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Nucleic Acids Res
2009 Nov 01;3721:e143. doi: 10.1093/nar/gkp752.
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MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes.
Rho M
,
Tang H
.
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Computational methods for genome-wide identification of mobile genetic elements (MGEs) have become increasingly necessary for both genome annotation and evolutionary studies. Non-long terminal repeat (non-LTR) retrotransposons are a class of MGEs that have been found in most eukaryotic genomes, sometimes in extremely high numbers. In this article, we present a computational tool, MGEScan-non-LTR, for the identification of non-LTR retrotransposons in genomic sequences, following a computational approach inspired by a generalized hidden Markov model (GHMM). Three different states represent two different protein domains and inter-domain linker regions encoded in the non-LTR retrotransposons, and their scores are evaluated by using profile hidden Markov models (for protein domains) and Gaussian Bayes classifiers (for linker regions), respectively. In order to classify the non-LTR retrotransposons into one of the 12 previously characterized clades using the same model, we defined separate states for different clades. MGEScan-non-LTR was tested on the genome sequences of four eukaryotic organisms, Drosophila melanogaster, Daphnia pulex, Ciona intestinalis and Strongylocentrotus purpuratus. For the D. melanogaster genome, MGEScan-non-LTR found all known ''full-length'' elements and simultaneously classified them into the clades CR1, I, Jockey, LOA and R1. Notably, for the D. pulex genome, in which no non-LTR retrotransposon has been annotated, MGEScan-non-LTR found a significantly larger number of elements than did RepeatMasker, using the current version of the RepBase Update library. We also identified novel elements in the other two genomes, which have only been partially studied for non-LTR retrotransposons.
Figure 1. The model for identifying and classifying non-LTR retrotransposons. The circles represent states corresponding to protein domains and linker regions. The shaded ovals represent super states corresponding to clades. This model classifies the elements in 12 clades independently.
Figure 2. The distribution of E-values estimated by the pHMMs of 12 clades in Drosophila genomes. The x-axis represents each element (listed in the Supplementary Table S2) and the y-axis represents E-values. For each element, the E-values measured by 12 clades pHMMs are plotted. Each element was assigned to the clade from which the lowest E-value was obtained. Note that the highest point in each element (x-axis) does not mean that they belong to the same clade. Lines connecting each point were added for visualization purpose.
Figure 3. (a) The distribution of hydrophobicity values in KD, (b) WW and (c) HH hydrophobicity scales, and (d) probability for linker region. In (a)−(c), the x-axis represents the hydrophobicity scale and the y-axis represents the frequency. The distribution on the left-hand side with green dots was plotted with the values obtained from random sequences. The distribution on the right-hand side with blue dots was plotted with the values obtained from the elements in the training set. The yellow and red lines represent Gaussian distribution fitting of the data plotted. In (d), the x-axis represents the probability for the linker region and the y-axis represents the frequency.
Figure 4. Phylogenetic analysis of RT domain sequences in the D. pulex elements, along with previously known elements from other genomes. For the D. pulex elements, LOA elements are highlighted in red, I elements in blue, L2 elements in green, L1 elements in pink and NeSL elements in cyan. A cluster of L2 elements (L2_Tr_AF086712, L2_Maul_2, L2_Poll_AAN15747, L2 Danio, L2_Oryzlas, L2_Xlphophorus and L2_L2_Mars_1) from fish genomes were indicated by green circle.
Figure 5. (a) Phylogenetic tree and (b) schematic representation of the elements in five ancient clades of CRE, GENIE, R2, R4 and NeSL. The neighbor-joining tree was built with 1000 rounds of bootstrapping. Note that the cluster of D. pulex elements is connected with the cluster of HEROs in the NeSL clades with a very high-bootstrap value (100%). The schematic representation of the D. pulex NeSL elements is most similar with one of the HERO elements. The gray bars downstream of the RT are cysteine−histidine motif (C-X2-C-X8-H-X4-C). The blank bars downstream of RT represent the REL domain motif (PD..D).
Figure 6. Multiple sequence alignments of the RT domain sequences from CiI, CiL1, CiL2, CiLOA and CiRTE in the C. intestinalis genome. Seven well conserved regions are highlighted in boxes.
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