The string decomposition problem and its applications to centromere analysis and assembly

Abstract

Motivation Recent attempts to assemble extra-long tandem repeats (such as centromeres) faced the challenge of translating long error-prone reads from the nucleotide alphabet into the alphabet of repeat units. Human centromeres represent a particularly complex type of high-order repeats (HORs) formed by chromosome-specific monomers. Given a set of all human monomers, translating a read from a centromere into the monomer alphabet is modeled as the String Decomposition Problem. The accurate translation of reads into the monomer alphabet turns the notoriously difficult problem of assembling centromeres from reads (in the nucleotide alphabet) into a more tractable problem of assembling centromeres from translated reads. Results We describe a StringDecomposer (SD) algorithm for solving this problem, benchmark it on the set of long error-prone Oxford Nanopore reads generated by the Telomere-to-Telomere consortium and identify a novel (rare) monomer that extends the set of known X-chromosome specific monomers. Our identification of a novel monomer emphasizes the importance of identification of all (even rare) monomers for future centromere assembly efforts and evolutionary studies. To further analyze novel monomers, we applied SD to the set of recently generated long accurate Pacific Biosciences HiFi reads. This analysis revealed that the set of known human monomers and HORs remains incomplete. SD opens a possibility to generate a complete set of human monomers and HORs for using in the ongoing efforts to generate the complete assembly of the human genome. Availability and implementation StringDecomposer is publicly available on https://github.com/ablab/stringdecomposer. Supplementary information Supplementary data are available at Bioinformatics online.

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

“…First, the sequence scaffold and underlying ONT reads were subjected to RepeatMasker (v.3.3.0) to ensure that read overlaps were concordant in repeat structure. Second, the centromeric scaffold and underlying ONT reads were subjected to StringDecomposer 42 to validate the HOR organization in overlapping reads. Finally, the sequence scaffold for each target region was incorporated into the CHM13 chromosome 8 assembly previously generated 5 , thereby filling the gaps in the chromosome 8 assembly.…”

“…The in silico digestion analysis indicates that the chromosome 8 centromeric HOR array consists of 1,462 HOR units: 283 4-monomer HORs, 4 5-monomer HORs, 13 6-monomer HORs, 356 7- monomer HORs, 295 8-monomer HORs, and 511 11-monomer HORs. As an alternative approach, we subjected the centromere assembly to StringDecomposer 42 ( https://github.com/ablab/stringdecomposer ; version from 28 February 2020) using a set of 11 α-satellite monomers derived from a chromosome 8 11-mer HOR unit. The sequence of the α-satellite monomers used are as follows: A: AGCATTCTCAGAAACACCTTCGTGATGTTTGCAATCAAGTCACAGAGTTGAACCTTCCGTTTCATAGAGCAGGTTGGAAACA CTCTTATTGTAGTATCTGGAAGTGGACATTTGGAGCGCTTTCAGGCCTATGGTGAAAAAGGAAATATCTTCCCATAAAAACGACATAGA; B: AGCTATCTCAGGAACTTGTTTATGATGCATCTAATCAACTAACAGTGTTGAACCTTTGTACTGACAG AGCACTTTGAAACACTCTTTTTTGGAATCTGCAAGTGGATATTTGGATCGCTTTGAGGATTTCGTTGGAAACGGGATGCAATATAAAACGTACACAGC; C: AGCATACTCAGAAAATACTTTGCCATATTTCCATTCAAGTCACAGAGTGGAACATTCCCATTCATAGAGCAGGTTGGAAACACTCTTTTTGGAGTATCTGGAAGTGGACATTTGGAGCGCTTTCTGAACTATGGTGAAAAAGGAAATATCTTCCAATGAAAACAAGACAGA; D: AGCATTCTGAGAAACTTATTTGTGATGTGTGTCCTCAACAAACGGACTTGAACCTTTCGTTTCATGCAGTACTTCTGGAACACTCTTTTT GAAGATTCTGCATGCGGATATTTGGATAGCTTTGAGGATTTCGTTGGAAACGGGCTTACATGTAAAAATTAGACAGC; E: AGCATTCTCAGAAACTTCTTTGTGGTG TCTGCATTCAAGTCACAGAATTGAACTTCTCCTCACATAGAGCAGTTGTGCAGCACTCTATTTGTAGTATCTGGAAGTGGACATTTGGAGGGCTTTGTAGCCTATCTGGAAAAAGGAAATATCTTCCCATGAATGCGAGATAGA; F: AGTAATCTCAGAAACATGTTTATGCTGTATCTACTCAACTAACTGTGCTGAACATTTCTATTGATAGAGCAGTTTTGAGACCCTCTTCTTTTGGAATCTGCAAGTGGATATTTGGATAGATTTGAGGATTTCGTTGGAAACGGGATTATATATAAAAAGTAGACAGC; G: AGCATTCTCAGAAACTTCTTTGTGATGTTTGCATCCAGCTCTCAGAGTTGAACATTCCCTTTCATAGAGTAGGTTTGAAACCCTCTTTTTATAGTGTCTGGAAGCGGGCATTTGGAGCGCTTTCAGGCCTATGCTGAAAAAGGAAATATCTACATATAGAAACTAGACAGA; H: AGCATTCTGAGAATCAAGTTTGTGATGTGGGTACTCAACTAACAGTGTTGATCCATTCTTTTGATACAGCAGTTTTGAACCACACTTTTTGTAGAATCTGCAAGTGGATATTTGGATAGCTGTGAGGATTTCGTTGGAAACGGGAATGTCTTCATAGAAAATTTAGACAGA; I: AGCATTCTCAGAACCTTGATTGTGATGTGTGTTCTCCACTAACAGAGTTGAACCTTTCTTTTGACAGAACTGTTCTGAAACATTCTTTTTATAGAATCTGGAAGTGGATATTTGGAAAGCTTTGAGGATTTCGTTGGAAACGGGAATATCTTCAAATAAAATCTAGCCAGA; J: AGCATTCTAAGAAACATCTTAGGGATGTTTACATTCAAGTCACAGAGTTGAACATTCC CTTTCACAGAGCAGGTTTGAAACAATCTTCTCGTACTATCTGGCAGTGGACATTTTGAGCTCTTTGGGGCCTATGCTGAAAAAGGAAATATCTTCCGACAAAAACTAGTCAGA; K: AGCATTCGCAGAATCCCGTTTGTGATGTGTGCACTCAACTGTCAGAATTGAACCTTGGTTTGGAGAGAGCACTTTTGAAACACACT TTTTGTAGAATCTGCAGGTGGATATTTGGCT AGCTTTGAGGATTTCGTTGGAAACGGTAATGTCTTCAAAGAAAATCTAGACAGA.…”

“…To assess the phylogenetic relationship between α-satellite repeats, we first masked every non-α-satellite repeat in the human and NHP centromere assemblies using RepeatMasker 78 (v.4.1.0). Then, we subjected the masked assemblies to StringDecomposer 42 (version available 28 February 2020) using a set of 11 α-satellite monomers derived from a chromosome 8 11-monomer HOR unit (described in the ‘Analysis of α-satellite organization’ section above). This tool identifies the location of α-satellite monomers in the assemblies, and we used this to extract the α-satellite monomers from the HOR/dimeric array and monomeric regions into multi-FASTA files.…”

“…The sequence of the α-satellite monomers used are as fol- This analysis indicated that the CHM13 chromosome 8 centromeric HOR array consists of 1,515 HOR units: 286 4-monomer HORs, 12 6-monomer HORs, 366 7-monomer HORs, 303 8-monomer HORs, 3 10-monomer HORs, 539 11-monomer HORs, 2 12-monomer HORs, 2 13-monomer HORs, 1 17-monomer HOR, and 1 18-monomer HOR, which is concordant with the in silico restriction enzyme digestion results. The predominant HOR types from StringDecomposer 42 are presented in Extended Data Fig. 8.…”

Computational methods for chromosome-scale haplotype reconstruction

“…Recent developments in long, accurate long reads (Hifi) as well as ultra-long nanopore reads could pave the way for new advancements in finishing centromeric and other highly repetitive regions in humans and polyploids. Computationally, Hifi reads can be decomposed into monomers [ 139 ] that are represented in the graph, where monomers are nodes and edges represent the adjacencies of node sequences from reads. In this process, the haplotype variation is also considered in the monomers that can result in a haplotype-aware graph.…”