HORmon: automated annotation of human centromeres

Kunyavskaya, Olga; Dvorkina, Tatiana; Bzikadze, Andrey V.; Alexandrov, I. A.; Pevzner, Pavel A.

doi:10.1101/2021.10.12.464028

Cited by 7 publications

(17 citation statements)

References 35 publications

(37 reference statements)

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“…Further, we did not identify any new SatDNA family organized in multi-unit higher-order repeats, although we confirmed the previously described pBuM-2 α/β alternating repeats of D. seriema ( Kuhn et al 2008 ; de Lima et al 2017 ). However, future long-read sequencing approaches are necessary for a proper study of higher-order repeats ( Kunyavskaya et al 2021 ).…”

Section: Resultsmentioning

confidence: 99%

In-Depth Satellitome Analyses of 37 Drosophila Species Illuminate Repetitive DNA Evolution in the Drosophila Genus

Ruiz‐Ruano

2022

Genome Biology and Evolution

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Satellite DNAs (SatDNA) are ubiquitously present in eukaryotic genomes and have been recently associated with several biological roles. Understanding the evolution and significance of SatDNA requires an extensive comparison across multiple phylogenetic depths. We combined the RepeatExplorer pipeline and cytogenetic approaches to conduct a comprehensive identification and analysis of the satellitome in 37 species from the genus Drosophila. We identified 188 SatDNA-like families, 112 of them being characterized for the first time. Repeat analysis within a phylogenetic framework has revealed the deeply divergent nature of SatDNA sequences in the Drosophila genus. The SatDNA content varied from 0.54% of the D. arizonae genome to 38.8% of the D. albomicans genome, with the SatDNA content often following a phylogenetic signal. Monomer size and GC-content also showed extreme variation ranging 2-570 bp and 9.1-71.4%, respectively. SatDNA families are shared among closely related species, consistent with the SatDNA library hypothesis. However, we uncovered the emergence of species-specific SatDNA families through amplification of unique or low abundant sequences in a lineage. Finally, we found that genome sizes of the Sophophora subgenus are positively correlated with transposable element content, whereas genome size in the Drosophila subgenus is positively correlated with SatDNA. This finding indicates genome size could be driven by different categories of repetitive elements in each subgenus. Altogether, we conducted the most comprehensive satellitome analysis in Drosophila from a phylogenetic perspective and generated the largest catalog of SatDNA sequences to date, enabling future discoveries in SatDNA evolution and Drosophila genome architecture.

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Section: Resultsmentioning

confidence: 99%

In-Depth Satellitome Analyses of 37 Drosophila Species Illuminate Repetitive DNA Evolution in the Drosophila Genus

Ruiz‐Ruano

2022

Genome Biology and Evolution

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“…5b) but different in CEN13 monomer 1 and CEN18 monomers 2 and 3 due to a few-nucleotide difference (Additional file 1: Fig. S5c, d) [14].…”

Section: Comparison With Hormon Annotationmentioning

confidence: 99%

“…Finally, hybrid monomers, which are a concatenate of two or even more monomers, are also important for comprehensively studying centromere architecture and evolution. Hybrid monomers were hypothesized as the "birth" of new frequent monomers and were reported in human CEN5 and CEN8 [14].…”

Section: Annotation Of Centromere Structures In the Plant Genomementioning

confidence: 99%

“…We obtained active alpha satellite arrays from the complete sequence of the human CHM13 cell line assembled by the T2T Consortium (version 1.0) [11,14] monomer TR detection module (Additional file 1: Fig. S2a and Additional file 1: Supplementary method) to detect new TRs with a given TR unit length.…”

Section: Datasets In Humans and Arabidopsis Thalianamentioning

confidence: 99%

“…To address this question, Dvorkina et al proposed the first automatic centromere annotation tool, CentromereArchitect [10], which was based on StringDecomposer (SD) [4], an algorithm for detecting sequence blocks by taking monomer templates to decompose centromere DNA sequences. In CentromereArchitect, monomer inference and HOR detection were considered two separate problems without interconnections, which often led to biologically inadequate annotation [14]. The authors next proposed HORmon [14] based on the centromere evolution postulate (CE postulate, where each monomer appears only once in the HOR 4 unit) to address the lack of interconnection issue in CentromereArchitect.…”

Section: Introductionmentioning

confidence: 99%

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HiCAT: A tool for automatic annotation of centromere structure

Gao

Yang

Zhao

et al. 2022

Preprint

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Significant improvements in long-read sequencing technologies have unlocked complex genomic areas, such as centromeres, in the genome and introduced the centromere annotation problem. Currently, centromeres are annotated in a semi-manual way. Here, we propose HiCAT, a generalizable automatic centromere annotation tool, based on hierarchical tandem repeat mining and maximization of tandem repeat coverage to facilitate decoding of centromere architecture. We applied HiCAT to human CHM13-T2T and gapless Arabidopsis thaliana genomes. Our results not only were generally consistent with previous inferences but also greatly improved annotation continuity and revealed additional fine structures, demonstrating HiCAT's performance and general applicability.

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Complete genomic and epigenetic maps of human centromeres

Altemose¹,

Rogaev²,

Alexandrov³

et al. 2021

Preprint

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Existing human genome assemblies have almost entirely excluded highly repetitive sequences within and near centromeres, limiting our understanding of their sequence, evolution, and essential role in chromosome segregation. Here, we present an extensive study of newly assembled peri/centromeric sequences representing 6.2% (189.9 Mb) of the first complete, telomere-to-telomere human genome assembly (T2T-CHM13). We discovered novel patterns of peri/centromeric repeat organization, variation, and evolution at both large and small length scales. We also found that inner kinetochore proteins tend to overlap the most recently duplicated subregions within centromeres. Finally, we compared chromosome X centromeres across a diverse panel of individuals and uncovered structural, epigenetic, and sequence variation at single-base resolution across these regions. In total, this work provides an unprecedented atlas of human centromeres to guide future studies of their complex and critical functions as well as their unique evolutionary dynamics.

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HORmon: automated annotation of human centromeres

Cited by 7 publications

References 35 publications

In-Depth Satellitome Analyses of 37 Drosophila Species Illuminate Repetitive DNA Evolution in the Drosophila Genus

In-Depth Satellitome Analyses of 37 Drosophila Species Illuminate Repetitive DNA Evolution in the Drosophila Genus

HiCAT: A tool for automatic annotation of centromere structure

Complete genomic and epigenetic maps of human centromeres

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