nucleotide polymorphism (SNP)-based trees, and the genetic makeup of the isolate was determined following assembly of the genome sequences and genome annotation with several bioinformatics tools. The presence of a complete package of general-secretory-pathway (gsp) genes, grouped in an operon identical to a well-characterized type II secretion system (T2SS), was confirmed by genome mining of Shigella sp. GCP5. The operon's gsp genes shared the most homology with Escherichia coli gsp genes. A few more high-pathogenicity islands (HPIs) in the GCP5 genome were validated using the pan-genomes analysis pipeline (PGAP) and island viewer. Several antibiotic-resistance genes were found in this genome, as well as the existence of key antibiotic efflux pump families, allowing for the creation of a gene network of several antibiotic efflux transporters. In addition, the genome contained genes specific for nickel transport, the nikABCD system, and the RND family transporter cusCFBA, which confers resistance to copper and silver by effluxing out Cu+ and Ag+ ions.

Genomic analysis of enterovirus D68, including one strain isolated from a child with Wilson's disease in Taiwan.

North America experienced life-threatening outbreaks of enterovirus D68 (EV-D68) in 2014. We retrospectively detected EV-D68 from a child with Wilson's disease in 2008 in Taiwan. After comparing this EV-D68/Taiwan/2008 strain with EV-D68 genomes obtained from the public domain, it was classified as genome type 1-B; it is phylogenetically related to the predominant EV-D68 viruses that circulated in 2009 in Vietnam. It is necessary to strengthen EV-D68 detection globally, including in children with acute liver failure. Moreover, harmonization of genomic analysis of EV-D68 is desirable to understand global evolution of EV-D68.

A copy number variation in PKD1L2 is associated with colorectal cancer predisposition in korean population.

Recently reported genome-wide association studies have identified more than 20 common low-penetrance colorectal cancer (CRC) susceptibility loci. Recent studies have reported that copy number variations (CNVs) are considered important human genomic variants related to cancer, while the contribution of CNVs remains unclear. We performed array comparative genomic hybridization (aCGH) in 36 CRC patients and 47 controls. Using breakpoint PCR, we confirmed the breakpoint of the PKD1L2 deletion region. High frequency of PKD1L2 CNV was observed in CRC cases. We validated the association between PKD1L2 variation and CRC risk in 1,874 cases and 2,088 controls (OR = 1.44, 95% CI = 1.04-1.98, p = 0.028). Additionally, PKD1L2 CNV is associated with increased CRC risk in patients younger than 50 years (OR = 2.14, 95% CI 1.39-3.30, p = 5.8 × 10-4 ). In subgroup analysis according to body mass index (BMI), we found that the CN loss of PKD1L2 with BMI above or equal to 25 exhibited a significant increase in CRC risk (OR = 2.29, 95% CI 1.29-4.05, p = 0.005). PKD1L2 CNV with BMI above or equal to 25 and age below 50 is associated with a remarkably increased risk of colorectal cancer (OR = 5.24, 95% CI 2.36-11.64, p= 4.8 × 10-5 ). Moreover, we found that PKD1L2 variation in obese patients (BMI ≥ 25) was associated with poor survival rate (p = 0.026). Our results suggest that the common PKD1L2 CNV is associated with CRC, and PKD1L2 CNV with high BMI and/or age below 50 exhibited a significant increased risk of CRC. In obese patients, PKD1L2 variation was associated with poor survival.

Complete genome sequence and comparative genome analysis of the Paenibacillus mucilaginosus K02.

AIM: Paenibacillus mucilaginosus (P. mucilaginosus) K02 is implicated in mineral weathering. However, relevant molecular mechanisms remain obscure. The study aims to uncover the bacterium's physiological processes using genomic approaches. METHODS AND RESULTS: Genomic DNA from P. mucilaginosus K02 was sequenced using high-throughput Solexa sequencing technology and then conducted for Clusters of Orthologous Group (COG) annotation. Thereafter, genome sequences of K02 were compared with two strains, 3016 and KNP414. Mummer was applied for collinearity analysis of three P. mucilaginosus genomes. BLAST was used to identify pan and core genes in these strains. Finally, a phylogenetic tree was constructed using the maximum likelihood method by TreeBeST. Complete genome sequence of P. mucilaginosus K02 indicated the strain comprises one circular chromosome with 8,819,200 bases containing 58.3% GC content and 84.75% coding regions. A total of 7299 predicted ORFs were identified in the genome, among them, several genes were related to carbonic anhydrase (CA), and exopolysaccharide biosynthesis and secretion. Moreover, proteins of the predicted genes were annotated in COG categories such as "Carbohydrate transport and metabolism" and "Inorganic ion transport and metabolism." In comparison with KNP414 and 3016, K02 exhibited chromosomal recombination or transposition. A total of 6662 core genes were identified among three P. mucilaginosus strains. The phylogenomic study indicated that P. mucilaginosus K02 was clustered with P. mucilaginosus strains 3016 and KNP414. CONCLUSIONS: In P. mucilaginosus K02, genes related to CA and exopolysaccharide biosynthesis and secretion, and that involved in metabolism-related processes might play significant roles in mineral weathering.

Innovations in functional genomics and molecular breeding of pea: exploring advances and opportunities.

The garden pea (Pisum sativum L.) is a significant cool-season legume, serving as crucial food sources, animal feed, and industrial raw materials. The advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea breeding. Notably, the release of the pea reference genome has enhanced our understanding of plant architecture, symbiotic nitrogen fixation (SNF), flowering time, floral organ development, seed development, and stress resistance. However, a considerable gap remains between pea functional genomics and molecular breeding. This review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.

Mechanisms underlying key agronomic traits and implications for molecular breeding in soybean.

Soybean (Glycine max [L.] Merr.) is an important crop that provides protein and vegetable oil for human consumption. As soybean is a photoperiod-sensitive crop, its cultivation and yield are limited by the photoperiodic conditions in the field. In contrast to other major crops, soybean has a special plant architecture and a special symbiotic nitrogen fixation system, representing two unique breeding directions. Thus, flowering time, plant architecture, and symbiotic nitrogen fixation are three critical or unique yield-determining factors. This review summarizes the progress made in our understanding of these three critical yield-determining factors in soybean. Meanwhile, we propose potential research directions to increase soybean production, discuss the application of genomics and genomic-assisted breeding, and explore research directions to address future challenges, particularly those posed by global climate changes.

Ethical, legal and social implications of human genome studies in radiation research: a workshop report for studies on atomic bomb survivors at the Radiation Effects Research Foundation.

The Radiation Effects Research Foundation (RERF) is the primary organization in Japan dedicated to studying the health consequences of the Hiroshima and Nagasaki atomic bombings in World War II. In December 2020, RERF held a virtual international workshop on the ethical, legal and social implications (ELSI) of genome studies. In this workshop, the ELSI considerations of future human genome studies on radiation research including atomic bomb survivors and their families were discussed. Since genome sequencing (GS) is now practical and affordable, RERF now plans GS of parents/child trios to examine genetic effects of atomic bomb radiation. As such studies may engender some novel risks and benefits, ethics review and engagement with families (including consent) need to be considered. These include protection of individual privacy, use of samples from deceased prior participants, return of results to the participants, public sharing of genome data and advance science and social welfare. Specifically with regard to social welfare, the results of such studies may have implications for public and government decision-making regarding social benefits of victims and other important questions. Based on these broad-ranging discussions we have developed the following concepts to guide this work: "trust," "compromise" and "relationship building," inclusive of the concerned stakeholders, scientific aims and Japanese society at large. We conclude that in order to realize, establish and maintain these concepts, it is essential to put procedures into place to ensure the successful, consensus-based implementation of the RERF studies.

Lifestyle, genomic types and non-communicable diseases in Korea: a protocol for the Korean Medicine Daejeon Citizen Cohort study (KDCC).

INTRODUCTION: Non-communicable diseases (NCDs) are the leading cause of death worldwide, including in Korea; thus, customised techniques for chronic disease management for the prevention, early diagnosis and treatment of NCDs are crucial. The Korean Medicine Daejeon Citizen Cohort (KDCC) study has been tasked with developing precise health promotion model for preventing and managing chronic diseases that considers individual traits, lifestyle factors and clinical data based on traditional Korean medicine. METHODS AND ANALYSIS: The KDCC study is a prospective cohort study of the community-based population in Korea. This study will sample 2000 adults aged 30-55 years in Daejeon area using stratified cluster sampling. The baseline survey began in 2017 and was completed in 2019, and follow-up surveys will be conducted three times every 2 years until 2025. In follow-ups, factors related to cardiovascular disease, metabolic syndrome and relevant diseases, as well as respondents' health status information, will be examined via questionnaire surveys and health examinations. DISCUSSION: The KDCC study will investigate the effects of an interaction of Korean medicine type with genome based, lifestyle and various clinical information on chronic diseases and individuals' health status using longitudinal epidemiological data. These findings are expected to inform the development of tailored health promotion programmes based on precision Korean medicine. TRIAL REGISTRATION NUMBER: KCT0004297.

Experiences and attitudes of residents regarding a community-based genome cohort study in Japan: a population-based, cross-sectional study.

BACKGROUND: Because of the rapid development in genomics, more research findings have emerged. However, the association between society and research results remains controversial. This article examines the experiences and attitudes of residents regarding a community-based genomic cohort study. METHODS: This study was conducted as a part of the health survey of the City Health Promotion section. At the conclusion of the first stage of the project, a self-administered questionnaire was mailed to a random sample of 2,500 residents in 2012. RESULTS: The response rate was 59 % (n = 1477/2500). The findings show that 70 % of males and 50 % of females knew nothing about the project. Females and elderly people were more likely to have knowledge of the study, indicating that self-rated understanding of the terminology is statistically associated with the level of awareness regarding the project. In addition, those who were aware of the project were also aware of the benefits of research utilizing genetic information, whereas unaware respondents, particularly males, believed that unexpected negative effects may occur. Those with higher self-rated understanding of the terminology and higher awareness of benefit of the research utilizing genetic information had more positive attitudes toward undergoing drug susceptibility genetic testing, indicating that the awareness of project in females and concerns toward genetic research are not statistically associated with the willingness to undergo. CONCLUSIONS: This study suggests that a community-based genome cohort project helps raise awareness of benefit of genetic research and that knowledge, however, does not directly affect the willingness to participate in related activities, such as drug susceptibility genetic testing. Therefore, additional research that focuses on the circular relationship between risk and action must be conducted in the future.

Residents' awareness and attitudes about an ongoing community-based genome cohort study in Nagahama, Japan.

This study's objective was to examine residents' attitudes toward and factors associated with an ongoing, real genome cohort study based on a community in Japan. After the genome cohort study's launch in 2007, in November and December 2009, a self-administered questionnaire survey was conducted with 2500 randomly sampled residents aged 30-74 years, living in Nagahama, Japan. Responses were received from 1363 people (response rate = 54.5%), of whom 187 respondents had already participated in the study. Although the local government and researchers disseminated information through leaflets and citizen-information papers to every household, sent notices by personalized letter, and held symposia and other meetings, 65.7% of males and 47.2% of females first became aware of the study when they received our questionnaire. Among all respondents, 81.2% of those who knew that the genome cohort study had begun and 68.6% of those who did not know had a positive attitude toward the study. Their attitudes were significantly associated with high health consciousness and the desire for an extensive health check-up. Although for males there were no particular negative aspects of the genome study, for females, positive aspects were associated with participating in community activities and desiring an extensive health check-up. Although promoting a community-based genome cohort study requires huge effort, it is essential to popularize it. Actions are vital both for monitoring public awareness and attitudes at a community level and for keeping communication channels open.