Additional file 1: Table S1. Prier used in this study. Table S2. List of 392 Glycine soja accessions and acumulated temperature zones. Table S3. 92 SNPs that significantly associated with flowering time in average across the two-year experiment (2020 and 2021). Table S4. The genes conresponding to the genomic regions surrounding ~50Kb of 92 SNPs that signficantly associated with flowering time in average in 2020 and 2021. Table S5. 28 candidate genes related to flowering...

Interkingdom competition occurs between hymenopteran parasitoids and insect viruses sharing the same insect hosts. It has been assumed that parasitoid larvae die with the death of infected host or as result of competition for host resources. Herein we describe a gene family, parasitoid killing factor (pkf), that encodes proteins toxic to parasitoids of the Microgastrinae group and determines parasitism success. Pkfs are found in several entomopathogenic DNA virus families and in some lepidopteran genomes. We...

Acalypha (Euphorbiaceae Acalyphoideae) is a large, monophyletic genus distributed worldwide in tropical and subtropical regions, with a few species extending into temperate Asia and North America. We reconstructed phylogenetic relationships within the genus using DNA sequences from the plastid ndhF and trnL-F regions and the nuclear ribosomal ITS region, sampling 143 species to represent the geographic, morphologic, and taxonomic diversity with the genus, resulting in a 162 (158 in Acalypha) terminal and 3847 character combined...

Fusarium head blight (FHB), primarily incited by Fusarium graminearum Schwabe, is the most devastating disease of barley (Hordeum vulgare L.) in Canada. Contaminated grains are unsuitable for use as livestock feed or by the malting industry, primarily due to contamination by mycotoxins such as deoxynivalenol (DON). Reducing DON content has been a long-term goal of barley breeders; however, the complex genetics of resistance and laborious testing required have made it difficult to develop resistant cultivars....

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

Additional file 4. Annotation of genes present within the 143 kb Starship transposon ‘Horizon’ present in the race 8 isolate I-73-1.

Additional file 4. Annotation of genes present within the 143 kb Starship transposon ‘Horizon’ present in the race 8 isolate I-73-1.

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 14: Table S9. The list of differentially expressed (DE) genes and their functional enrichment.

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

The genus Pythium (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of Pythium, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into Pythium sensu stricto (s.s.), Elongisporangium, Globisporangium, Ovatisporangium (= Phytopythium), and Pilasporangium using morphological characters and phylogenies of the mt cytochrome c oxidase subunit 2 (cox2) and D1–D2 domains of nuc 28S rDNA. Although...

Fusarium head blight (FHB), primarily incited by Fusarium graminearum Schwabe, is the most devastating disease of barley (Hordeum vulgare L.) in Canada. Contaminated grains are unsuitable for use as livestock feed or by the malting industry, primarily due to contamination by mycotoxins such as deoxynivalenol (DON). Reducing DON content has been a long-term goal of barley breeders; however, the complex genetics of resistance and laborious testing required have made it difficult to develop resistant cultivars....

Several members of Alternaria section Alternaria are economically important plant-pathogenic fungi that cause disease on a wide range of host types and plant tissues. The production of Alternaria-derived mycotoxins can lead to significant post-harvest losses due to contamination of agricultural products. Multiple Alternaria species are listed as regulated organisms, which are monitored by international plant protection programmes. These taxa often share high levels of both morphological and phylogenetic similarity, and the establishment of molecular markers...

The dataset is a tab-deliminted text file with genotyping information for a diploid potato progeny population derived from a cross of diploid potato clones 12120-03 X 07506-01. The SolCap 8303 Infinium Chip was used for SNP genotyping. It was originally generated for study on genetic mapping of Verticillium wilt resistance. The data was used again for analysis of segregation distortion in the most recent manuscript.

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.

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.