MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

By Yujun Han, S. Wessler. Nucleic Acids Research, 2010

565 citations recorded by the source corpus.

Miniature inverted-repeat transposable elements (MITEs) are a special type of Class 2 non-autonomous transposable element (TE) that are abundant in the non-coding regions of the genes of many plant and animal species. The accurate identification of MITEs has been a challenge for existing programs because they lack coding sequences and, as such, evolve very rapidly. Because of their importance to gene and genome evolution, we developed MITE-Hunter, a program pipeline that can identify MITEs as well as other small Class 2 non-autonomous TEs from genomic DNA data sets. The output of MITE-Hunter is composed of consensus TE sequences grouped into families that can be used as a library file for homology-based TE detection programs such as RepeatMasker. MITE-Hunter was evaluated by searching the rice genomic database and comparing the output with known rice TEs. It discovered most of the previously reported rice MITEs (97.6%), and found sixteen new elements. MITE-Hunter was also compared with two other MITE discovery programs, FINDMITE and MUST. Unlike MITE-Hunter, neither of these programs can search large genomic data sets including whole genome sequences. More importantly, MITE-Hunter is significantly more accurate than either FINDMITE or MUST as the vast majority of their outputs are false-positives.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/a37fbc3c0f7b473fc344846437860b51604d3bd7

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Citations in the corpus

RepeatModeler2 for automated genomic discovery of transposable element families (2020, background): “However, the large number of well-characterized MITEs in the rice genomes (46) did not appear underrepresented in the RepeatModeler2 libraries compared to their long, coding peers (53% and 32% of families found for MITEs and coding DNA-TIRs, respectively).”
Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline (2019, background): “For TIR candidates identified by TIR-Learner, sequences are reclassified as MITEs if their length is ≤ 600 bp. MITE-Hunter results are masked using TIR-Learner results to remove duplicated candidates.”
LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons1[OPEN] (2017, methodology): “MITEs are most abundant in plant genomes in terms of copy number, and MITE libraries can be generated through programs such as MITE-Hunter (Han and Wessler, 2010) and detectMITE (Ye et al., 2016).”
MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations1[W][OPEN] (2013, methodology): “Brie ﬂ y, sequences of miniature inverted repeat transposable elements were collected using MITE-Hunter (Han and Wessler, 2010) with all default parameters.”
The genome of the pear (Pyrus bretschneideri Rehd.) (2013, unknown): “MITEs were detected by MITE_Hunter (Han and Wessler 2010).”
Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower (2016, methodology): “These structure features have been incorporated into an annotation pipeline MITE-Hunter 646 (Han and Wessler, 2010), which was primarily designed to search Miniature Inverted repeat 647 Transposable Elements (MITEs), but also can be used to search other non-autonomous cut-and-paste 648 TEs.”
RepeatModeler2: automated genomic discovery of transposable element families (2019, background): “…modular architecture of RepeatModeler2, it should be relatively straightforward to add other modules tailored to the discovery of specific subclass of elements such as those dedicated to the identification of MITEs (Han and Wessler 2010) or Helitrons (Yang and Bennetzen 2009; Xiong et al. 2014).”