The structure, function, and evolution of a complete human chromosome 8

Abstract

The complete assembly of each human chromosome is essential for understanding human biology and evolution. Using complementary long-read sequencing technologies, we complete the first linear assembly of a human autosome, chromosome 8. Our assembly resolves the sequence of five previously long-standing gaps, including a 2.08 Mbp centromeric α-satellite array, a 644 kbp defensin copy number polymorphism important for disease risk, and an 863 kbp variable number tandem repeat at chromosome 8q21.2 that can function as a neocentromere. We show that the centromeric α-satellite array is generally methylated except for a 73 kbp hypomethylated region of diverse higher-order α-satellite enriched with CENP-A nucleosomes, consistent with the location of the kinetochore. Using a dual long-read sequencing approach, we complete the assembly of the orthologous chromosome 8 centromeric regions in chimpanzee, orangutan, and macaque for the first time to reconstruct its evolutionary history. Comparative and phylogenetic analyses show that the higher-order α-satellite structure evolved specifically in the great ape ancestor, and the centromeric region evolved with a layered symmetry, with more ancient higher-order repeats located at the periphery adjacent to monomeric α-satellites. We estimate that the mutation rate of centromeric satellite DNA is accelerated at least 2.2-fold, and this acceleration extends beyond the higher-order α-satellite into the flanking sequence.

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

“…We generated a de novo multiplatform assembly of a female bird-of-paradise genome by combining the cutting-edge technologies that are now being implemented in many assembly projects (Bickhart et al, 2017;Faino et al, 2015;Gordon et al, 2016;Michael et al, 2018;Rhie et al 2020;Seo et al, 2016;Teeling et al, 2018;Weissensteiner et al, 2017;Yoshimura et al, 2019), namely Illumina short reads, 10X Genomics linked reads, PacBio long reads and two proximity ligation maps with Dovetail CHiCAGO and Phase…”

“…(i) Hi-C heatmaps were used to identify and correct misassemblies between and within chromosome models. This multiplatform approach is similar to those of large-scale sequencing projects such as the Bat1K Initiative (Teeling et al, 2018) and the Vertebrate Genomes Project (Rhie et al, 2020) [Colour figure can be viewed at wileyonlinelibrary.com] blastn 2.7.1 + results were collected, extended by 2 kb on both sides and aligned to one another with mafft 7.4.07. The alignments were manually curated applying the majority rule and the superfamily of repeats assessed following the Wicker et al (2007) classification.…”

“…Even though no single technology is currently able to yield telomere-to-telomere assemblies, it is still possible to bridge separate contigs into scaffolds using long-range physical data and obtain chromosome-level assemblies (Miga et al, 2020). Such scaffolding technologies are becoming more and more commonly used (Belser et al, 2018;Deschamps et al, 2018;Dudchenko et al, 2017;Li et al, 2019;Rhie et al, 2020;Wallberg et al, 2019). The two most common ones are linked reads (Weisenfeld et al, 2017) and proximity ligation techniques (reviewed in Sedlazeck et al, 2018).…”

Architecture and evolution of subtelomeres in the unicellular green algaChlamydomonas reinhardtii

“…But because of their intrinsically complex and repetitive nature, telomeres and subtelomeres are often misassembled or altogether absent in reference genomes of most species. For example, the human reference genome still lacks a comprehensive and accurate representation of its subtelomeres, although recent advances improved the assembly (Stong et al 2014; Logsdon et al 2020; Miga et al 2020; Young et al 2020). With the advent of long read sequencing technologies (Li et al 2017; Yue et al 2017; Kim et al 2019), we can look forward to better assemblies and descriptions of subtelomeres, enabling the mechanisms underlying their structural variations and evolution to be inferred for a diverse range of organisms.…”

Genomic architecture of 5S rDNA cluster and its variations within and between species

“…Availability of ultra-long reads from ONT or PacBio platforms is expected to accelerate the generation of complete genome sequence from telomere to telomere. With these technologies, the human chromosome 8, X, and Y were assembled with no gap albeit with some manual corrections [55–57]. With ultra-long reads of a higher read accuracy, the structure of 45S rDNA and other highly repetitive regions such as centromeres and telomeres are expected to be resolved in the coming years, leading to a gap-free genome, in human, model organisms and economically significant species in the years to come.…”