Pan-genome analysis of the R2R3-MYB genes family in unveils phylogenetic divergence and expression profiles under hormone and abiotic stress treatments.

Introduction: The R2R3-MYB transcription factors (TFs) are pivotal regulators of plant growth, development, and stress responses. However, their genetic diversity and functional roles in remain underexplored at a pan-genome scale.

Methods: We identified R2R3-MYB genes in 18 published rapeseed genomes and analyzed their genomic distribution patterns, gene duplication, selective pressure, gene structure, conserved motifs, and phylogenetic relationships using a pan-genome approach.

Association between Systemic Inflammation and Worsening Renal Function in Cardiovascular-Kidney-Metabolic Syndrome.

Introduction: As a concept recently proposed by the American Heart Association (AHA), cardiovascular-kidney-metabolic (CKM) syndrome is characterized by the interplay of cardiovascular, renal, and metabolic dysfunctions. However, previous studies constantly focused on the cardiovascular outcomes, and there is scarce evidence addressing the association between chronic systemic inflammation and long-term changes in kidney function in the progression of CKM syndrome. This study aimed to investigate the association between the systemic inflammation and worsening renal function (WRF) in individuals with CKM syndrome.

Construction of a postoperative liver metastasis prediction model for colorectal cancer based on spectral CT imaging, CEA, and CA19-9.

Background: Most existing models for predicting liver metastasis primarily rely on single clinical indicators or traditional imaging features, which, while useful, offer limited accuracy and reliability. In recent years, spectral computed tomography (CT) has emerged as a dual-energy imaging technology that provides detailed quantitative analyses of the blood supply characteristics and metabolic activity of tumors. The integration of serum biomarkers such as carcinoembryonic antigen (CEA) and cancer antigen 19-9 (CA19-9) with spectral CT features holds great potential for significantly enhancing the accuracy of liver metastasis predictions.

Telomere-to-telomere gapless genome assembly of Triplophysa yaopeizhii.

The genus Triplophysa exhibits remarkable adaptability to the unique environment found at the Qinghai-Tibet Plateau (QTP). Higher quality genomes are helpful to the study of the adaptability to the extreme environment in the plateau. This study utilized PacBio HiFi, Ultra-long ONT, and Hi-C sequencing of Triplophysa yaopeizhii to construct the first telomere-to-telomere (T2T) gapless genome assembly of the genus Triplophysa.

Correction to: The pan-NLRome analysis based on 23 genomes reveals the diversity of NLRs in .

[This corrects the article DOI: 10.1007/s11032-024-01522-4.].

The pan-NLRome analysis based on 23 genomes reveals the diversity of NLRs in .

, a globally significant oilseed crop, exhibits a wide distribution across diverse climatic zones. is being increasingly susceptible to distinct diseases, such as blackleg, clubroot and sclerotinia stem rot, leading to substantial reductions in yield. Nucleotide-binding site leucine-rich repeat genes (), the most pivotal family of resistance genes, can be effectively harnessed by identifying and uncovering their diversity to acquire premium disease-resistant gene resources.

AMIR: a multi-omics data platform for Asteraceae plants genetics and breeding research.

As the largest family of dicotyledon, the Asteraceae family comprises a variety of economically important crops, ornamental plants and numerous medicinal herbs. Advancements in genomics and transcriptomic have revolutionized research in Asteraceae species, generating extensive omics data that necessitate an efficient platform for data integration and analysis. However, existing databases face challenges in mining genes with specific functions and supporting cross-species studies.

PCMD: A multilevel comparison database of intra- and cross-species metabolic profiling in 530 plant species.

Comparative metabolomics plays a crucial role in investigating gene function, exploring metabolite evolution, and accelerating crop genetic improvement. However, a systematic platform for intra- and cross-species comparison of metabolites is currently lacking. Here, we report the Plant Comparative Metabolome Database (PCMD; http://yanglab.

Natural variation in BnaA07.MKK9 confers resistance to Sclerotinia stem rot in oilseed rape.

Sclerotinia stem rot (SSR), caused by the necrotrophic fungus Sclerotinia sclerotiorum, is one of the most devastating diseases for several major oil-producing crops. Despite its impact, the genetic basis of SSR resistance in plants remains poorly understood. Here, through a genome-wide association study, we identify a key gene, BnaA07.

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore.

Domesticated herbivores are an important agricultural resource that play a critical role in global food security, particularly as they can adapt to varied environments, including marginal lands. An understanding of the molecular basis of their biology would contribute to better management and sustainable production. Thus, we conducted transcriptome sequencing of 100 to 105 tissues from two females of each of seven species of herbivore (cattle, sheep, goats, sika deer, horses, donkeys, and rabbits) including two breeds of sheep.

PeNAC67-PeKAN2-PeSCL23 and B-class MADS-box transcription factors synergistically regulate the specialization process from petal to lip in Phalaenopsis equestris.

The molecular basis of orchid flower development involves a specific regulatory program in which MADS-box transcription factors play a central role. The recent 'perianth code' model hypothesizes that two types of higher-order heterotetrameric complexes, namely SP complex and L complex, play pivotal roles in the orchid perianth organ formation. Therefore, we explored their roles and searched for other components of the regulatory network.

Direct Bilirubin, but not Indirect Bilirubin, is Associated with Short-term Adverse Events in HFpEF.

Objective: Abnormal live function tests have been identified as independent risk factors for ominous prognosis in patients with heart failure. However, most of the previous studies have failed to determine the contribution of direct bilirubin (DBIL) and indirect bilirubin (IBIL) separately. Hence, we aimed to explore whether DBIL or IBIL is correlated with the prognosis of heart failure with preserved ejection fraction (HFpEF).

AnimalMetaOmics: a multi-omics data resources for exploring animal microbial genomes and microbiomes.

The Animal Meta-omics landscape database (AnimalMetaOmics, https://yanglab.hzau.edu.

SoyMD: a platform combining multi-omics data with various tools for soybean research and breeding.

Advanced multi-omics technologies offer much information that can uncover the regulatory mechanisms from genotype to phenotype. In soybean, numerous multi-omics databases have been published. Although they cover multiple omics, there are still limitations when it comes to the types and scales of omics datasets and analysis methods utilized.

INSurVeyor: improving insertion calling from short read sequencing data.

Insertions are one of the major types of structural variations and are defined as the addition of 50 nucleotides or more into a DNA sequence. Several methods exist to detect insertions from next-generation sequencing short read data, but they generally have low sensitivity. Our contribution is two-fold.

Comparative transcriptome profiling reveals the multiple levels of crosstalk in phytohormone networks in Brassica napus.

Plant hormones are the intrinsic factors that control plant development. The integration of different phytohormone pathways in a complex network of synergistic, antagonistic and additive interactions has been elucidated in model plants. However, the systemic level of transcriptional responses to hormone crosstalk in Brassica napus is largely unknown.