Project description:Nematodes encompass over 24,000 described species, which were discovered in almost every ecological habitat, and make up over 80% of metazoan taxonomic diversity in soils. The last common ancestor of nematodes is believed to date back to around 650–750 million years, generating a large and phylogenetically diverse group to be explored. However, for most species high quality gene annotations are incomprehensive or missing. Combining short-read RNA sequencing with mass spectrometry-based proteomics and machine learning quality control in an approach called proteotranscriptomics, we improve gene annotations for 9 genome-sequenced nematode species and provide new gene annotations for 3 additional species without genome assemblies. Emphasizing the sensitivity of our methodology, we provide evidence for two hitherto undescribed genes in the model organism Caenorhabditis elegans. Extensive phylogenetic systems analysis using this comprehensive proteome annotation provides new insights into evolutionary processes of this metazoan group.
2022-11-12 | PXD034107 | Pride
Project description:Deception Bay metazoan eDNA metagenomics
Project description:Some features underlying replication origin activation in metazoan cells have been identified, but little is known about their regulation during metazoan development. Using the nascent strand purification method, we identified replication origins throughout Caenorhabditis elegans embryonic development and found that the origin repertoire is thoroughly reorganized after gastrulation onset. During the pluripotent embryonic stages (pre-gastrula), potential cruciform structures and open chromatin are determinant factors to establish replication origins. The enrichment of replication origins in transcription factor binding sites and their presence inside promoters of highly transcribed genes, particularly operons, argue that transcriptional activity contributes to replication initiation before gastrulation. After the gastrula transition, when differentiation programs are set in the embryos, origins are particularly selected at enhancers, in the vicinity of CGI-like sequences, and non-coding genes. Our findings suggest that origin selection coordinates replication initiation with transcriptional programs during metazoan development.
2017-01-22 | GSE86651 | GEO
Project description:COI environmental DNA sequencing of metazoan communities across Indonesia
Project description:Proteomics data from gel band excision in support of "The proteasome as a drug target in the metazoan pathogen, Schistosoma mansoni"