Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods

Abstract

BackgroundInsertion Sequences (ISs) and their non-autonomous derivatives (MITEs) are important components of prokaryotic genomes inducing duplication, deletion, rearrangement or lateral gene transfers. Although ISs and MITEs are relatively simple and basic genetic elements, their detection remains a difficult task due to their remarkable sequence diversity. With the advent of high-throughput genome and metagenome sequencing technologies, the development of fast, reliable and sensitive methods of ISs and MITEs detection become an important challenge. So far, almost all studies dealing with prokaryotic transposons have used classical BLAST-based detection methods against reference libraries. Here we introduce alternative methods of detection either taking advantages of the structural properties of the elements (de novo methods) or using an additional library-based method using profile HMM searches.ResultsIn this study, we have developed three different work flows dedicated to ISs and MITEs detection: the first two use de novo methods detecting either repeated sequences or presence of Inverted Repeats; the third one use 28 in-house transposase alignment profiles with HMM search methods. We have compared the respective performances of each method using a reference dataset of 30 archaeal and 30 bacterial genomes in addition to simulated and real metagenomes. Compared to a BLAST-based method using ISFinder as library, de novo methods significantly improve ISs and MITEs detection. For example, in the 30 archaeal genomes, we discovered 30 new elements (+20%) in addition to the 141 multi-copies elements already detected by the BLAST approach. Many of the new elements correspond to ISs belonging to unknown or highly divergent families. The total number of MITEs has even doubled with the discovery of elements displaying very limited sequence similarities with their respective autonomous partners (mainly in the Inverted Repeats of the elements). Concerning metagenomes, with the exception of short reads data (<300 bp) for which both techniques seem equally limited, profile HMM searches considerably ameliorate the detection of transposase encoding genes (up to +50%) generating low level of false positives compare to BLAST-based methods.ConclusionCompared to classical BLAST-based methods, the sensitivity of de novo and profile HMM methods developed in this study allow a better and more reliable detection of transposons in prokaryotic genomes and metagenomes. We believed that future studies implying ISs and MITEs identification in genomic data should combine at least one de novo and one library-based method, with optimal results obtained by running the two de novo methods in addition to a library-based search. For metagenomic data, profile HMM search should be favored, a BLAST-based step is only useful to the final annotation into groups and families.

A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

“…2b ). This confirms that the combining of multiple tools, using several approaches improves the detection of different TE families, with complete sequences, as previously indicated [ 66 , 67 , 71 ]. In this comparison, TEdenovo was efficient and displayed the second highest percentage of detected TE families (75%) (Fig.…”

“…These tools represent the four major TE detection approaches (presented above), so as to be as exhaustive as possible. Combining tools is recognised to improve TE detection efficiency [ 66 , 67 , 71 ]. We then applied a clustering method to decrease the redundancy of the detected sequences, by selecting the larger detected sequences of each cluster.…”

The chromosomal organization of horizontal gene transfer in bacteria

“…Hits were regarded as significant when their e -value was smaller than 10 −3 and their alignment covered at least 50% of the protein profile. Insertion sequences (ISs) were detected combining two approaches (i) using hmmsearch from the HMMer with IS HMM profiles (as previously proposed) 57 and (ii) by a BLAST-based method using the ISFinder database 58 . Integrases and transposases were defined as mobility-associated proteins (MAPs).…”

Transposons: the agents of antibiotic resistance in bacteria

“…The MITE Superfamily is more widely distributed in Archaea, such as Sulfolobus solfataricus , Sulfolobus tokodaii , Methanospirillum hungatei , Ferroplasma acidarmanus , Thermoplasma volcanium , Methanosarcina acetivorans , Methanosarcina mazei , Methanosarcina barkeri , Haloquadratum walsbyi , and Natronomonas pharaonis . MITE in these Archaea are flanked by IS 200 , IS 605 , IS 3 , IS 4 , IS 5 , IS 630 , IS 1634 , IS 1595 , and IS 1182 .…”