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# delfies: a Python package for the detection of DNA breakpoints with neo-telomere addition

Brice Letcher, Marie Delattre

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Brice Letcher, Marie Delattre. delfies: a Python package for the detection of DNA breakpoints with neo-telomere addition. Journal of Open Source Software, 2025, 10, 10.21105/joss.07385. hal-05393548

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Distributed under a Creative Commons Attribution 4.0 International License
# delfies: a Python package for the detection of DNA breakpoints with neo-telomere addition

Brice Letcher and Marie Delattre

1 Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR 5239, Inserm U1293, University Claude Bernard Lyon 1, Lyon, France Corresponding author

DOI: 10.21105/joss.07385

## Software

- Review

- Repository

- Archive

Editor: AHM Mahfuzur Rahman

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## Reviewers:

- @KatyBrown

- @natir

Submitted: 09 September 2024

Published: 12 January 2025

## License

Authors of papers retain copyright and release the work under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

## Summary

In multicellular organisms, all cells generally carry an identical genome, faithfully transmitted through cell divisions from the founding zygote. This is not the case in species that undergo Programmed DNA Elimination (PDE), the systematic destruction of portions of the genome in somatic cells during early development. In these species, somatic cells carry a reduced genome, while germline cells maintain an intact genome.

PDE was first documented in 1887 in a parasitic nematode (Boveri, 1887), and since then various forms of PDE have been found in a wide variety of organisms including birds, fish, insects, mammals, crustaceans, other nematodes and ciliates (Dedukh & Krasikova, 2021; Drotos et al., 2022). Some species eliminate entire chromosomes (birds, fish, insects, mammals) while others eliminate portions of chromosomes, with or without changes in chromosome number (copepod crustaceans, nematodes, ciliates).

In species that eliminate portions of chromosomes, two main types of elimination have been documented. The first is the elimination of small sequences (~100s of bp) called 'IESs', by a splicing process: a double-strand break is produced at each IES extremity, the IES is excised, and the two extremities are rejoined. This form has so far been documented in ciliates only. The second type is the elimination of large fragments of chromosomes (up to >1Mbp): a single double-strand break is produced, one side is eliminated, and telomeres on the retained side allow the new 'mini-chromosome' to be maintained in the soma. This form occurs in ciliates (Yu & Blackburn, 1991), nematodes (Gonzalez de la Rosa et al., 2020; Rey et al., 2023), and probably also in copepods (Beermann, 1977). While IES elimination in ciliates has been well-characterised genomically and functionally, chromosome fragmentation with neo-telomere addition has not.

Here, we present a tool called delfies to systematically detect sites of chromosome breakage and neo-telomere addition. delfies enables rapidly and comprehensively mapping the locations of elimination breakpoints in all species in which this form of DNA elimination occurs.

## Statement of need

Several other tools for the detection of DNA elimination breakpoints have been developed and tested, all in the context of ciliates: parTIES (Denby Wilkes et al., 2015), SIGAR (Feng et al., 2020), ADFinder (Zheng et al., 2020) and bleTIES (Seah & Swart, 2021). Of these, parTIES, ADFinder and SIGAR allow the detection of IESs only, not sites of chromosome breakage with neo-telomere addition, and were primarily designed for short-read sequencing data. bleTIES was designed to detect and reconstruct IESs in the context of long-read sequencing data, and also includes a module for detecting chromosome breakage sites with telomere addition called MILTEL (Seah & Swart, 2021).
delfies was developed when studying PDE in nematodes, and presents several new features compared to MILTEL. Both tools output the locations of breakpoints in standard bioinformatics formats: MILTEL in a GFF3-formatted file, delfies in a BED-formatted file. While MILTEL expresses each putative breakpoint in isolation, delfies can merge multiple breakpoints occurring in close proximity in a user-configurable way. This allows for directly detecting more or less sharply-defined breakpoints, a feature that is known to vary in both ciliates and nematodes (Bétermier et al., 2023; Dockendorff et al., 2022; Estrem & Wang, 2023; Gonzalez de la Rosa et al., 2020). delfies also outputs the strand of breakpoints in the appropriate BED column, enabling subsequently classifying the genome into 'retained' and 'eliminated' compartments (details in the software repository).

delfies also explicitly models and outputs two types of breakpoints: in the first, the assembled genome is 'complete' and reads from the 'reduced' genome contain telomeres after the breakpoint. In the second, the assembled genome is 'reduced' and contains telomeres, and reads from the 'complete' genome contain unique non-telomeric sequence. These two types can be treated separately. For example, in the case of a reduced assembled genome, reads coming from the reduced genome can be specifically depleted at breakpoints and the new read-set used to assemble the complete genome (instructions provided in the software repository).

In addition to breakpoint locations, delfies extracts and outputs the sequences around the
breakpoints in a Fasta-formatted file. This enables searching for motifs specifying breakpoints,
e.g. using MEME (Bailey et al., 2015).

In practical terms, delfies has a highly configurable command-line interface, enabling specify-
ing how much to filter read alignments, which regions of the genome to analyse and the types
of breakpoints to look for. On a nematode genome of size 240Mbp sequenced at 85X average
coverage with PacBio HiFi data, delfies finds all breakpoints in less than 2 minutes, using a
single thread. For further speed, delfies also supports multi-threading.

delfies has already been used to successfully characterise the breakpoints, motifs, and
retained/eliminated genomes of several nematode genera in the family *Rhabditidae*, supporting
two upcoming publications (Letcher *et al.* and Stevens *et al.*, in preparation). For testing
purposes, the author has prepared a subset of publicly-available data from the nematode
*Oscheius onirici*, whose elimination breakpoint motif has been previously described (Estrem &
Wang, 2023). The data are available on Zenodo (Letcher, 2024), and consist of a small genome
region containing a single elimination breakpoint and alignment files for reads sequenced using
three distinct technologies: Illumina NovaSeq, Oxford Nanopore Technologies PromethION and
Pacific Biosciences Sequel II. The reads span a range of average lengths (151bp to 11.9kbp)
and per-base qualities (Q11 to Q28). delfies recovered a single, identical breakpoint across
all three datasets.

We anticipate this tool can be of broad use to researchers studying Programmed DNA
Elimination, to characterise species known to eliminate but also to discover or screen for
elimination in new species. This is especially relevant as new long-read and high-coverage
sequencing data (of both germline and somatic cells) of eukaryotic species become increasingly
available (Blaxter et al., 2022; Lewin et al., 2022). delfies may also be useful in other fields
of research in which modified chromosomes with neo-telomeres are formed and maintained,
such as cancer biology.

Acknowledgements

We acknowledge the many interactions with Lewis Stevens and Pablo Manuel Gonzalez de la Rosa at the Wellcome Sanger Institute and Marie Delattre at the Laboratory of Biology and Modelling of the Cell, which helped foster the development of delfies.

This work was supported by a grant from the Agence Nationale de la Recherche: ANR-22-
CE12-0027.
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