Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
Project description:The complete assembly of vast and complex plant genomes, like the hexaploid wheat genome, remains challenging. Here, we present CS-IAAS, a comprehensive telomere-to-telomere (T2T) gap-free Triticum aestivum L. reference genome, encompassing 14.51 billion base pairs and featuring all 21 centromeres and 42 telomeres. Annotation revealed 90.8 Mb additional centromeric satellite arrays and 5,611 ribosomal DNA(rDNA) units. Genome-wide rearrangements, centromeric elements, TE expansion, and segmental duplications were deciphered during tetraploidization and hexaploidization, providing a comprehensive understanding of wheat subgenome evolution. Among them, TE insertions during hexaploidization greatly influenced gene expression balances, thus increasing the genome plasticity of transcriptional levels. Additionally, we generated 163,329 full-length cDNA sequences and proteomic data that helped annotate 141,035 high-confidence (HC) protein-coding genes. However, in such a hexaploidy genome, 20.05%, 33.43%, and 42.76% of gene transcript levels, alternative splicing events, and protein levels were detected unbalancing among subgenomes. The complete T2T reference genome (CS-IAAS), along with its transcriptome and proteome, represents a significant step in our understanding of wheat genome complexity, and provides insights for future wheat research and breeding.
Project description:Here we performed a comprehensive genomic and proteomics analysis of P. stutzeri in aerobic and oxygen-limiting conditions. We combined de novo genome assembly relying on 3rd generation long read sequencing technologies to report the first complete P. stutzeri ATCC14405 genome, which added over 110 kb of sequence and contains 126 full length CDS that were only partially covered in the fragmented short read-based genome assembly available for this strain. With this optimal basis for downstream functional genomics, we next carried out state of the art bottom-up and top-down proteomics analyses to report the most detailed study of proteome remodeling in response to oxygen limitation in P. stutzeri. We identified more than 2900 proteins, i.e. greater than 70% of the theoretical proteome, including 160 annotated small proteins. The proteins included well-established enzymes involved in denitrification and metabolic adaptation to oxygen-limiting conditions, as well as uncharacterized proteins. Notably, we identified 16 novel small proteins that had so far been missed in the genome annotation.