@article{bleties:2021,
    author = {Seah, Brandon K B and Swart, Estienne C},
    title = "{BleTIES: annotation of natural genome editing in ciliates using long read sequencing}",
    journal = {Bioinformatics},
    volume = {37},
    number = {21},
    pages = {3929-3931},
    year = {2021},
    month = {09},
    abstract = "{Ciliates are single-celled eukaryotes that eliminate specific, interspersed DNA sequences (internally eliminated sequences, IESs) from their genomes during development. These are challenging to annotate and assemble because IES-containing sequences are typically much less abundant in the cell than those without, and IES sequences themselves often contain repetitive and low-complexity sequences. Long-read sequencing technologies from Pacific Biosciences and Oxford Nanopore have the potential to reconstruct longer IESs than has been possible with short reads but require a different assembly strategy. Here we present BleTIES, a software toolkit for detecting, assembling, and analyzing IESs using mapped long reads.BleTIES is implemented in Python 3. Source code is available at https://github.com/Swart-lab/bleties (MIT license) and also distributed via Bioconda.Supplementary data are available at Bioinformatics online.}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btab613},
    url = {https://doi.org/10.1093/bioinformatics/btab613},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/37/21/3929/56741888/btab613.pdf},
}



@article{parties:2015,
    author = {Denby Wilkes, Cyril and Arnaiz, Olivier and Sperling, Linda},
    title = "{ParTIES: a toolbox for Paramecium interspersed DNA elimination studies}",
    journal = {Bioinformatics},
    volume = {32},
    number = {4},
    pages = {599-601},
    year = {2015},
    month = {11},
    abstract = "{Motivation: Developmental DNA elimination occurs in a wide variety of multicellular organisms, but ciliates are the only single-celled eukaryotes in which this phenomenon has been reported. Despite considerable interest in ciliates as models for DNA elimination, no standard methods for identification and characterization of the eliminated sequences are currently available.Results: We present the Paramecium Toolbox for Interspersed DNA Elimination Studies (ParTIES), designed for Paramecium species, that (i) identifies eliminated sequences, (ii) measures their presence in a sequencing sample and (iii) detects rare elimination polymorphisms.Availability and implementation: ParTIES is multi-threaded Perl software available at https://github.com/oarnaiz/ParTIES. ParTIES is distributed under the GNU General Public Licence v3.Contact:  linda.sperling@i2bc.paris-saclay.frSupplementary information:  Supplementary data are available at Bioinformatics online.}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btv691},
    url = {https://doi.org/10.1093/bioinformatics/btv691},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/32/4/599/49017591/bioinformatics\_32\_4\_599.pdf},
}


@article{sigar:2020,
    author = {Feng, Yi and Beh, Leslie Y and Chang, Wei-Jen and Landweber, Laura F},
    title = "{SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping}",
    journal = {Genome Biology and Evolution},
    volume = {12},
    number = {10},
    pages = {1711-1718},
    year = {2020},
    month = {08},
    abstract = "{Ciliates are microbial eukaryotes with distinct somatic and germline genomes. Postzygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programed genome rearrangements. Current studies usually focus on a few model species, where rearrangement features are annotated by aligning reference germline and somatic genomes. Although many high-quality somatic genomes have been assembled, a high-quality germline genome assembly is difficult to obtain due to its smaller DNA content and abundance of repetitive sequences. To overcome these hurdles, we propose a new pipeline, SIGAR (Split-read Inference of Genome Architecture and Rearrangements) to infer germline genome architecture and rearrangement features without a germline genome assembly, requiring only short DNA sequencing reads. As a proof of principle, 93\\% of rearrangement junctions identified by SIGAR in the ciliate Oxytricha trifallax were validated by the existing germline assembly. We then applied SIGAR to six diverse ciliate species without germline genome assemblies, including Ichthyophthirius multifilii, a fish pathogen. Despite the high level of somatic DNA contamination in each sample, SIGAR successfully inferred rearrangement junctions, short eliminated sequences, and potential scrambled genes in each species. This pipeline enables pilot surveys or exploration of DNA rearrangements in species with limited DNA material access, thereby providing new insights into the evolution of chromosome rearrangements.}",
    issn = {1759-6653},
    doi = {10.1093/gbe/evaa147},
    url = {https://doi.org/10.1093/gbe/evaa147},
    eprint = {https://academic.oup.com/gbe/article-pdf/12/10/1711/34033595/evaa147.pdf},
}



@article{adfinder:2020,
    author = {Zheng, Weibo and Chen, Jing and Doak, Thomas G and Song, Weibo and Yan, Ying},
    title = "{ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data}",
    journal = {Bioinformatics},
    volume = {36},
    number = {12},
    pages = {3632-3636},
    year = {2020},
    month = {04},
    abstract = "{Programmed DNA elimination (PDE) plays a crucial role in the transitions between germline and somatic genomes in diverse organisms ranging from unicellular ciliates to multicellular nematodes. However, software specific for the detection of DNA splicing events is scarce. In this paper, we describe Accurate Deletion Finder (ADFinder), an efficient detector of PDEs using high-throughput sequencing data. ADFinder can predict PDEs with relatively low sequencing coverage, detect multiple alternative splicing forms in the same genomic location and calculate the frequency for each splicing event. This software will facilitate research of PDEs and all down-stream analyses.By analyzing genome-wide DNA splicing events in two micronuclear genomes of Oxytricha trifallax and Tetrahymena thermophila, we prove that ADFinder is effective in predicting large scale PDEs.The source codes and manual of ADFinder are available in our GitHub website: https://github.com/weibozheng/ADFinder.Supplementary data are available at Bioinformatics online.}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btaa226},
    url = {https://doi.org/10.1093/bioinformatics/btaa226},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/36/12/3632/50747364/bioinformatics\_36\_12\_3632.pdf},
}


@article{Boveri1887,
  author    = {Theodor Boveri},
  title     = {{\"U}ber Differenzierung der Zellkerne w{\"a}hrend der Furchung des Eies von Ascaris megalocephala},
  journal   = {Anatomischer Anzeiger},
  volume    = {2},
  pages     = {688 -- 693},
  year      = {1887},
}

@article{Beermann1977,
author={Beermann, Sigrid},
title={The diminution of heterochromatic chromosomal segments in Cyclops (Crustacea, Copepoda)},
journal={Chromosoma},
year={1977},
month={Dec},
day={01},
volume={60},
number={4},
pages={297-344},
issn={1432-0886},
doi={10.1007/BF00292858},
url={https://doi.org/10.1007/BF00292858}
}

@article{Yu1991,
  title = {Developmentally programmed healing of chromosomes by telomerase in Tetrahymena},
  volume = {67},
  ISSN = {0092-8674},
  url = {http://dx.doi.org/10.1016/0092-8674(91)90077-C},
  DOI = {10.1016/0092-8674(91)90077-c},
  number = {4},
  journal = {Cell},
  publisher = {Elsevier BV},
  author = {Yu,  Guo-Liang and Blackburn,  Elizabeth H.},
  year = {1991},
  month = nov,
  pages = {823–832}
}



@article{Dedukh2021,
  title = {Delete and survive: strategies of programmed genetic material elimination in eukaryotes},
  volume = {97},
  ISSN = {1469-185X},
  url = {http://dx.doi.org/10.1111/brv.12796},
  DOI = {10.1111/brv.12796},
  number = {1},
  journal = {Biological Reviews},
  publisher = {Wiley},
  author = {Dedukh,  Dmitrij and Krasikova,  Alla},
  year = {2021},
  month = sep,
  pages = {195–216}
}

@article{Drotos2022,
  title = {Throwing away DNA: programmed downsizing in somatic nuclei},
  volume = {38},
  ISSN = {0168-9525},
  url = {http://dx.doi.org/10.1016/j.tig.2022.02.003},
  DOI = {10.1016/j.tig.2022.02.003},
  number = {5},
  journal = {Trends in Genetics},
  publisher = {Elsevier BV},
  author = {Drotos,  Katherine H.I. and Zagoskin,  Maxim V. and Kess,  Tony and Gregory,  T. Ryan and Wyngaard,  Grace A.},
  year = {2022},
  month = may,
  pages = {483–500}
}

@article{Bailey2015,
  title = {The MEME Suite},
  volume = {43},
  ISSN = {1362-4962},
  url = {http://dx.doi.org/10.1093/nar/gkv416},
  DOI = {10.1093/nar/gkv416},
  number = {W1},
  journal = {Nucleic Acids Research},
  publisher = {Oxford University Press (OUP)},
  author = {Bailey,  Timothy L. and Johnson,  James and Grant,  Charles E. and Noble,  William S.},
  year = {2015},
  month = may,
  pages = {W39–W49}
}

@article{Betermier2023,
  title = {Programmed chromosome fragmentation in ciliated protozoa: multiple means to chromosome ends},
  volume = {87},
  ISSN = {1098-5557},
  url = {http://dx.doi.org/10.1128/mmbr.00184-22},
  DOI = {10.1128/mmbr.00184-22},
  number = {4},
  journal = {Microbiology and Molecular Biology Reviews},
  publisher = {American Society for Microbiology},
  author = {Bétermier,  Mireille and Klobutcher,  Lawrence A. and Orias,  Eduardo},
  editor = {Lodoen,  Melissa Bruckner},
  year = {2023},
  month = dec 
}

@article{Estrem2023,
  title = {Programmed DNA elimination in the parasitic nematode Ascaris},
  volume = {19},
  ISSN = {1553-7374},
  url = {http://dx.doi.org/10.1371/journal.ppat.1011087},
  DOI = {10.1371/journal.ppat.1011087},
  number = {2},
  journal = {PLOS Pathogens},
  publisher = {Public Library of Science (PLoS)},
  author = {Estrem,  Brandon and Wang,  Jianbin},
  editor = {Kafsack,  Bjorn F.C.},
  year = {2023},
  month = feb,
  pages = {e1011087}
}

@article{Rey2023,
  title = {Programmed DNA elimination in Mesorhabditis nematodes},
  volume = {33},
  ISSN = {0960-9822},
  url = {http://dx.doi.org/10.1016/j.cub.2023.07.058},
  DOI = {10.1016/j.cub.2023.07.058},
  number = {17},
  journal = {Current Biology},
  publisher = {Elsevier BV},
  author = {Rey,  Carine and Launay,  Caroline and Wenger,  Eva and Delattre,  Marie},
  year = {2023},
  month = sep,
  pages = {3711--3721.e5}
}

@article{GonzalezdelaRosa2020,
  title = {A telomere-to-telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes},
  volume = {11},
  ISSN = {2160-1836},
  url = {http://dx.doi.org/10.1093/g3journal/jkaa020},
  DOI = {10.1093/g3journal/jkaa020},
  number = {1},
  journal = {G3 Genes|Genomes|Genetics},
  publisher = {Oxford University Press (OUP)},
  author = {Gonzalez de la Rosa,  Pablo Manuel and Thomson,  Marian and Trivedi,  Urmi and Tracey,  Alan and Tandonnet,  Sophie and Blaxter,  Mark},
  editor = {Rockman,  M},
  year = {2020},
  month = dec 
}


@article{Dockendorff2022,
  title = {The nematode Oscheius tipulae as a genetic model for programmed DNA elimination},
  volume = {32},
  ISSN = {0960-9822},
  url = {http://dx.doi.org/10.1016/j.cub.2022.10.043},
  DOI = {10.1016/j.cub.2022.10.043},
  number = {23},
  journal = {Current Biology},
  publisher = {Elsevier BV},
  author = {Dockendorff,  Thomas C. and Estrem,  Brandon and Reed,  Jordan and Simmons,  James R. and Zadegan,  Sobhan Bahrami and Zagoskin,  Maxim V. and Terta,  Vincent and Villalobos,  Eduardo and Seaberry,  Erin M. and Wang,  Jianbin},
  year = {2022},
  month = dec,
  pages = {5083--5098.e6}
}

@article{DTOL2022,
  title = {Sequence locally,  think globally: The Darwin Tree of Life Project},
  volume = {119},
  ISSN = {1091-6490},
  url = {http://dx.doi.org/10.1073/pnas.2115642118},
  DOI = {10.1073/pnas.2115642118},
  number = {4},
  journal = {Proceedings of the National Academy of Sciences},
  publisher = {Proceedings of the National Academy of Sciences},
  author = {Blaxter,  Mark and Mieszkowska,  Nova and Di Palma,  Federica and Holland,  Peter and Durbin,  Richard and Richards,  Thomas and Berriman,  Matthew and Kersey,  Paul and Hollingsworth,  Peter and Wilson,  Willie and Twyford,  Alex and Gaya,  Ester and Lawniczak,  Mara and Lewis,  Owen and Broad,  Gavin and Howe,  Kevin and Hart,  Michelle and Flicek,  Paul and Barnes,  Ian},
  year = {2022},
  month = jan 
}

@article{EBGP2022,
  title = {The Earth BioGenome Project 2020: Starting the clock},
  volume = {119},
  ISSN = {1091-6490},
  url = {http://dx.doi.org/10.1073/pnas.2115635118},
  DOI = {10.1073/pnas.2115635118},
  number = {4},
  journal = {Proceedings of the National Academy of Sciences},
  publisher = {Proceedings of the National Academy of Sciences},
  author = {Lewin,  Harris A. and Richards,  Stephen and Lieberman Aiden,  Erez and Allende,  Miguel L. and Archibald,  John M. and Bálint,  Miklós and Barker,  Katharine B. and Baumgartner,  Bridget and Belov,  Katherine and Bertorelle,  Giorgio and Blaxter,  Mark L. and Cai,  Jing and Caperello,  Nicolette D. and Carlson,  Keith and Castilla-Rubio,  Juan Carlos and Chaw,  Shu-Miaw and Chen,  Lei and Childers,  Anna K. and Coddington,  Jonathan A. and Conde,  Dalia A. and Corominas,  Montserrat and Crandall,  Keith A. and Crawford,  Andrew J. and DiPalma,  Federica and Durbin,  Richard and Ebenezer,  ThankGod E. and Edwards,  Scott V. and Fedrigo,  Olivier and Flicek,  Paul and Formenti,  Giulio and Gibbs,  Richard A. and Gilbert,  M. Thomas P. and Goldstein,  Melissa M. and Graves,  Jennifer Marshall and Greely,  Henry T. and Grigoriev,  Igor V. and Hackett,  Kevin J. and Hall,  Neil and Haussler,  David and Helgen,  Kristofer M. and Hogg,  Carolyn J. and Isobe,  Sachiko and Jakobsen,  Kjetill Sigurd and Janke,  Axel and Jarvis,  Erich D. and Johnson,  Warren E. and Jones,  Steven J. M. and Karlsson,  Elinor K. and Kersey,  Paul J. and Kim,  Jin-Hyoung and Kress,  W. John and Kuraku,  Shigehiro and Lawniczak,  Mara K. N. and Leebens-Mack,  James H. and Li,  Xueyan and Lindblad-Toh,  Kerstin and Liu,  Xin and Lopez,  Jose V. and Marques-Bonet,  Tomas and Mazard,  Sophie and Mazet,  Jonna A. K. and Mazzoni,  Camila J. and Myers,  Eugene W. and O’Neill,  Rachel J. and Paez,  Sadye and Park,  Hyun and Robinson,  Gene E. and Roquet,  Cristina and Ryder,  Oliver A. and Sabir,  Jamal S. M. and Shaffer,  H. Bradley and Shank,  Timothy M. and Sherkow,  Jacob S. and Soltis,  Pamela S. and Tang,  Boping and Tedersoo,  Leho and Uliano-Silva,  Marcela and Wang,  Kun and Wei,  Xiaofeng and Wetzer,  Regina and Wilson,  Julia L. and Xu,  Xun and Yang,  Huanming and Yoder,  Anne D. and Zhang,  Guojie},
  year = {2022},
  month = jan 
}


@misc{ZenodoData2024,
  author    = {Brice Letcher},
  title     = {Dataset supporting the tool 'delfies: a Python package for the detection of DNA breakpoints with neo-telomere addition'},
  year      = {2024},
  doi       = {10.5281/zenodo.14101797},
  publisher = {Zenodo},
}
