Abstract
A majority of facioscapulohumeral muscular dystrophy (FSHD) is caused by contraction of macrosatellite repeats called D4Z4 that are located in the subtelomeric region of human chromosome 4q35. Sequencing the FSHD locus has been technically challenging due to its long size and nearly identical nature of repeat elements. Here we report sequencing and partial assembly of a BAC clone carrying an entire FSHD locus by a single molecule real time (SMRT) sequencing technology which could produce long reads up to about 18 kb containing D4Z4 repeats. De novo assembly by Hierarchical Genome Assembly Process 1 (HGAP.1) yielded a contig of 41 kb containing all but a part of the most distal D4Z4 element. The validity of the sequence model was confirmed by an independent approach employing anchored multiple sequence alignment by Kalign using reads containing unique flanking sequences. Our data will provide a basis for further optimization of sequencing and assembly conditions of D4Z4.
Highlights
About half [1] and possibly more [2] of the human genome comprise repetitive elements
Even long reads of more than several kb produced by the single molecule real time (SMRT) sequence technology of PacBio RS cannot be precisely mapped if not provided with anchors that can be unambiguously placed
SMRT reads closed 50 gaps and extended 60 boundaries out of 160 gaps remaining in the human reference genome GRCh37, the chromosome 4 subtelomeric gap was not closed because highly identical repeats could not be resolved
Summary
About half [1] and possibly more [2] of the human genome comprise repetitive elements. Macrosatellite repeats, consisting of units longer than 100 bp and often spanning several kilobases (kb), have attracted attention in recent years for their possible structural and regulatory roles [3]. In the subtelomeric region of human chromosome 4 are tandem arrays of 3.3 kb PLOS ONE | DOI:10.1371/journal.pone.0151963. PacBio Sequencing of D4Z4 Repeats funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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