High-quality chromosome scale genome assemblies of two important Sorghum inbred lines, Tx2783 and RTx436.

Sorghum bicolor (L.) Moench is a significant grass crop globally, known for its genetic diversity. High quality genome sequences are needed to capture the diversity. We constructed high-quality, chromosome-level genome assemblies for two vital sorghum inbred lines, Tx2783 and RTx436. Through advanced single-molecule techniques, long-read sequencing and optical maps, we improved average sequence continuity 19-fold and 11-fold higher compared to existing Btx623 v3.0 reference genome and obtained 19 and 18 scaffolds (N50 of 25.6 and 14.4) for Tx2783 and RTx436, respectively. Our gene annotation efforts resulted in 29 612 protein-coding genes for the Tx2783 genome and 29 265 protein-coding genes for the RTx436 genome. Comparative analyses with 26 plant genomes which included 18 sorghum genomes and 8 outgroup species identified around 31 210 protein-coding gene families, with about 13 956 specific to sorghum. Using representative models from gene trees across the 18 sorghum genomes, a total of 72 579 pan-genes were identified, with 14% core, 60% softcore and 26% shell genes. We identified 99 genes in Tx2783 and 107 genes in RTx436 that showed functional enrichment specifically in binding and metabolic processes, as revealed by the GO enrichment Pearson Chi-Square test. We detected 36 potential large inversions in the comparison between the BTx623 Bionano map and the BTx623 v3.1 reference sequence. Strikingly, these inversions were notably absent when comparing Tx2783 or RTx436 with the BTx623 Bionano map. These inversion were mostly in the pericentromeric region which is known to have low complexity regions and harder to assemble and suggests the presence of potential artifacts in the public BTx623 reference assembly. Furthermore, in comparison to Tx2783, RTx436 exhibited 324 883 additional Single Nucleotide Polymorphisms (SNPs) and 16 506 more Insertions/Deletions (INDELs) when using BTx623 as the reference genome. We also characterized approximately 348 nucleotide-binding leucine-rich repeat (NLR) disease resistance genes in the two genomes. These high-quality genomes serve as valuable resources for discovering agronomic traits and structural variation studies.

Analysis of the effects of early screening combined with blood lactate on the severity of patients with sepsis.

This work aimed to investigate the adoption value of blood lactic acid (BLA) combined with the National Early Warning Score (NEWS) in the early screening of sepsis patients and assessing their severity. The data and materials utilized in this work were obtained from the electronic medical record system of 537 anonymized sepsis patients who received emergency rescue in the emergency rescue area of Liuzhou People's Hospital, Guangxi, from July 1, 2020, to December 26, 2020. Based on the 28-day outcomes of sepsis patients, the medical records were rolled into Group S (407 survival cases) and Group D (130 dead cases). Basic information such as the mode of hospital admission, initial management, use of emergency ventilator within 24 h of admission, NEWS score, arterial oxygen pressure/alveolar oxygen pressure ratio (PaO2/PAO2), alveolar-arterial oxygen difference (A-aDO2), serum creatinine (SCr), blood urea nitrogen (BUN), oxygenation index (OI), Glasgow Coma Scale (GCS), D-dimer, use of vasoactive drugs within 24 h of admission, C-reactive protein (CRP), procalcitonin (PCT), interleukin-6 (IL-6), N-terminal pro-B-type natriuretic peptide (NT-proBNP), quick Sequential Organ Failure Assessment (qSOFA) score, SOFA score, BLA level, NEWS with lactate (NEWS-L) score, SOFA score including lactate level (SOFA-L) score, Intensive Care Unit (ICU) length of stay, total hospital stay, ICU stay/total hospital stay, and septic shock condition were compared between groups. Logistic regression analysis was performed to assess the impact of various predictive factors on prognosis and to plot the receiver operating characteristic (ROC) curve. The results suggested marked differences between Group S and Group D in terms of mean age (t = -5.620; OR = -9.96, 95 % CI: -13.44∼-6.47; P < 0.001). Group S showed drastic differences in terms of mode of hospital admission (χ2 = 9.618, P < 0.01), method of initial management (χ2 = 51.766, P < 0.001), use of emergency ventilator within 24 h of admission (χ2 = 98.564, P < 0.001), incidence of septic shock (χ2 = 77.545, P < 0.001), use of vasoactive drugs within 24 h of admission (χ2 = 102.453, P < 0.001), heart rate (t = -4.063, P < 0.001), respiratory rate (t = -4.758, P < 0.001), oxygenation status (χ2 = 20.547, P < 0.001), NEWS score (t = -6.120, P < 0.001), PaO2/PAO2 ratio (t = 2.625, P < 0.01), A-aDO2 value (Z = -3.581, P < 0.001), OI value (Z = -3.106, P < 0.01), PLT value (Z = -2.305, P < 0.05), SCr value (Z = -3.510, P < 0.001), BUN value (Z = -3.170, P < 0.01), D-dimer (Z = -4.621, P < 0.001), CRP level (Z = -4.057, P < 0.001), PCT value (Z = -2.783, P < 0.01), IL-6 level (Z = -2.904, P < 0.001), length of hospital stay (Z = -4.138, P < 0.001), total hospital stay (Z = -8.488, P < 0.001), CCU/total hospital stay (Z = -9.118, P < 0.001), NEWS score (t = -6.120, P < 0.001), SOFA score (t = -6.961, P < 0.001), SOFA-L score (Z = -4.609, P < 0.001), NEWS-L score (Z = -5.845, P < 0.001), BLA level (Z = -6.557, P < 0.001), and GCS score (Z = 6.909, P < 0.001) when compared to Group D. The use of ventilators, septic shock, PCT, NEWS score, GCS score, SOFA score, SOFA-L score, NEWS-L score, and BLA level were identified as independent risk factors for predicting the prognosis of sepsis patients (P < 0.001). The areas under ROC curve (AUC) of blood lactic acid, PCT, NEWS, NEWS-L, GCS, SOFA, and SOFA-L were 0.695, 0.665, 0.692, 0.698, 0.477, 0.700, and 0.653, respectively. These findings indicate that the combination of BLA with NEWS (NEWS-L) score and SOFA score has certain advantages in assessing the prognosis of sepsis.

Integrated transcriptomic and pathway analyses of sorghum plants revealed the molecular mechanisms of host defense against aphids.

Sugarcane aphid has emerged as a major pest of sorghum recently, and a few sorghum accessions were identified for resistance to this aphid so far. However, the molecular and genetic mechanisms underlying this resistance are still unclear. To understand these mechanisms, transcriptomics was conducted in resistant Tx2783 and susceptible BTx623 sorghum genotypes infested with sugarcane aphids. A principal component analysis revealed differences in the transcriptomic profiles of the two genotypes. The pathway analysis of the differentially expressed genes (DEGs) indicated the upregulation of a set of genes related to signal perception (nucleotide-binding, leucine-rich repeat proteins), signal transduction [mitogen-activated protein kinases signaling, salicylic acid (SA), and jasmonic acid (JA)], and plant defense (transcription factors, flavonoids, and terpenoids). The upregulation of the selected DEGs was verified by real-time quantitative PCR data analysis, performed on the resistant and susceptible genotypes. A phytohormone bioassay experiment showed a decrease in aphid population, plant mortality, and damage in the susceptible genotype when treated with JA and SA. Together, the results indicate that the set of genes, pathways, and defense compounds is involved in host plant resistance to aphids. These findings shed light on the specific role of each DEG, thus advancing our understanding of the genetic and molecular mechanisms of host plant resistance to aphids.

Genome-wide identification and characterization of greenbug-inducible NAC transcription factors in sorghum.

BACKGROUND: Sorghum (Sorghum bicolor) is an important cereal crop grown worldwide because of its multipurpose uses such as food, forage, and bioenergy feedstock and its wide range of adaption even in marginal environments. Greenbug can cause severe damage to sorghum plants and yield loss. Plant NAC transcription factors (TFs) have been reported to have diverse functions in plant development and plant defense but has not been studied in sorghum yet. METHODS AND RESULTS: In this study, a comprehensive analysis of the sorghum NAC (SbNAC) gene family was conducted through genome-wide analysis. A total of 112 NAC genes has been identified in the sorghum genome. These SbNAC genes are phylogenetically clustered into 15 distinct subfamilies and unevenly distribute in clusters at the telomeric ends of each chromosome. Twelve pairs of SbNAC genes are possibly involved in the segmental duplication among nine chromosomes except chromosome 10. Structure analysis showed the diverse structures with a highly variable number of exons in the SbNAC genes. Furthermore, most of the SbNAC genes showed specific temporal and spatial expression patterns according to the results of RNA-seq analysis, suggesting their diverse functions during sorghum growth and development. We have also identified nine greenbug-inducible SbNAC genes by comparing the expression profiles between two sorghum genotypes (susceptible BTx623 and resistant PI607900) in response to greenbug infestation. CONCLUSIONS: Our systematic analysis of the NAC gene expression profiles provides both a preliminary survey into their roles in plant defense against insect pests and a useful reference for in-depth characterization of the SbNAC genes and the regulatory network that contributes genetic resistance to aphids.

Spectrum of PHEX Mutations and FGF23 Profiles in a Taiwanese Cohort With X-Linked Hypophosphatemia Including 102 Patients.

BACKGROUND/AIM: X-linked hypophosphatemia (XLH), the most common form of hereditary rickets, results from loss-of-function mutations in the phosphate-regulating PHEX gene. Elevated fibroblast growth factor 23 (FGF23) contributes to hypophosphatemia in XLH. This study aimed to characterize PHEX variants and serum FGF23 profiles in Taiwanese patients with XLH. PATIENTS AND METHODS: We retrospectively reviewed the records of 102 patients clinically suspected of having hypophosphatemic rickets from 2006 to 2022. Serum intact Fibroblast growth factor-23 (iFGF23) levels were measured on clinic visit days. PHEX mutations were identified using Sanger sequencing, and negative cases were analyzed using whole-exome sequencing. RESULTS: The majority (92.1%) of patients exhibited elevated FGF23 compared with normal individuals. Among 102 patients, 44 distinct PHEX mutations were identified. Several mutations recurred in multiple unrelated Taiwanese families. We discovered a high frequency of novel PHEX mutations and identified variants associated with extreme FGF23 elevation and tumorigenesis. CONCLUSION: Our findings revealed the PHEX genotypic variants and FGF23 levels in Taiwanese patients with XLH. These results are crucial given the recent approval of burosumab, a monoclonal FGF23 antibody, for XLH therapy. This study provides key insights into the clinical management of XLH in Taiwan.

Correction to: Decreased sustained attention, processing speed and verbal learning memory in patients with insomnia in Chinese young and middle-aged adults: a cross-sectional study.

[This corrects the article DOI: 10.1007/s41105-020-00262-0.].