BIROn - Birkbeck Institutional Research Online

    Aiming off the target: recycling target capture sequencing reads for investigating repetitive DNA

    Costa, L. and Marques, A. and Buddenhagen, C. and Wayt Thomas, W. and Huettel, B. and Schubert, V. and Dodsworth, Steven and Houben, A. and Souza, G. and Pedrosa-Harand, A. (2021) Aiming off the target: recycling target capture sequencing reads for investigating repetitive DNA. Annals of Botany 128 (7), pp. 835-848. ISSN 0305-7364.

    [img] Text
    mcab063.pdf - Published Version of Record
    Restricted to Repository staff only

    Download (2MB)

    Abstract

    Background and Aims: With the advance of high-Throughput sequencing, reduced-representation methods such as target capture sequencing (TCS) emerged as cost-efficient ways of gathering genomic information, particularly from coding regions. As the off-Target reads from such sequencing are expected to be similar to genome skimming (GS), we assessed the quality of repeat characterization in plant genomes using these data. Methods: Repeat composition obtained from TCS datasets of five Rhynchospora (Cyperaceae) species were compared with GS data from the same taxa. In addition, a FISH probe was designed based on the most abundant satellite found in the TCS dataset of Rhynchospora cephalotes. Finally, repeat-based phylogenies of the five Rhynchospora species were constructed based on the GS and TCS datasets and the topologies were compared with a gene-Alignment-based phylogenetic tree. Key Results: All the major repetitive DNA families were identified in TCS, including repeats that showed abundances as low as 0.01 in the GS data. Rank correlations between GS and TCS repeat abundances were moderately high (r=0.58-0.85), increasing after filtering out the targeted loci from the raw TCS reads (r=0.66-0.92). Repeat data obtained by TCS were also reliable in developing a cytogenetic probe of a new variant of the holocentromeric satellite Tyba. Repeat-based phylogenies from TCS data were congruent with those obtained from GS data and the gene-Alignment tree. Conclusions: Our results show that off-Target TCS reads can be recycled to identify repeats for cyto-and phylogenomic investigations. Given the growing availability of TCS reads, driven by global phylogenomic projects, our strategy represents a way to recycle genomic data and contribute to a better characterization of plant biodiversity.

    Metadata

    Item Type: Article
    Keyword(s) / Subject(s): Genome skimming, holocentric, reduced-representation sequencing, RepeatExplorer, Rhynchospora, satellite DNA, transposable elements
    School: Birkbeck Faculties and Schools > Faculty of Science > School of Natural Sciences
    Research Centres and Institutes: Structural Molecular Biology, Institute of (ISMB)
    Depositing User: Steven Dodsworth
    Date Deposited: 26 Sep 2024 09:44
    Last Modified: 26 Sep 2024 14:14
    URI: https://eprints.bbk.ac.uk/id/eprint/54025

    Statistics

    Activity Overview
    6 month trend
    1Download
    6 month trend
    18Hits

    Additional statistics are available via IRStats2.

    Archive Staff Only (login required)

    Edit/View Item
    Edit/View Item