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How Long Are Long Tandem Repeats? A Challenge for Current Methods of Whole-Genome Sequence Assembly: The Case of Satellites in Caenorhabditis elegans

1
Department of Computer Science, Universitat Politècnica de Catalunya, Jordi Girona 1-3, 08034 Barcelona, Spain
2
Evolutionary Genomics Group, Research Program on Biomedical Informatics (GRIB)–Hospital del Mar Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Dr. Aiguader 86, 08003 Barcelona, Spain
*
Author to whom correspondence should be addressed.
Genes 2018, 9(10), 500; https://doi.org/10.3390/genes9100500
Received: 18 September 2018 / Revised: 11 October 2018 / Accepted: 11 October 2018 / Published: 16 October 2018
(This article belongs to the Section Molecular Genetics and Genomics)
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Abstract

Repetitive genome regions have been difficult to sequence, mainly because of the comparatively small size of the fragments used in assembly. Satellites or tandem repeats are very abundant in nematodes and offer an excellent playground to evaluate different assembly methods. Here, we compare the structure of satellites found in three different assemblies of the Caenorhabditis elegans genome: the original sequence obtained by Sanger sequencing, an assembly based on PacBio technology, and an assembly using Nanopore sequencing reads. In general, satellites were found in equivalent genomic regions, but the new long-read methods (PacBio and Nanopore) tended to result in longer assembled satellites. Important differences exist between the assemblies resulting from the two long-read technologies, such as the sizes of long satellites. Our results also suggest that the lengths of some annotated genes with internal repeats which were assembled using Sanger sequencing are likely to be incorrect. View Full-Text
Keywords: satellite DNA; tandem repeat sequences; Caenorhabditis elegans; genome sequencing satellite DNA; tandem repeat sequences; Caenorhabditis elegans; genome sequencing
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Subirana, J.A.; Messeguer, X. How Long Are Long Tandem Repeats? A Challenge for Current Methods of Whole-Genome Sequence Assembly: The Case of Satellites in Caenorhabditis elegans. Genes 2018, 9, 500.

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