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Open Genomes Telomere-to-Telomere (T2T) Reference Realignment Project

ABSTRACT: This project realigns reads from publicly available genomes to the new Telomere-to-Telomere (T2T) CHM13-HG002 reference genome.

PROVIDER: PRJEB11561 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10012059.fastq.gz	Fastqsanger.gz
	ERR10012060.fastq.gz	Fastqsanger.gz
	ERR10012061.fastq.gz	Fastqsanger.gz
	ERR10012062.fastq.gz	Fastqsanger.gz
	ERR12015054.fastq.gz	Fastqsanger.gz

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Epigenetic centromere identity is precisely maintained through DNA replication but is uniquely specified among human cells

Project description:Centromere identity is defined and maintained epigenetically by the presence of the histone variant CENP-A. How centromeric CENP-A position is specified and precisely maintained through DNA replication is not fully understood. The recently released Telomere-to-Telomere (T2T-CHM13) genome assembly containing the first complete human centromere sequences provides a new resource for examining CENP-A position. Mapping CENP-A position in clones of the same cell line to T2T-CHM13 identified highly similar CENP-A position following multiple cell divisions. In contrast, centromeric CENP-A epialleles were evident at several centromeres of different human cell lines, demonstrating the location of CENP-A enrichment and site of kinetochore recruitment varies among human cells. Across the cell cycle, CENP-A molecules deposited in G1 phase are maintained at their precise position through DNA replication. Thus, despite CENP-A dilution during DNA replication, CENP-A is precisely reloaded onto the same sequences within the daughter centromeres, maintaining unique centromere identity among human cells.

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A complete telomere-to-telomere genome of bread wheat presents insights into the evolution, transcriptome, and proteome of a hexaploid genome

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.

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Project description:Curated publicly available nanopore datasets

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The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis

Project description:BACKGROUND: Traditional Chinese medicine has used Peucedanum praeruptorum Dunn (Apiaceae) for a long time. Various coumarins, including the significant root constituents Praeruptorin (A-E), are the active constituents of the dried roots of P. praeruptorum. Previous transcriptomic and metabolomic studies attempted to elucidate the distribution and biosynthetic network of these medicinal-valuable compounds. However, the lack of a high-quality reference genome impedes an in-depth understanding of genetic traits and, thus, the development of better breeding strategies.RESULTS: The authors assembled a telomere-to-telomere genome by combining PacBio HiFi, ONT ultra- long and Hi-C data. The final genome assembly was approximately 1.798 Gb, assigned to 11 chromosomes and genome completeness >98%. Comparative genomic analysis suggested that P. praeruptorum experienced two WGD events like the ones in the Apiaceae family. By the transcriptomic and metabolomic analysis of the coumarin metabolic pathway, we presented coumarins' spatial and temporal distribution and the expression patterns of critical genes for its biosynthesis. Notably, the COSY and cytochrome P450 genes showed tandem duplications on several chromosomes, which may be responsible for the high accumulation of coumarins.CONCLUSIONS: The authors obtained a T2T genome for P. praeruptorum, which provides molecular insights into the chromosomal distribution of the coumarin biosynthetic genes. This high-quality genome is an essential resource for designing engineering strategies for improving the production of these valuable compounds.

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