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

Lucas Costa, André Marques, Chris Buddenhagen, William Wayt Thomas, Bruno Huettel, Veit Schubert, Steven Dodsworth, Andreas Houben, Gustavo Souza, Andrea Pedrosa-Harand*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)835-848
Number of pages14
JournalAnnals of Botany
Issue number7
Early online date29 May 2021
Publication statusPublished - 9 Nov 2021


  • Genome skimming
  • holocentric
  • reduced-representation sequencing
  • RepeatExplorer
  • Rhynchospora
  • satellite DNA
  • transposable elements


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