The complete Ac/Ds transposon family of maize

Du, Chunguang; Hoffman, Andrew S.; He, Limei; Caronna, Jason; Dooner, Hugo K.

doi:10.1186/1471-2164-12-588

Cited by 22 publications

(15 citation statements)

References 54 publications

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“…On an element basis, we found over half (4,104 out of 13,317 novel TIR elements and 11,885 out of 18,093 novel MITEs) of the elements shared similar TIR sequences with our curated library, but included variation in their internal sequences, with few elements showing potential to be autonomous (Figure 5D). Such variation is typical for nonautonomous TIR transposons, such as Ds elements [56]. For MITE candidates with novel TIRs, the majority had more than three copies in the rice genome (Figure 5D), suggesting these are likely novel TEs that were not included in the curated library.…”

Section: Resultsmentioning

confidence: 99%

Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline

Liao

et al. 2019

Preprint

173

239

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20Sequencing technology and assembly algorithms have matured to the point that high-21 quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse 22 transposable elements (TEs) and allow for annotation of TEs. There are numerous methods for 23 each class of elements with unknown relative performance metrics. We benchmarked existing 24 programs based on a curated library of rice TEs. Using the most robust programs, we created a 25 comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) that produces a 26 condensed TE library for annotations of structurally intact and fragmented elements. EDTA is 27 open-source and freely available: https://github.com/oushujun/EDTA. 28 Keywords 29 Transposable element; Annotation; Genome; Benchmarking; Pipeline 30 31Long-read sequencing (e.g., PacBio and Oxford Nanopore) and assembly scaffolding 50 (e.g., Hi-C and BioNano) techniques have progressed rapidly within the last few years. These 51 innovations have been critical for high-quality assembly of the repetitive fraction of genomes. In 52 fact, Ou et al. [8] demonstrated that the assembly contiguity of repetitive sequences in recent 53 long-read assemblies is even better than traditional BAC-based reference genomes. With these 54 developments, inexpensive and high-quality assembly of an entire genome is now possible. 55Knowing where features (i.e., genes, TEs, etc.) exist in a genome assembly is important 56 4 information for using these assemblies for biological findings. However, unlike the relatively 57 straightforward and comprehensive pipelines established for gene annotation [9][10][11], current 58 methods for TE annotation can be piecemeal, inaccurate, and are highly specific to classes of 59 transposable elements. 60Transposable elements fall into two major classes. Class I elements, also known as 61 retrotransposons, use an RNA intermediate in their "copy and paste" mechanism of 62 transposition [12]. Class I elements can be further divided into long terminal repeat (LTR) 63 retrotransposons, as well as those that lack LTRs (non-LTRs), which include long interspersed 64 nuclear elements (LINEs), and short interspersed nuclear elements (SINEs). Structural features 65 of these elements can facilitate automated de novo annotation in a genome assembly. For 66 example, LTR elements have a 5-bp target site duplication (TSD), while non-LTRs have either 67 variable length TSDs or lack TSDs entirely, being instead associated with deletion of flanking 68 sequences upon insertion [13]. There are also standard terminal sequences associated with 69 LTR elements (i.e., 5'-TG…C/G/TA-3' for LTR-Copia and 5'-TG…CA-3' for LTR-Gypsy 70 elements), and non-LTRs often have a terminal poly-A tail at the 3' end of the element (see [14] 71 for a complete description of structural features of each superfamily). 72The second major class of TEs, Class II elements, also known as DNA transposons, use 73 a DNA intermediate in their "cut and paste" mechanism of transposition [15]. As with Class I 74...

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Section: Resultsmentioning

confidence: 99%

Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline

Liao

et al. 2019

Preprint

173

239

View full text Add to dashboard Cite

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“…Thus the real frequency of duplications derived from the P1-ovov454 allele may be closer to 1%. Given this high frequency, we asked whether Ac/Ds -induced tandem duplications could be detected in the maize B73 genome, which contains ∼50 Ac / Ds elements [44]. However, we failed to find any Ac/Ds copies adjacent to a tandem duplication, possibly because the Ac / Ds elements in the B73 genome are widely separated, and efficient reversed-ends Ac/Ds transposition requires two elements in close proximity and correct orientation [29].…”

Section: Discussionmentioning

confidence: 96%

Generation of Tandem Direct Duplications by Reversed-Ends Transposition of Maize Ac Elements

2013

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Tandem direct duplications are a common feature of the genomes of eukaryotes ranging from yeast to human, where they comprise a significant fraction of copy number variations. The prevailing model for the formation of tandem direct duplications is non-allelic homologous recombination (NAHR). Here we report the isolation of a series of duplications and reciprocal deletions isolated de novo from a maize allele containing two Class II Ac/Ds transposons. The duplication/deletion structures suggest that they were generated by alternative transposition reactions involving the termini of two nearby transposable elements. The deletion/duplication breakpoint junctions contain 8 bp target site duplications characteristic of Ac/Ds transposition events, confirming their formation directly by an alternative transposition mechanism. Tandem direct duplications and reciprocal deletions were generated at a relatively high frequency (∼0.5 to 1%) in the materials examined here in which transposons are positioned nearby each other in appropriate orientation; frequencies would likely be much lower in other genotypes. To test whether this mechanism may have contributed to maize genome evolution, we analyzed sequences flanking Ac/Ds and other hAT family transposons and identified three small tandem direct duplications with the structural features predicted by the alternative transposition mechanism. Together these results show that some class II transposons are capable of directly inducing tandem sequence duplications, and that this activity has contributed to the evolution of the maize genome.

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“…These observations indicate that although MMEJ appears to be common in MITE formation, the formation of different MITE families may involve different mechanisms for internal deletions of ancestral autonomous elements. These miniaturization processes may have also led to the non-MITE miniature versions TEs that are much more abundant than autonomous elements such as the Ac/Ds elements in maize (Du et al 2011). …”

Section: Discussionmentioning

confidence: 99%

Birth of Three Stowaway-like MITE Families via Microhomology-Mediated Miniaturization of a Tc1/Mariner Element in the Yellow Fever Mosquito

Yang

Fattash

Lee

et al. 2013

Genome Biology and Evolution

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Eukaryotic genomes contain numerous DNA transposons that move by a cut-and-paste mechanism. The majority of these elements are self-insufficient and dependent on their autonomous relatives to transpose. Miniature inverted repeat transposable elements (MITEs) are often the most numerous nonautonomous DNA elements in a higher eukaryotic genome. Little is known about the origin of these MITE families as few of them are accompanied by their direct ancestral elements in a genome. Analyses of MITEs in the yellow fever mosquito identified its youngest MITE family, designated as Gnome, that contains at least 116 identical copies. Genome-wide search for direct ancestral autonomous elements of Gnome revealed an elusive single copy Tc1/Mariner-like element, named as Ozma, that encodes a transposase with a DD37E triad motif. Strikingly, Ozma also gave rise to two additional MITE families, designated as Elf and Goblin. These three MITE families were derived at different times during evolution and bear internal sequences originated from different regions of Ozma. Upon close inspection of the sequence junctions, the internal deletions during the formation of these three MITE families always occurred between two microhomologous sites (6–8 bp). These results suggest that multiple MITE families may originate from a single ancestral autonomous element, and formation of MITEs can be mediated by sequence microhomology. Ozma and its related MITEs are exceptional candidates for the long sought-after endogenous active transposon tool in genetic control of mosquitoes.

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The complete Ac/Ds transposon family of maize

Cited by 22 publications

References 54 publications

Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline

Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline

Generation of Tandem Direct Duplications by Reversed-Ends Transposition of Maize Ac Elements

Birth of Three Stowaway-like MITE Families via Microhomology-Mediated Miniaturization of a Tc1/Mariner Element in the Yellow Fever Mosquito

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