Aiming off the target: recycling target capture sequencing reads for investigating repetitive DNA.
Ann Bot
; 128(7): 835-848, 2021 11 09.
Article
em En
| MEDLINE
| ID: mdl-34050647
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. KEYRESULTS:
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 (râ =â 0.58-0.85), increasing after filtering out the targeted loci from the raw TCS reads (râ =â 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.Palavras-chave
Texto completo:
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Base de dados:
MEDLINE
Assunto principal:
Genoma de Planta
/
Sequenciamento de Nucleotídeos em Larga Escala
Idioma:
En
Revista:
Ann Bot
Ano de publicação:
2021
Tipo de documento:
Article
País de afiliação:
Brasil