Subirana, Juan A.Messeguer, Xavier2019-05-082019-05-082018Subirana JA, 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 (Basel). 2018 Oct 16;9(10):500. DOI: 10.3390/genes91005002073-4425http://hdl.handle.net/10230/37187Repetitive 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.application/pdfeng©2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open accessarticle distributed under the terms and conditions of the Creative Commons Attribution(CC BY) license http://creativecommons.org/licenses/by/4.0/.Genomainfo:eu-repo/semantics/articlehttp://dx.doi.org/10.3390/genes9100500Caenorhabditis elegansGenome sequencingSatellite DNATandem repeat sequencesinfo:eu-repo/semantics/openAccess