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Introduction Legume crops are an important source of protein and oil for human health and in fixing atmospheric N2 for soil enrichment. With an objective to accelerate much-needed genetic analyses and breeding applications, draft genome assemblies were generated in several legume crops; many of them are not high quality because they are mainly based on short reads. However, the superior quality of genome assembly is crucial for a detailed understanding of genomic architecture, genome evolution, and crop improvement. Objectives Present study was undertaken with an objective of developing improved chromosome-length genome assemblies in six different legumes followed by their systematic investigation to unravel different aspects of genome organization and legume evolution. Methods We employed in situ Hi-C data to improve the existing draft genomes and performed different evolutionary and comparative analyses using improved genome assemblies. Results We have developed chromosome-length genome assemblies in chickpea, pigeonpea, soybean, subterranean clover, and two wild progenitor species of cultivated groundnut (A. duranensis and A. ipaensis). A comprehensive comparative analysis of these genome assemblies offered improved insights into various evolutionary events that shaped the present-day legume species. We highlighted the expansion of gene families contributing to unique traits such as nodulation in legumes, gravitropism in groundnut, and oil biosynthesis in oilseed legume crops such as groundnut and soybean. As examples, we have demonstrated the utility of improved genome assemblies for enhancing the resolution of “QTL-hotspot” identification for drought tolerance in chickpea and marker-trait associations for agronomic traits in pigeonpea through genome-wide association study. Genomic resources developed in this study are publicly available through an online repository, ‘Legumepedia’. Conclusion This study reports chromosome-length genome assemblies of six legume species and demonstrates the utility of these assemblies in crop improvement. The genomic resources developed here will have significant role in accelerating genetic improvement applications of legume crops.

This study aimed to evaluate the effect of resistance exercise on peripheral inflammatory biomarkers in healthy adults.Four databases, including PubMed, Web of Science, Cochrane Library, and SPORTDiscus, were searched from inception until April 1st, 2022. A meta-analysis was conducted using a random-effects model, followed by sensitivity analysis, subgroup analysis, meta-regression analysis, and publication bias analysis.15 randomized controlled trials were included in the meta-analysis. The pooled results showed that resistance exercise significantly decreased TNF-α levels (SMD = -0.81, 95% CI: -1.42 to -0.20, p = 0.009) but did not affect IL-6 and CRP levels. Individuals with BMI 18.5-24.9 exhibited significantly decreased IL-6 levels, while moderate strength resistance exercise could significantly decrease TNF-α levels. Finally, age might be a confounding factor influencing the effect of resistance exercise on IL-6.Resistance exercise could reduce TNF-α levels in healthy adults, and resistance exercise with moderate intensity could reduce TNF-α levels more effectively.

Breeding for good meat quality performance while maintaining large body size and desirable carcass traits has been the major challenge for modern swine selective breeding. To address this goal, in the present work we studied five related populations produced by two commercial breeds (Berkshire and Duroc) and two Chinese breeds (Licha black pig and Lulai black pig). A single-trait GWAS performed on 20 body size and carcass traits using a self-developed China Chip-1 porcine SNP50K BeadChip identified 11 genome-wide significant QTL on nine chromosomes and 22 suggestive QTL on 15 chromosomes. For the 11 genome-wide significant QTL, eight were detected in at least two populations, and the rest were population-specific and only mapped in Shanxia black pig. Most of the genome-wide significant QTL were pleiotropic; for example, the QTL around 75.65 Mb on SSC4 was associated with four traits at genome-wide significance level. After screening the genes within 50 kb of the top SNP for each genome-wide significant QTL, NR6A1 and VRTN were chosen as candidate genes for vertebrae number; PLAG1 and BMP2 were identified as candidate genes for body size; and MC4R was the strong candidate gene for body weight. The four genes have been reported as candidates for thoracic vertebrae number, lumbar vertebrae number, carcass length and body weight respectively in previous studies. The effects of VRTN on thoracic vertebrae number, carcass length and body length have been verified in Shanxia black pig. Therefore, the VRTN genotype could be used in gene-assisted selection, and this could accelerate genetic improvement of body size and carcass traits in Shanxia black pig.

Coronavirus disease (COVID-19) and tuberculosis (TB) are two respiratory infectious diseases with a high incidence of transmission, mainly via respiratory droplets and both can weaken the immune system and lower the number of CD4新型冠状病毒（简称新冠病毒）肺炎（COVID-19）和结核病是两种主要经呼吸道飞沫传播力极强的呼吸道传染病，发病率高，均可导致患者免疫力下降，CD4

Algae characterize their high diversity, taxonomy and morphology for wide-used studying the plant origins and terrestrialization, as well as multicellular evolution. Due to the genome assembly challenge of algae caused by symbionts with microbiome, the published algae genomes are relatively less than the terrestrial plants. Here we comprehensively collected and re-annotated 191 available algae genomes distributed in nine major lineages. We systemically investigated the genome features including genome size, assembly continuity and integrity, GC content, abundance of repetitive sequences and protein-coding gene number. We construct the phylogenetic trees using 193 algae genomes, which is consistent with the well-known evolution path that Glaucophyte is the most ancient, going through eight lineages, and finally evolved to terrestrial plants. We also examined the Horizontal Gene Transfer (HGT) genes distribution in algae genomes and provides a substantial genomic resource for functional gene origins and plant evolution.

The mechanism of osteoarthritis is still not completely clear,the current treatment can not effectively prevent the disease from progressing.In order to study osteoarthritis,researchers have developed various models,including骨关节炎的发病机制尚不明确，目前的治疗方法仍不能有效阻止疾病进展。生物模型是研究疾病的重要工具，二维、三维细胞培养模型及生物反应器培养模型等体外模型，以及自发性、遗传修饰性、侵入性及非侵入性模型等动物体内模型，可模拟疾病的阶段性变化或发展全过程。对以上模型的研究是探索骨关节炎发生、发展过程的重要手段，亦是开发和评价治疗方法的重要依据。本文对骨关节炎模型及其特点进行综述，以期为骨关节炎的研究提供参考。.

Marine mammals are important models for studying convergent evolution and aquatic adaption, and thus reference genomes of marine mammals can provide evolutionary insights. Here, we present the first chromosome-level marine mammal genome assembly based on the data generated by the BGISEQ-500 platform, for a stranded female sperm whale (Physeter macrocephalus). Using this reference genome, we performed chromosome evolution analysis of the sperm whale, including constructing ancestral chromosomes, identifying chromosome rearrangement events and comparing with cattle chromosomes, which provides a resource for exploring marine mammal adaptation and speciation. We detected a high proportion of long interspersed nuclear elements and expanded gene families, and contraction of major histocompatibility complex region genes which were specific to sperm whale. Using comparisons with sheep and cattle, we analysed positively selected genes to identify gene pathways that may be related to adaptation to the marine environment. Further, we identified possible convergent evolution in aquatic mammals by testing for positively selected genes across three orders of marine mammals. In addition, we used publicly available resequencing data to confirm a rapid decline in global population size in the Pliocene to Pleistocene transition. This study sheds light on the chromosome evolution and genetic mechanisms underpinning sperm whale adaptations, providing valuable resources for future comparative genomics.

The purpose of this article is twofold. One is to establish a proximal point algorithm for finding a minimizer of a proper convex and lower semi-continuous function and fixed points of quasi-pseudo-contractive mappings in CAT(0) spaces. The other is to point out and correct a basic and conceptual error in a paper of Ugwunnadi et al. [Theorem 3.1, J. Fixed Point Theory Appl. (2018) 20: 82].

Decontamination is necessary for eliminating the effect of foreign genomes on the symbiont studies and biomedical discoveries. However, direct extraction of host sequencing reads with no references remains challenging. Here, we present a triobased method to classify the host error-prone long reads or sparse co-barcoded reads prior to assembly, free of any alignments against DNA or protein references. This method first identifies high-confident host reads by haplotype-specific k-mers inherited from parents, and then groups remaining host reads by the unsupervised clustering. Experimental results demonstrated that this approach successfully classified up to 97.38% of the host human long reads with the precision rate of 99.9999%, and 79.95% host co-barcoded reads with the precision rate of 98.36% using an artificially mixed data. Moreover, the tool also exhibited a good performance on the decontamination of the real algae data. The purified reads reconstructed two haplotypes and improved the assembly with larger contig NGA50 value and less misassemblies. Symbiont-Screener can be freely downloaded at https://github.com/BGI-Qingdao/Symbiont-Screener.

The aim of this study was to clarify the role of microRNA-433-5p (miRNA-433-5p) in influencing pathological lesions following acute spinal cord injury (SCI) by targeting mitogen-activated protein kinase 1 (MAPK1).SCI model was successfully established in mice by performing hitting injury procedures. Serum levels of miRNA-433-5p and MAPK1 in SCI patients and mice were determined. Grip strengths of both forelimbs in SCI mice and controls were determined. Dual-Luciferase reporter gene assay was applied to verify the binding relation between miRNA-433-5p and MAPK1. After overexpression of miRNA-433-5p and MAPK1 in vivo, the grip strength changes in SCI mice were assessed. Furthermore, the protein level of inflammatory factor iNOS in 293T cells influenced by miRNA-433-5p and MAPK1 was detected by Western blot.MiRNA-433-5p was significantly downregulated in the serum of SCI patients and mice, whereas MAPK1 was up-regulated. Grip strengths of SCI mice were significantly lower than those of controls at different postoperative time points. However, this could be markedly reversed by the in vivo overexpression of miRNA-433-5p. Western blot indicated that the protein level of iNOS was remarkably downregulated in 293T cells overexpressing miRNA-433-5p. MAPK1 was confirmed as the target of miRNA-433-5p, whose expression level was negatively regulated by miRNA-433-5p. Importantly, MAPK1 partially reversed the protective role of miRNA-433-5p in grip strength of SCI mice and inflammatory response at post-SCI.Overexpression of miRNA-433-5p protects SCI-induced motor dysfunction and inflammatory response by targeting MAPK1.

Background and objectives Coronavirus disease 2019 (COVID-19) has become a pandemic Preliminary data reported that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) might not be found in the semen of patients in the early stages of COVID-19;however, the virus may be seen in the semen in the late, severe stages To determine the effects of SARS-CoV-2 infection on the male reproductive system Materials and methods We reviewed the relationship between previously reported infections with mumps virus (MuV), HIV, Zika virus, hepatitis virus B, hepatitis virus C, SARS-CoV, and influenza viruses that could possibly damage the male reproductive system, and then investigated whether SARS-CoV-2 infection could cause any damage to the male reproductive system Results There were various reports that viruses could impair male reproduction by entering into the testicular cells, inducing inflammation, or both Regarding SARS-CoV-2, five recent independent studies showed no evidence to suggest that SARS-CoV-2 could be found in the semen and testicular tissues, suggesting that SARS-CoV-2 would not directly damage the blood-testis barrier (BTB) in the early stages of COVID-19 infection However, a study found that viral RNA was found in 6 out of 38 patients Three studies found that there were some changes in the sexual hormone levels Discussion and conclusion There is a lack of substantial evidence to determine how SARS-CoV-2 affects male reproduction at this moment Understanding of the relationship between SARS-CoV-2 and male infertility requires further research

The aim of this study was to determine the expression levels of TTK in clear cell renal cell carcinoma (ccRCC) tissues and its possible link with the clinical pathologic characteristics and the prognosis of patients suffering this disease, and to further explore the potential role of TTK in the progression of ccRCC. Immunohistochemical (IHC) assays were performed to detect the expression levels of TTK in 112 samples of ccRCC tissues and corresponding non-tumor tissues. According to the results of IHC assays, patients were divided into TTK high expression and low expression group. Clinical analysis related to the clinical features (age, gender, T stage), and the potential link between TTK expression levels and clinical features were analyzed. In addition, the effects of TTK on the proliferation and invasion of ccRCC cells were detected through colony formation assay and transwell assays, respectively. The possible effects of TTK on tumor growth and metastasis were measured in mice. We found a high expression level of TTK in human ccRCC tissues from patients who received surgical treatment. We also found its expression level was obviously associated with clinical characteristics, such as T stage (p=0.008) and lymphatic metastasis (p=0.023). We further confirmed that knockdown of TTK suppressed cell proliferation and invasion in 2 types of ccRCC cells, HTB-47 and CRL-1932 cells. Furthermore, TTK contributes to tumor growth and metastasis of ccRCC in mice. We found that TTK affected the progression of ccRCC and further mechanically confirmed it could be a novel therapeutic target for ccRCC treatment.

With the continuing development of sequencing technology, genomics has been applied in a variety of biological research areas. In particular, the application of genomics to marine species, which boast a high diversity, promises great scientific and industrial potential. Significant progress has been made in marine genomics especially over the past few years. Consequently, BGI, leveraging its prominent contributions in genomics research, established BGI-Qingdao, an institute specifically aimed at exploring marine genomics. In order to accelerate marine genomics research and related applications, BGI-Qingdao initiated the International Conference on Genomics of the Ocean (ICG-Ocean) to develop international collaborations and establish a focused and coherent global research plan. Last year, the first ICG-Ocean conference was held in Qingdao, China, during which 47 scientists in marine genomics from all over the world reported on their research progress to an audience of about 300 attendees. This year, we would like to build on that success, drafting a report on marine genomics to draw global attention to marine genomics. We summarized the recent progress, proposed future directions, and we would like to enable additional profound insights on marine genomics. Similar to the annual report on plant and fungal research by Kew Gardens, and the White Paper of ethical issues on experimental animals, we hope our first report on marine genomics can provide some useful insights for researchers, funding agencies as well as industry, and that future versions will expand upon the foundation established here in both breadth and depth of knowledge.This report summarizes the recent progress in marine genomics in six parts including: marine microorganisms, marine fungi, marine algae and plants, marine invertebrates, marine vertebrates and genomics-based applications.

Summary The Indo-Pacific humpback dolphin (Sousa chinensis) is a small inshore species of odontocete cetacean listed as Vulnerable on the IUCN Red List. Here, we report on the evolution of S. chinensis chromosomes from its cetruminant ancestor and elucidate the evolutionary history and population genetics of two neighboring S. chinensis populations. We found that breakpoints in ancestral chromosomes leading to S. chinensis could have affected the function of genes related to kidney filtration, body development, and immunity. Resequencing of individuals from two neighboring populations in the northwestern South China Sea, Leizhou Bay and Sanniang Bay, revealed genetic differentiation, low diversity, and small contemporary effective population sizes. Demographic analyses showed a marked decrease in the population size of the two investigated populations over the last ~4,000 years, possibly related to climatic oscillations. This study implies a high risk of extinction and strong conservation requirement for the Indo-Pacific humpback dolphin., Graphical Abstract, Highlights • Deducing chromosome evolution from ancestral Cetruminantia and ancestral Odontoceti • Reconstructing the demographic history of Sousa chinensis • Implying high risk of extinction and strong conservation requirement for S. chinensis, Evolutionary Biology; Genetics; Genomics

To explore whether lncRNA UCA1 (long non-coding RNA urothelial carcinoma associated 1) could promote the development of papillary thyroid carcinoma (PTC) via Wnt pathway and its underlying mechanism.UCA1 expression in PTC tissues, paracancerous tissues, and thyroid cancer cells were detected by quantitative Real Time-Polymerase Chain Reaction (qRT-PCR). UCA1 lentivirus was then constructed for the following in vitro experiments. Proliferative ability of MTC and SW579 cells was detected by cell counting kit-8 (CCK-8) and colony formation assay. Cell apoptosis after altering UCA1 expression in MTC and SW579 cells was detected by flow cytometry and Western blot. Invasive ability of MTC and SW579 cells was detected by transwell and wound healing assay. Finally, protein expressions of Wnt pathway-related genes were detected by Western blot.UCA1 was overexpressed in PTC tissues and thyroid cancer cells. UCA1 expression was positively correlated to tumor size, tumor stage, and metastasis of PTC. Overexpressed UCA1 promoted proliferation and invasion, whereas inhibited apoptosis of thyroid cancer cells via Wnt pathway.Overexpressed UCA1 promotes PTC development by stimulating proliferation, migration, and anti-apoptosis of thyroid cancer cells via activating Wnt pathway.

Penicillium is an ascomycetous genus widely distributed in the natural environment and is one of the dominant fungi involved in the decomposition of mangroves, which can produce a variety of antitumor compounds and bioactive substances. However, in mangrove ecosystems there is no complete genome in this genus. In this study, we isolated a fungus strain named Penicillium variabile HXQ-H-1 from coast mangrove (Fujian Province, China). We generated a chromosome-level genome with total size of 33.32 Mb, scaffold N50 of 5.23 Mb and contig N50 of 96.74 kb. Additionally, we anchored about 95.91% assembly sequences into the longest seven scaffolds, and predicted 10,622 protein-coding genes, in which 99.66% could be annotated by eight protein databases. The secondary metabolites analysis reveals the strain has various gene clusters involving polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS) and terpene synthase that may have a largely capacity of biotechnological potential. Comparison genome analysis between Penicillium variabile and Talaromyces islandicus reveals a small difference in the total number of genes, whereas HXQ-H-1 has a higher gene number with COG functional annotation. Evolutionary relationship of Penicillum based on genome-wide data was carried out for the first time, showing the strain HXQ-H-1 is closely related to Talaromyces islandicus. This genomic resource may provide a new resource for development of novel bioactive antibiotics, drug candidates and precursors in Penicillium variabile.