Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases

Abstract

The widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. This multi-level problem can lead to errors in genome and protein databases that are often not recognized or acknowledged. As a consequence, end users working with sequences with repetitive regions are faced with ‘ready-to-use’ deposited data whose trustworthiness is difficult to determine, let alone to quantify. Here, we provide a review of the problems associated with tandem repeat sequences that originate from different stages during the sequencing-assembly-annotation-deposition workflow, and that may proliferate in public database repositories affecting all downstream analyses. As a case study, we provide examples of the Atlantic cod genome, whose sequencing and assembly were hindered by a particularly high prevalence of tandem repeats. We complement this case study with examples from other species, where mis-annotations and sequencing errors have propagated into protein databases. With this review, we aim to raise the awareness level within the community of database users, and alert scientists working in the underlying workflow of database creation that the data they omit or improperly assemble may well contain important biological information valuable to others.

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

“…In brief, high quality Illumina reads were prepared using TrimGalore (https://github.com/FelixKrueger/TrimGalore) based on the following criteria: (i) no “N” base, (ii) trimming of adaptor sequences and low quality bases (Q<20), (iii) no trimmed reads < 100 bp. To avoid mis-assembly due to repetitive sequences (Tørresen et al, 2019), PacBio SEQUEL subreads with repetitive sequences comprised over 85% of total sequences were filtered out. The GC content criteria (<25% and >85%) was applied for filtering low complexity DNA sequences before assembly.…”

A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder

“…Despite much interest [8,[14][15][16], the most recent and commonly cited census of protein TRs summarizing repeats in the curated protein knowledge base UniProtKB/Swiss-Prot [17] dates back two decades [18]. Since then this popular data bank has grown more than seven-fold ( Figure S1).…”

“…This allows our study to provide an unprecedented detail of the universe of protein TRs. We respond to the call [14] and apply the state-of-the-art method for TR detection followed by filtering through a sound statistical framework.…”

Reevaluation of theToxoplasma gondiiandNeospora caninumgenomes reveals misassembly, karyotype differences and chromosomal rearrangements

“…Widely used sequencing technologies, such as Sanger, 454 and Illumina, have played a pivotal part in these advancements. However, the limitations of these technologies, namely their trouble reading through repetitive regions and their short read outputs, have led to assembly artifacts that are currently widely distributed in genome and proteome databases 43 . A number of protozoan parasite genomes have been recently revisited using third generation sequencing technologies.…”