Project description:Duckweeds are a monophyletic group of rapidly reproducing aquatic monocots in the Lemnaceae family. Spirodela polyrhiza, the Greater Duckweed, has the largest body plan yet the smallest genome size in the family (1C = 150 Mb). Given their clonal, exponentially fast reproduction, a key question is whether genome structure is conserved across the species in the absence of meiotic recombination. We generated a highly contiguous, chromosome-scale assembly of Spirodela polyrhiza line Sp7498 using Oxford Nanopore plus Hi-C scaffolding (Sp7498_HiC) that is highly syntenic with a related line (Sp9509). Both the Sp7498_HiC and Sp9509 genome assemblies reveal large chromosomal misorientations in a recent PacBio assembly of Sp7498, highlighting the necessity of orthogonal long-range scaffolding techniques like Hi-C and BioNano optical mapping. Proteome analysis of Sp7498 verified the expression of nearly 2,250 proteins and revealed a high level of proteins involved in photosynthesis and carbohydrate metabolism among other functions. In addition, a strong increase in chloroplast proteins was observed that correlated to chloroplast density. This Sp7498_HiC genome was generated cheaply and quickly with a single Oxford Nanopore MinION flow cell and one Hi-C library in a classroom setting. Combining these data with a mass spectrometry-generated proteome, demonstrates that duckweed is a model for genomics- and proteomics-based education.
Project description:The Global Pandemic Lineage (GPL) of the amphibian pathogen Batrachochytrium dendrobatidis (Bd) has been described as a main driver of amphibian extinctions on nearly every continent. Near complete genome of three Bd-GPL strains have enabled studies of the pathogen but the genomic features that set Bd-GPL apart from other Bd lineages is not well understood due to a lack of high-quality genome assemblies and annotations from other lineages. We used long-read DNA sequencing to assemble high-quality genomes of three Bd-BRAZIL isolates and one non-pathogen outgroup species Polyrhizophydium stewartii (Ps) strain JEL0888, and compared these to genomes of previously sequenced Bd-GPL strains. The Bd-BRAZIL assemblies range in size between 22.0 and 26.1 Mb and encode 8495-8620 protein-coding genes for each strain. Our pan-genome analysis provided insight into shared and lineage-specific gene content. The core genome of Bd consists of 6278 conserved gene families, with 202 Bd-BRAZIL and 172 Bd-GPL specific gene families. We discovered gene copy number variation in pathogenicity gene families between Bd-BRAZIL and Bd-GPL strains though none were consistently expanded in Bd-GPL or Bd-BRAZIL strains. Comparison within the Batrachochytrium genus and two closely related non-pathogenic saprophytic chytrids identified variation in sequence and protein domain counts. We further test these new Bd-BRAZIL genomes to assess their utility as reference genomes for transcriptome alignment and analysis. Our analysis examines the genomic variation between strains in Bd-BRAZIL and Bd-GPL and offers insights into the application of these genomes as reference genomes for future studies.
2024-01-31 | GSE253912 | GEO
Project description:Chromosome-level genome assemblies of sunflower oilseed and confectionery cultivars
Project description:Background: In both Turner syndrome (TS) and Klinefelter syndrome (KS) copy number aberrations of the X chromosome lead to various developmental symptoms. To date there has not been a comprehensive and directly comparative analysis of TS vs. KS regarding the changes on the molecular level Methods: We analyzed gene expression patterns with RNA-Seq and DNA methylation patterns with the CpGiant assay in lymphocytes, and chromatin conformation with in situ Hi-C in lymphoblastoid cell lines, from TS and KS patients together with their same gender controls. Results: In TS, differentially expressed escape genes were downregulated but differentially expressed inactive genes were upregulated. In KS, differentially expressed escape genes were upregulated while inactive genes appeared unchanged. Interestingly, 81 differentially expressed genes (DEGs) were associated with both TS and KS, and uniformly displayed expression changes into opposite directions. DEGs on the X chromosome and the autosomes were coexpressed in both TS and KS, indicating that there are molecular ripple effects of the changes in X chromosome dosage that extend to autosomes. Four potentially candidate genes (RPS4X, SEPT6, NKRF and CX0rf57) for KS were identified on Xq. Broad hypomethylation of the X chromosome is observed in TS whereas hypermethylation of chromosome X is present in KS. Only promoters of inactive genes were differentially methylated in both TS and KS while escape genes remained unchanged. The intrachromosomal contact map of the X chromosome in TS was partitioned into two superdomains and exhibited the structure of an active X chromosome. Conclusions: Components of the molecular basis of TS and KS were identified on the levels of the transcriptome and the epigenome, with candidate central genes on Xp for TS and on Xq for KS. The discovery of shared DEGs indicates the existence of common molecular mechanisms for gene regulation in TS and KS that are transmitting the gene dosage changes to the transcriptome.