Additional file 1: Summary of the NORMAN-SLE datasets (CSV format) as of 4 May 2022 [81].

Additional file 10: Table S5. The list of DMRs and annotation.

Additional file 11: Table S6. The list of genes harboring DMCs or overlapping with DMRs.

Additional file 13: Table S8. The list of differentially methylated haplotype blocks (dMHBs) and functional enrichment for hyper dMHBs.

Additional file 17: Table S12. The cluster of functional annotations enriched by differential methylated and expressed genes (MetGDE genes).

Additional file 7: Table S2. Read mapping statistics of whole-genome bisulfite sequencing data and RNA sequencing data of six cows.

Additional file 10. List of GenBank accession numbers associated with the genomes generated by this study and of the genomes downloaded and used for comparison.

Verticillium dahliae is an important soil-borne pathogen causing Verticillium wilt. It is also the primary causal agent of the Potato Early Dying, a disease complex involving the root-lesion nematode. Here, we report the whole-genome sequencing of 192 isolates of V. dahliae originating from the major potato production areas across Canada. Our results yielded a resource of 277,010 genetic variations that will be useful for genetic analyses and revealed the presence of two major lineages, both...

The emerging COVID-19 caused by SARS-CoV-2 infection poses severe challenges to global public health. Serum antibody testing is becoming one of the critical methods for the diagnosis of COVID-19 patients. We investigated IgM and IgG responses against SARS-CoV-2 nucleocapsid (N) and spike (S) protein after symptom onset in the intensive care unit (ICU) and non-ICU patients. 130 blood samples from 38 COVID-19 patients were collected. The levels of IgM and IgG specific to N and...

Basidiomycete yeasts have recently been reported as stably associated secondary fungal symbionts (SFSs) of many lichens, but their role in the symbiosis remains unknown. Attempts to sequence their genomes have been hampered both by the inability to culture them and their low abundance in the lichen thallus alongside two dominant eukaryotes (an ascomycete fungus and chlorophyte alga). Using the lichen Alectoria sarmentosa, we selectively dissolved the cortex layer in which SFSs are embedded to enrich...

Additional file 1. Genomic sequences and their corresponding annotations of 25 flowering plants.

Additional file 6. The collected transcriptome analysis data.

Additional file 4 Significant enrichment functions (n = 39) of conserved lncRNA set (n = 196).

The emerging COVID-19 caused by SARS-CoV-2 infection poses severe challenges to global public health. Serum antibody testing is becoming one of the critical methods for the diagnosis of COVID-19 patients. We investigated IgM and IgG responses against SARS-CoV-2 nucleocapsid (N) and spike (S) protein after symptom onset in the intensive care unit (ICU) and non-ICU patients. 130 blood samples from 38 COVID-19 patients were collected. The levels of IgM and IgG specific to N and...

Additional file 4: Summary of Zenodo citations plus DOIs per list (CSV format) as of 1 May 2022 [236].

Additional file 3. Curated output from dbCAN for grouping and counting the number of genes in specific CAZyme families.

Additional file 6. Number of core, accessory, and singleton genes on individual contigs of the long-read assemblies of I-73-1 and D308.

Additional file 10. List of GenBank accession numbers associated with the genomes generated by this study and of the genomes downloaded and used for comparison.

Additional file 10: Table S5. The list of DMRs and annotation.

Additional file 9: Table S4. The number of DMCs (CpG, CHG and CHH) in different genetic regions.

Additional file 9: Table S4. The number of DMCs (CpG, CHG and CHH) in different genetic regions.

Additional file 15: Table S10. The genome-wide correlation between DNA methylation and gene expression and list of MetGDE genes.

Additional file 15: Table S10. The genome-wide correlation between DNA methylation and gene expression and list of MetGDE genes.

Additional file 16: Table S11. The results of functional enrichment differentially methylated and expressed genes (MetGDE genes).

Patients with acute myeloid leukaemia (AML) have poor prognoses and low overall survival (OS) rates owing to its heterogeneity and the complexity of its tumour microenvironment (TME). N6-methyladenosine (m6A) modification plays a key role in the initiation and progression of haematopoietic malignancies. However, the underlying function of m6A regulators in AML remains elusive. This study thoroughly analysed the m6A modification features of 177 AML patients based on 22 m6A regulators. Utilizing unsupervised clustering, we determined...