- Genome-wide characterization of LTR. - retrotransposons in the non-model deep- sea annelid Lamellibrachia luymesi. - Available data on LTR retrotransposons have facilitated comparative studies and provided insight on genome evolution. - Here, we focus on genome of Lamellibrachia luymesi, a vestimentiferan tubeworm from deep-sea hydrocarbon seeps, to gain knowledge of LTR retrotransposons in a deep-sea annelid.. - Results: We characterized LTR retrotransposons present in the genome of L. - luymesi using bioinformatic approaches and found that intact LTR retrotransposons makes up about 0.1% of L. - Previous characterization of the genome has shown that this tubeworm hosts several known LTR-retrotransposons. - Here we describe and classify LTR retrotransposons in L. - In addition, analysis of insertion times indicated that several LTR-retrotransposons were recently transposed into the genome of L. - Conclusions: Our analysis contributes to knowledge on diversity of LTR-retrotransposons in marine settings and also serves as an important step to assist our understanding of the potential role of retroelements in marine organisms. - However, several new groups of LTR retrotransposons were discovered suggesting that the representation of LTR retrotransposons may be different in marine settings. - Further study would improve understanding of the diversity of retrotransposons across animal groups and environments.. - They often make up a substantial fraction of the host genome in which they reside, occupying more than 40% of the human genome [2] and more than 50% of the maize genome [3]. - For this reason, we explored the genome of the deep-sea tubeworm Lamellibrachia luymesi (Sibo- glinidae, Annelida) [5] which employs chemoauto- trophic endosymbionts to inhabit hydrocarbon seeps in the Gulf of Mexico.. - Retrotransposons are usually classified into two cat- egories: LTR retrotransposons and non-LTR retrotran- sposons. - LTR retrotransposons usually serve as a model for the study of retroviruses [6], because both are structurally similar and phylogenetic- ally related [7]. - The main distinguishing characteristic is the presence of an envelope (env) gene in retroviruses which is absent in LTR retrotransposons. - LTR retrotransposons (Fig. - In contrast, function of the aORF located in the antisense orientation is not clearly known, however , studies carried out so far suggests that they may be play- ing a regulatory role in retrotransposition . - However, to the best of our knowledge, there has been minimal effort to characterize the LTR retrotransposons present in deep-sea (>200m) animals or in annelids. - Available stud- ies tend to only consider transposable ele- ments in context of their role in genome composition rather than detailed assessment of the elements and their evolution. - Their result showed that 2.52% of the genome consisted of LTR retroelements. - However, the goal of the analysis was to see how much of the genome’s DNA was derived from repetitive elements using RepeatMode- ler [28] and RepeatMasker [29]. - luymesi’s genome composition rather than an exploration of the LTR ret- roelements biology. - In the current study, we further characterized and classified LTR retrotransposons. - 1 Structure of a LTR retrotransposon. - present in the genome of Lamellibrachia luymesi to shed light on the representation of LTR retrotransposon superfamilies, as well as augment understanding of the potential function and structure of intact elements. - Identification and classification of LTR-retrotransposon A total of 223 intact LTR retrotransposons (Supplemen- tary Table 1, 2) were identified in the 688 Mb L. - Of the 223 intact LTR-retrotransposon identified by LTR_retriever, 51 were classified as unknown, 1 was classified as Copia while 171 were classified as Gypsy.. - In addition, out of the 51 classified by LTR_retriever as unknown, 7 were classified as Gypsy, 2 were classified as Bel-pao while 1 was classified as Copia in TEsorter. - Hence, in total, TEsorter classi- fied 182 of the 223 intact LTR retrotransposons identi- fied by LTR-retriever (Supplementary Table 2).. - Results showed that 24 of the elements lacked domains match- ing any known profiles in the databases, 10 had domains that were unrelated to LTR retrotransposons (e.g., a transmembrane receptor, coagulation-inhibition site etc. - Summary details of the 182 LTR retrotransposons used for downstream analysis, which includes 178 Gypsy, 2 Bel-pao and 2 Copia elements are shown in Table 1.. - Of the 182 identified LTR retrotransposons, 32 elements had all domains (Gag and Pol – RT, INT, RH, PR) present with the remainder having at least one domain present. - The target site duplication flanking ends of identified LTR retrotransposons ranged from 3 to 5 bp in length, with majority of them being 5 bp in length. - Palindromic motifs detected in the elements includes TGCA, TACA, TATA, TCGT, TGAA, TGAC, TGAT and TTAT, with 89% of the LTR-retrotransposons having TGCA motif.. - In addition, differences in length of identified LTR- retrotransposons were substantial, ranging from 1389 bp-8866 bp while the length of the LTRs ranged from 103 to 1468 bp (Supplementary Table 2).. - Insertion times of LTR retrotransposon elements in L.. - Phylogenetic analysis of LTR-retrotransposons. - Naming conventions based on phylogenetic analyses are described in the Methods section.. - For Gypsy elements, phylogenetic analysis of the RT, RH and INT sequences showed that some elements fall into recognized families such as CSRN1 [32], Gmr1 [33]. - Table 1 Summary of LTR retrotransposons in L. - Elements in the 2 previously described fam- ilies. - Three of the novel families (LFG8, LFG9 and LFG7) clustered within Mag elements, sug- gesting that they might be distinct lineage within the Mag radiation.. - In the RH tree, LLCO2 clus- tered within the GalEa family (LCF2) with a bootstrap. - Elements in red are elements identified in the genome of L. - The deep-sea annelid Lamellibrachia luymesi genome contained at least 182 intact LTR retrotransposons which clustered into 12 families, 6 of which appear to be novel. - although several elements could not be classified in the existing families of these superfamilies.. - Generally, LTR retrotransposons are known to be more abundant in plant genomes (e.g. - only 0.02% of the genome of C. - In the genome se- quencing study of L. - luymesi done by Li et al., 2.52% of the genome were reported to be made up of LTR ele- ments. - Here, we expand this earlier effort to show that only ~0.1% of the genome is made up of intact LTR ele- ments comprising mainly Gypsy representatives with a few Bel-pao and Copia elements. - Our results, when compared to Li et al., indicates that most of the hits recovered by RepeatModeler and. - However, a better understanding of LTR retro- transposon domains and a more robust database for LTR retrotransposon in non-model animals would likely allow a more accurate assessment as to the number, rep- resentation, and completeness of LTR retrotransposons in L. - Examination of LTR retrotransposons in L. - luymesi genome corroborates these observations as 97% of the elements classified were Gypsy elements. - Ac- cording to our phylogenetic analysis, 3 previously de- scribed families including A-clade and C-clade of the Mag family, Gmr1 and CSRN1 were present in L.. - Given their ubiquitous nature, Mag elements been the most common of the Gypsy elements found in L.. - Gmr1 elements differ from other Gypsy LTR-retroelements in that the integrase domain usually lie upstream of the reverse transcriptase domain, an arrangement mostly seen in Copia elements [33].. - The previously described family, GalEa, has been known to be one of the most predominant Copia retrotransposon as they are widely distributed among metazoans [10, 46]. - The distribution of inferred insertion times of LTR retrotransposons found in L. - augments the fact that these elements are indeed recent in the genome of L. - However, to infer the possible role of transposable elements more fully in the animal genomes, other types of retrotranspo- sons such as non-LTR retrotransposons or other trans- posable elements needs to be identified and annotated in these organisms.. - Assembled whole genomic sequence of the siboglinid annelid Lamellibrachia luymesi generated by Li et al.. - conducted a scaffold-level assembly of the genome using Illumina paired-end and mate-pair and se- quence data. - Identification of LTR retrotransposons. - The bioinformatics pipeline (Figure 2) used to identify LTR retrotransposon candidates in the L. - Classification of discovered LTR retrotransposons. - Classification of LTR retrotransposons is dependent upon the presence and order of protein domains within the pol gene [11] (Fig 1). - LTR_retriever based the classi- fication of LTR retrotransposons on identification of conserved protein domains of each LTR retrotransposon candidate using profile Hidden Markov Models (pHMMs) of LTR retrotransposon domains from Pfam database [30]. - Classification into superfamilies and families were based on hits of the pol and gag genes to curated database. - To facilitate communication, naming conventions for LTR retrotransposons families and elements identified in this study were created. - For individual elements, identified LTR retrotransposons were designated as LLXY#, where LL denotes 2 letters representing L. - luymesi, XY denotes the first two letters of the superfamily it belongs to and # denotes the elem- ent number (e.g., LLGY1 represents a Gypsy element).. - To infer phylogenetic trees, amino acid sequence of INT,RH and RT from other known organisms were obtained from the GYDB database and recent studies and aligned using MAFFT v7.407 [64] to amino acid sequence of INT, RT and RH from LTR retrotransposons found in L. - Each of the 3 domains was analyzed separately and a com- bined analysis was not done due to difference in taxon sampling and the fact that the domains may have distinct evolutionary histories. - Time since initial insertion of LTR retrotransposon can- didates was estimated using scripts implemented in the LTR_retriever package. - Details of each LTR- retrotransposons found in Lamellibrachia luymesi genome, including element sizes, LTR sizes and pair identity, TSD sizes and sequences,motif sequences.. - I would like to thank the members of the Molette Lab for their valuable information and guidance. - Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi. - Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside. - LTR Retrotransposons in Fungi. - Mollusc genomes reveal variability in patterns of LTR-retrotransposons dynamics. - The structure and retrotransposition mechanism of LTR-retrotransposons in the asexual yeast Candida albicans. - Systematic survey of plant LTR- retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. - Additional ORFs in Plant LTR-Retrotransposons.. - Recent expansion of heat- activated retrotransposons in the coral symbiont Symbiodinium microadriaticum. - LTR- retrotransposons in R. - CsRn1, a novel active retrotransposon in a parasitic trematode, Clonorchis sinensis, discloses a new phylogenetic clade of Ty3/gypsy-like LTR retrotransposons. - Structural and evolutionary analyses of the Ty3/gypsy group of LTR retrotransposons in the genome of Anopheles gambiae. - The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. - Sequence analysis of transposable elements in the sea squirt, Ciona intestinalis. - Molecular structure of a novel gypsy-Ty3-like retrotransposon (Kabuki) and nested retrotransposable elements on the W chromosome of the silkworm Bombyx mori. - Boudicca, a retrovirus-like long terminal repeat retrotransposon from the genome of the human blood fluke Schistosoma mansoni. - The Sinbad retrotransposon from the genome of the human blood fluke, Schistosoma mansoni, and the distribution of related Pao-like elements. - software for de novo detection of LTR retrotransposons. - LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. - Heterogeneity of the internal structure of PDR1, a family of Ty1/copia-like retrotransposons in pea. - Identification and characterization of a LTR retrotransposon from the genome of Cyprinus carpio var
Xem thử không khả dụng, vui lòng xem tại trang nguồn hoặc xem
Tóm tắt