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bioRxiv · 10.1101/2020.12.10.419515

Aiming off the target: studying repetitive DNA using target capture sequencing reads

Costa, L.·Marques, A.·Buddenhagen, C.·Thomas, W. W.·Huettel, B.·Schubert, V.·Dodsworth, S.·Houben, A.·Souza, G.·Pedrosa-Harand, A.
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Abstract

O_LIWith the advance of high-throughput sequencing (HTS), reduced-representation methods such as target capture sequencing (TCS) emerged as cost-efficient ways of gathering genomic information. As the off-target reads from such sequencing are expected to be similar to genome skims (GS), we assessed the quality of repeat characterization using this data. C_LIO_LIFor this, repeat composition from TCS datasets of five Rhynchospora (Cyperaceae) species were compared with GS data from the same taxa. C_LIO_LIAll the major repetitive DNA families were identified in TCS, including repeats that showed abundances as low as 0.01% in the GS data. Rank correlation 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 was also reliable to develop a cytogenetic probe and solve phylogenetic relationships of Rhynchospora species with high support. C_LIO_LIIn light of our results, TCS data can be effectively used for cyto- and phylogenomic investigations of repetitive DNA. Given the growing availability of HTS reads, driven by global phylogenomic projects, our strategy represents a way to recycle genomic data and contribute to a better characterization of plant biodiversity. C_LI

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Costa, L., Marques, A., Buddenhagen, C., Thomas, W. W., Huettel, B., Schubert, V., Dodsworth, S., Houben, A., Souza, G., Pedrosa-Harand, A.. 2020-12-11. Aiming off the target: studying repetitive DNA using target capture sequencing reads. https://doi.org/10.1101/2020.12.10.419515

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