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: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.
Project description:Recent completion of the telomere-to-telomere (T2T) genome assembly has enabled a comprehensive characterization of pericentromeric SatⅠ, SatII, SatⅢ and centromeric α-satellite repeats. SatⅢ DNA constitutes ~1.56% of the genome with a reported localization across 16 chromosomes. The transcription activity of SatⅢ DNA across genome and the sequence of SatⅢ transcripts remained largely unclear. We performed nanopore long-read RNA sequencing (RNA-seq) in untreated (UN), sodium arsenite (SA: 0.1mM, 5 h) and heat shock (HS: 42°C, 2 h; 37°C, 1 h) stressed HeLa cells to characterize SatⅢ transcripts . Since a portion of SatⅢ transcripts is non-polyadenylated, We performed polyadenylated (poly(A)+) and rRNA-depleted (ribo-) nanopore cDNA long-read RNA-seq.