Non-autonomous Transposable Elements Research Articles

Unveiling host-parasite relationships through conserved MITEs in prokaryote and viral genomes.

Transposable elements (TEs) play a pivotal role in the evolution of genomes across all life domains. 'Miniature Inverted-repeat Transposable-Elements' (MITEs) are non-autonomous TEs mainly located in intergenic regions, relying on external transposases for mobilization. The extent of MITEs' mobilome was explored across nearly 1700 prokaryotic genera, 183 232 genomes, revealing a broad distribution. MITEs were identified in 56.5% of genomes, totaling over 1.4 million cMITEs (cellular MITEs). Cluster analysis revealed that 97.4% of cMITEs were specific within genera boundaries, with up to 23% being species-specific. Subsequently, this genus-specificity was evaluated as a method to link microbial host to their viruses. A total of 51 655 cMITEs had counterparts in viral sequences, termed vMITEs (viral MITEs), resulting in the identification of 2500 viral sequences with them. Among these, 1501 sequences were positively assigned to a previously known host (41.8% were isolated viruses and 12.3% were assigned through CRISPR data), while 379 new host-virus associations were predicted. Deeper analysis in Neisseria and Bacteroidota groups allowed the association of 242 and 530 new viral sequences, respectively. MITEs are proposed as a novel approach to establishing valid virus-host relationships.

Characterization of active transposable elements and their new insertions in tuber propagated greater yam (Dioscorea alata)

BackgroundGreater yam is a key staple crop grown in tropical and subtropical regions, while its asexual propagation mode had led to non-flowering mutations. How transposable elements contribute to its genetic variations is rarely analyzed. We used transcriptome and whole genome sequencing data to identify active transposable elements (TEs) and genetic variation caused by these active TEs. Our aim was to shed light on which TEs would lead to its intraspecies variation.ResultsAnnotation of de novo assembly transcripts indicated that 0.8 − 0.9% of transcripts were TE related, with LTR retrotransposons (LTR-RTs) accounted for 65% TE transcripts. A large portion of these transcripts were non-autonomous TEs, which had incomplete functional domains. The majority of mapped transcripts were distributed in genic deficient regions, with 9% of TEs overlapping with genic regions. Moreover, over 90% TE transcripts exhibited low expression levels and insufficient reads coverage to support full-length structure assembly. Subfamily analysis of Copia and Gypsy, the two LTR-RTs revealed that a small number of subfamilies contained a significantly larger number of members, which play a key role in generating TE transcript. Based on resequencing data, 15,002 L-RT insertion loci were detected for active LTR-RT members. The insertion loci of LTR-RTs were highly divergent among greater yam accessions.ConclusionsThis study showed the ongoing transcription and transpositions of TEs in greater yam, despite low transcription levels and incomplete proteins insufficient for autonomous transposition. While our research did not directly link these TEs to specific yam traits such as tuber yield and propagation mode, it lays a crucial foundation for further research on how these TE insertion polymorphisms (TIPs) might be related to variations in greater yam traits and its tuber propagation mode. Future research may explore the potential roles of TEs in trait variations, such as tuber yield and stress resistance, in greater yam.

RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes

Compared to eukaryotes, repetitive sequences are rare in bacterial genomes and usually do not persist for long. Yet, there is at least one class of persistent prokaryotic mobile genetic elements: REPINs. REPINs are non-autonomous transposable elements replicated by single-copy transposases called RAYTs. REPIN-RAYT systems are mostly vertically inherited and have persisted in individual bacterial lineages for millions of years. Discovering and analyzing REPIN populations and their corresponding RAYT transposases in bacterial species can be rather laborious, hampering progress in understanding REPIN-RAYT biology and evolution. Here we present RAREFAN, a webservice that identifies REPIN populations and their corresponding RAYT transposase in a given set of bacterial genomes. We demonstrate RAREFAN’s capabilities by analyzing a set of 49 Stenotrophomonas maltophilia genomes, containing nine different REPIN-RAYT systems. We guide the reader through the process of identifying and analyzing REPIN-RAYT systems across S. maltophilia, highlighting erroneous associations between REPIN and RAYTs, and providing solutions on how to find correct associations. RAREFAN enables rapid, large-scale detection of REPINs and RAYTs, and provides insight into the fascinating world of intragenomic sequence populations in bacterial genomes. RAREFAN is available at http://rarefan.evolbio.mpg.de.

A workflow for studying enigmatic non-autonomous transposable elements across bacteria

Compared to eukaryotes, repetitive sequences are rare in bacterial genomes and usually do not persist for long. Yet, there is at least one class of persistent prokaryotic mobile genetic elements: REPINs. REPINs are non-autonomous transposable elements replicated by single-copy transposases called RAYTs. REPIN-RAYT systems are mostly vertically inherited and have persisted in individual bacterial lineages for millions of years. Discovering and analyzing REPIN populations and their corresponding RAYT transposases in bacterial species can be rather laborious, hampering progress in understanding REPIN-RAYT biology and evolution. Here we present RAREFAN, a webservice that identifies REPIN populations and their corresponding RAYT transposase in a given set of bacterial genomes. We demonstrate RAREFAN’s capabilities by analyzing a set of 49 Stenotrophomonas maltophilia genomes, containing nine different REPIN-RAYT systems. We guide the reader through the process of identifying and analyzing REPIN-RAYT systems across S. maltophilia, highlighting erroneous associations between REPIN and RAYTs, and providing solutions on how to find correct associations. RAREFAN enables rapid, large-scale detection of REPINs and RAYTs, and provides insight into the fascinating world of intragenomic sequence populations in bacterial genomes. RAREFAN is available at http://rarefan.evolbio.mpg.de.

Transposable elements drive intron gain in diverse eukaryotes

There is massive variation in intron numbers across eukaryotic genomes, yet the major drivers of intron content during evolution remain elusive. Rapid intron loss and gain in some lineages contrast with long-term evolutionary stasis in others. Episodic intron gain could be explained by recently discovered specialized transposons called Introners, but so far Introners are only known from a handful of species. Here, we performed a systematic search across 3,325 eukaryotic genomes and identified 27,563 Introner-derived introns in 175 genomes (5.2%). Species with Introners span remarkable phylogenetic diversity, from animals to basal protists, representing lineages whose last common ancestor dates to over 1.7 billion years ago. Aquatic organisms were 6.5 times more likely to contain Introners than terrestrial organisms. Introners exhibit mechanistic diversity but most are consistent with DNA transposition, indicating that Introners have evolved convergently hundreds of times from nonautonomous transposable elements. Transposable elements and aquatic taxa are associated with high rates of horizontal gene transfer, suggesting that this combination of factors may explain the punctuated and biased diversity of species containing Introners. More generally, our data suggest that Introners may explain the episodic nature of intron gain across the eukaryotic tree of life. These results illuminate the major source of ongoing intron creation in eukaryotic genomes.

Miniature Inverted-Repeat Transposable Elements (MITEs) in the Two Lepidopteran Genomes of Helicoverpa armigera and Helicoverpa zea.

Simple SummaryMiniature inverted-repeat transposable elements (MITEs) are non-autonomous transposable elements that play important roles in genome organization and evolution. Helicoverpa armigera and Helicoverpa zea shows a high number of reported cases of insecticide resistance worldwide, having evolved resistance against pyrethroids, organophosphates, carbamates, organochlorines, and recently to macrocyclic lactone spinosad and several Bacillus thuringiensis toxins. In the present study, we conducted a genome screening of MITEs in the H. armigera and H. zea genomes using bioinformatics approaches, and the results revealed a total of 3570 and 7405 MITE sequences in the H. armigera and H. zea genomes, respectively. Among these MITEs, we highlighted eleven MITE insertions in the H. armigera defensome genes and only one MITE insertion in those of H. zea.Miniature inverted-repeat transposable elements MITEs are ubiquitous, non-autonomous class II transposable elements. The moths, Helicoverpa armigera and Helicoverpa zea, are recognized as the two most serious pest species within the genus. Moreover, these pests have the ability to develop insecticide resistance. In the present study, we conducted a genome-wide analysis of MITEs present in H. armigera and H. zea genomes using the bioinformatics tool, MITE tracker. Overall, 3570 and 7405 MITE sequences were identified in H. armigera and H. zea genomes, respectively. Comparative analysis of identified MITE sequences in the two genomes led to the identification of 18 families, comprising 140 MITE members in H. armigera and 161 MITE members in H. zea. Based on target site duplication (TSD) sequences, the identified families were classified into three superfamilies (PIF/harbinger, Tc1/mariner and CACTA). Copy numbers varied from 6 to 469 for each MITE family. Finally, the analysis of MITE insertion sites in defensome genes showed intronic insertions of 11 MITEs in the cytochrome P450, ATP-binding cassette transporter (ABC) and esterase genes in H. armigera whereas for H. zea, only one MITE was retrieved in the ABC-C2 gene. These insertions could thus be involved in the insecticide resistance observed in these pests.

Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome

BackgroundMiniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA transposable elements that play important roles in genome organization and evolution. Genome-wide identification and characterization of MITEs provide essential information for understanding genome structure and evolution.ResultsWe performed genome-wide identification and characterization of MITEs in the pineapple genome. The top two MITE families, accounting for 29.39% of the total MITEs and 3.86% of the pineapple genome, have insertion preference in (TA) n dinucleotide microsatellite regions. We therefore named these MITEs A. comosus microsatellite-associated MITEs (Ac-mMITEs). The two Ac-mMITE families, Ac-mMITE-1 and Ac-mMITE-2, shared sequence similarity in the terminal inverted repeat (TIR) regions, suggesting that these two Ac-mMITE families might be derived from a common or closely related autonomous elements. The Ac-mMITEs are frequently clustered via adjacent insertions. Among the 21,994 full-length Ac-mMITEs, 46.1% of them were present in clusters. By analyzing the Ac-mMITEs without (TA) n microsatellite flanking sequences, we found that Ac-mMITEs were likely derived from Mutator-like DNA transposon. Ac-MITEs showed highly polymorphic insertion sites between cultivated pineapples and their wild relatives. To better understand the evolutionary history of Ac-mMITEs, we filtered and performed comparative analysis on the two distinct groups of Ac-mMITEs, microsatellite-targeting MITEs (mt-MITEs) that are flanked by dinucleotide microsatellites on both sides and mutator-like MITEs (ml-MITEs) that contain 9/10 bp TSDs. Epigenetic analysis revealed a lower level of host-induced silencing on the mt-MITEs in comparison to the ml-MITEs, which partially explained the significantly higher abundance of mt-MITEs in pineapple genome. The mt-MITEs and ml-MITEs exhibited differential insertion preference to gene-related regions and RNA-seq analysis revealed their differential influences on expression regulation of nearby genes.ConclusionsAc-mMITEs are the most abundant MITEs in the pineapple genome and they were likely derived from Mutator-like DNA transposon. Preferential insertion in (TA) n microsatellite regions of Ac-mMITEs occurred recently and is likely the result of damage-limiting strategy adapted by Ac-mMITEs during co-evolution with their host. Insertion in (TA) n microsatellite regions might also have promoted the amplification of mt-MITEs. In addition, mt-MITEs showed no or negligible impact on nearby gene expression, which may help them escape genome control and lead to their amplification.

TnpAREP and REP sequences dissemination in bacterial genomes: REP recognition determinants.

REP, diverse palindromic DNA sequences found at high copy number in many bacterial genomes, have been attributed important roles in cell physiology but their dissemination mechanisms are poorly understood. They might represent non-autonomous transposable elements mobilizable by TnpAREP, the first prokaryotic domesticated transposase associated with REP. TnpAREP, fundamentally different from classical transposases, are members of the HuH superfamily and closely related to the transposases of the IS200/IS605 family. We previously showed that Escherichia coli TnpAREP processes cognate single stranded REP in vitro and that this activity requires the integrity of the REP structure, in particular imperfect palindromes interrupted by a bulge and preceded by a conserved DNA motif. A second group of REPs rather carry perfect palindromes, raising questions about how the latter are recognized by their cognate TnpAREP. To get insight into the importance of REP structural and sequence determinants in these two groups, we developed an in vitro activity assay coupled to a mutational analysis for three different TnpAREP/REP duos via a SELEX approach. We also tackled the question of how the cleavage site is selected. This study revealed that two TnpAREP groups have co-evolved with their cognate REPs and use different strategies to recognize their REP substrates.

Structural and sequence diversity of eukaryotic transposable elements.

The majority of eukaryotic genomes contain a large fraction of repetitive sequences that primarily originate from transpositional bursts of transposable elements (TEs). Repbase serves as a database for eukaryotic repetitive sequences and has now become the largest collection of eukaryotic TEs. During the development of Repbase, many new superfamilies/lineages of TEs, which include Helitron, Polinton, Ginger and SINEU, were reported. The unique composition of protein domains and DNA motifs in TEs sometimes indicates novel mechanisms of transposition, replication, anti-suppression or proliferation. In this review, our current understanding regarding the diversity of eukaryotic TEs in sequence, protein domain composition and structural hallmarks is introduced and summarized, based on the classification system implemented in Repbase. Autonomous eukaryotic TEs can be divided into two groups: Class I TEs, also called retrotransposons, and Class II TEs, or DNA transposons. Long terminal repeat (LTR) retrotransposons, including endogenous retroviruses, non-LTR retrotransposons, tyrosine recombinase retrotransposons and Penelope-like elements, are well accepted groups of autonomous retrotransposons. They share reverse transcriptase for replication but are distinct in the catalytic components responsible for integration into the host genome. Similarly, at least three transposition machineries have been reported in eukaryotic DNA transposons: DDD/E transposase, tyrosine recombinase and HUH endonuclease combined with helicase. Among these, TEs with DDD/E transposase are dominant and are classified into 21 superfamilies in Repbase. Non-autonomous TEs are either simple derivatives generated by internal deletion, or are composed of several units that originated independently.

Expression of CCD4 gene involved in carotenoid degradation in yellow-flowered Petunia × hybrida

Petunia is a popular commercial bedding plant that comes in many colors, but there are no petunia cultivars with deep yellow petals. The carotenoid degradation gene carotenoid cleavage dioxygenase (CCD4) was isolated from white and yellow-flowered petunia and we found the 226-bp insertion of a non-autonomous transposable element tourist-like miniature-inverted repeat (MITE) in the coding region of CCD4 only in yellow cultivars. The insertion interrupts gene expression because of a premature stop codon after the TE insertion and could form secondary structures in hairpin RNA that could then be processed into a mature miRNA. Here, the normal function of CCD4 isolated from a white cultivar was introduced to a yellow cultivar. The transformants showed more fading pale-yellow flowers and carotenoid content was decreased. These results indicate that transformed CCD4 expression promoted carotenoid degradation and the lack of CCD4 expression results in more carotenoid accumulation in wild-type yellow-flowered petunia.

Genome Size Evolution: Small Transposons with Large Consequences

Transposable elements (TEs) heavily influence genome size variation between organisms. A new study on larvacean tunicates now shows that even non-autonomous TEs - small TEs that parasitize the enzymatic machinery of large, autonomous TEs - can have a large impact on genome size.

Massive Changes of Genome Size Driven by Expansions of Non-autonomous Transposable Elements

In eukaryotes, genome size correlates little with the number of coding genes or the level of organismal complexity (C-value paradox). The underlying causes of variations in genome size, whether adaptive or neutral, remain unclear, although several biological traits often covary with it [1-5]. Rapid increases in genome size occur mainly through whole-genome duplications or bursts in the activity of transposable elements (TEs) [6]. The very small and compact genome of Oikopleura dioica, a tunicate of the larvacean class, lacks elements of most ancient families of animal retrotransposons [7, 8]. Here, we sequenced the genomes of six other larvaceans, all of which are larger than that of Oikopleura (up to 12 times) and which increase in size with greater body length. Although no evidence was found for whole-genome duplications within the group of species, the global amount of TEs strongly correlated with genome size. Compared to other metazoans, however, the TE diversity was reduced in all species, as observed previously in O.dioica, suggesting a common ancestor with a compacted genome. Strikingly, non-autonomous elements, particularly short interspersed nuclear elements (SINEs), massively contributed to genome size variation through species-specific independent amplifications, ranging from 3% in the smallest genome up to 49% in the largest. Variations in SINE abundance explain as much as 83% of interspecific genome size variation. These data support an indirect influence of autonomous TEs on genome size via their ability to mobilize non-autonomous elements.

Transposable elements contribute to fungal genes and impact fungal lifestyle

The last decade brought a still growing experimental evidence of mobilome impact on host’s gene expression. We systematically analysed genomic location of transposable elements (TEs) in 625 publicly available fungal genomes from the NCBI database in order to explore their potential roles in genome evolution and correlation with species’ lifestyle. We found that non-autonomous TEs and remnant copies are evenly distributed across genomes. In consequence, they also massively overlap with regions annotated as genes, which suggests a great contribution of TE-derived sequences to host’s coding genome. Younger and potentially active TEs cluster with one another away from genic regions. This non-randomness is a sign of either selection against insertion of TEs in gene proximity or target site preference among some types of TEs. Proteins encoded by genes with old transposable elements insertions have significantly less repeat and protein-protein interaction motifs but are richer in enzymatic domains. However, genes only proximal to TEs do not display any functional enrichment. Our findings show that adaptive cases of TE insertion remain a marginal phenomenon, and the overwhelming majority of TEs are evolving neutrally. Eventually, animal-related and pathogenic fungi have more TEs inserted into genes than fungi with other lifestyles. This is the first systematic, kingdom-wide study concerning mobile elements and their genomic neighbourhood. The obtained results should inspire further research concerning the roles TEs played in evolution and how they shape the life we know today.

PePIF1, a P-lineage of PIF-like transposable element identified in protocorm-like bodies of Phalaenopsis orchids

BackgroundOrchids produce a colorless protocorm by symbiosis with fungi upon seed germination. For mass production of orchids, the prevailing approaches are both generation of protocorm-like bodies (PLBs) from callus and multiplication of adventitious buds on inflorescence. However, somaclonal variations occur during micropropagation.ResultsWe isolated the two most expressed transposable elements belonging to P Instability Factor (PIF)-like transposons. Among them, a potential autonomous element was identified by similarity analysis against the whole-genome sequence of Phalaenopsis equestris and named PePIF1. It contains a 19-bp terminal inverted repeat flanked by a 3-bp target site duplication and two coding regions encoding ORF1- and transposase-like proteins. Phylogenetic analysis revealed that PePIF1 belongs to a new P-lineage of PIF. Furthermore, two distinct families, PePIF1a and PePIF1b, with 29 and 37 putative autonomous elements, respectively, were isolated, along with more than 3000 non-autonomous and miniature inverted-repeat transposable element (MITE)-like elements. Among them, 828 PePIF1-related elements were inserted in 771 predicted genes. Intriguingly, PePIF1 was transposed in the somaclonal variants of Phalaenopsis cultivars, as revealed by transposon display, and the newly inserted genes were identified and sequenced.ConclusionA PIF-like element, PePIF1, was identified in the Phalaenopsis genome and actively transposed during micropropagation. With the identification of PePIF1, we have more understanding of the Phalaenopsis genome structure and somaclonal variations during micropropagation for use in orchid breeding and production.

MiteFinderII: a novel tool to identify miniature inverted-repeat transposable elements hidden in eukaryotic genomes

BackgroundMiniature inverted-repeat transposable element (MITE) is a type of class II non-autonomous transposable element playing a crucial role in the process of evolution in biology. There is an urgent need to develop bioinformatics tools to effectively identify MITEs on a whole genome-wide scale. However, most of currently existing tools suffer from low ability to deal with large eukaryotic genomes.MethodsIn this paper, we proposed a novel tool MiteFinderII, which was adapted from our previous algorithm MiteFinder, to efficiently detect MITEs from genomics sequences. It has six major steps: (1) build K-mer Index and search for inverted repeats; (2) filtration of inverted repeats with low complexity; (3) merger of inverted repeats; (4) filtration of candidates with low score; (5) selection of final MITE sequences; (6) selection of representative sequences.ResultsTo test the performance, MiteFinderII and three other existing algorithms were applied to identify MITEs on the whole genome of oryza sativa. Results suggest that MiteFinderII outperforms existing popular tools in terms of both specificity and recall. Additionally, it is much faster and more memory-efficient than other tools in the detection.ConclusionMiteFinderII is an accurate and effective tool to detect MITEs hidden in eukaryotic genomes. The source code is freely accessible at the website: https://github.com/screamer/miteFinder.

Divergence of VRN-B3 alleles during the evolution of domesticated wheat.

Genetic changes accrued during the domestication of wheat have been crucial in improving the cultivation and yield of this strategic crop. Allelic variation at the VRN3 gene makes a significant contribution to the adaptability of wheat to a wide range of environmental conditions. In the present study, the origin and distribution of the Vrn-B3a and Vrn-B3b alleles during the evolution of wheat were investigated. Analysis of 214 accessions of 11 polyploid wheat species from different eco-geographical areas found the Vrn-B3a and Vrn-B3b alleles in accessions of tetraploid wheat T. dicoccum from Russia and hexaploid wheat of T. spelta from Iran, respectively. DNA sequence analysis of an insertion in the Vrn-B3b promoter region identified a new family of non-autonomous transposable hAT elements that originated in T. urartu lineage. Publicly available whole genome sequence assemblies of 11 T. aestivum and T. durum varieties, as well as WGS of T. dicoccoides were used to investigate the phylogeny and distribution of the TEs inserted in the Vrn-B3a and Vrn-B3b promoter regions, to determine the origin of these alleles. Results showed that both Vrn-B3a and Vrn-B3b diverged during the domestication of wheat, in the T. dicoccum lineage. However, while Vrn-B3a is common in T. dicoccum and T. durum from Ukraine and Russia the Vrn-B3b allele likely has a more recent origin in hexaploid wheat from the Near East.

LINEs Contribute to the Origins of Middle Bodies of SINEs besides 3' Tails.

Short interspersed elements (SINEs), which are nonautonomous transposable elements, require the transposition machinery of long interspersed elements (LINEs) to mobilize. SINEs are composed of two or more independently originating parts. The 5′ region is called the “head” and is derived mainly from small RNAs, and the 3′ region (“tail”) originates from the 3′ region of LINEs and is responsible for being recognized by counterpart LINE proteins. The origin of the middle “body” of SINEs is enigmatic, although significant sequence similarities among SINEs from very diverse species have been observed. Here, a systematic analysis of the similarities among SINEs and LINEs deposited on Repbase, a comprehensive database of eukaryotic repeat sequences was performed. Three primary findings are described: 1) The 5′ regions of only two clades of LINEs, RTE and Vingi, were revealed to have contributed to the middle parts of SINEs; 2) The linkage of the 5′ and 3′ parts of LINEs can be lost due to occasional tail exchange of SINEs; and 3) The previously proposed Ceph-domain was revealed to be a fusion of a CORE-domain and a 5′ part of RTE clade of LINE. Based on these findings, a hypothesis that the 5′ parts of bipartite nonautonomous LINEs, which possess only the 5′ and 3′ regions of the original LINEs, can contribute to the undefined middle part of SINEs is proposed.

Evolutionary modes of emergence of short interspersed nuclear element (SINE) families in grasses.

Short interspersed nuclear elements (SINEs) are non-autonomous transposable elements which are propagated by retrotransposition and constitute an inherent part of the genome of most eukaryotic species. Knowledge of heterogeneous and highly abundant SINEs is crucial for de novo (or improvement of) annotation of whole genome sequences. We scanned Poaceae genome sequences of six important cereals (Oryza sativa, Triticum aestivum, Hordeum vulgare, Panicum virgatum, Sorghum bicolor, Zea mays) and Brachypodium distachyon to examine the diversity and evolution of SINE populations. We comparatively analyzed the structural features, distribution, evolutionary relation and abundance of 32 SINE families and subfamilies within grasses, comprising 11052 individual copies. The investigation of activity profiles within the Poaceae provides insights into their species-specific diversification and amplification. We found that Poaceae SINEs (PoaS) fall into two length categories: simple SINEs of up to 180bp and dimeric SINEs larger than 240bp. Detailed analysis at the nucleotide level revealed that multimerization of related and unrelated SINE copies is an important evolutionary mechanism of SINE formation. We conclude that PoaS families diversify by massive reshuffling between SINE families, likely caused by insertion of truncated copies, and provide a model for this evolutionary scenario. Twenty-eight of 32 PoaS families and subfamilies show significant conservation, in particular either in the 5' or 3' regions, across Poaceae species and share large sequence stretches with one or more other PoaS families.

Rare horizontal transmission does not hide long-term inheritance of SINE highly conserved domains in the metazoan evolution.

Transposable elements (TEs) are self-replicating, mobile DNA sequences which constitute a significant fraction of eukaryotic genomes. They are generally considered selfish DNA, as their replication and random insertion may have deleterious effects on genome functionalities, although some beneficial effects and evolutionary potential have been recognized. Short interspersed elements (SINEs) are non-autonomous TEs with a modular structure: a small RNA-related head, a body, and a long interspersed element-related tail. Despite their high turnover rate and de novo emergence, the body may retain highly conserved domains (HCDs) shared among divergent SINE families: in metazoans, at least nine HCD-SINEs have been recognized. Data mining on public molecular databases allowed the retrieval of 16 new HCD-SINE families from cnidarian, molluscs, arthropods, and vertebrates. Tracking the ancestry of HCDs on the metazoan phylogeny revealed that some of them date back to the Radiata–Bilateria split. Moreover, phylogenetic and age versus divergence analyses of the most ancient HCDs suggested that long-term vertical inheritance is the rule, with few horizontal transfer events. We suggest that the evolutionary conservation of HCDs may be linked to their potential to serve as recombination hotspots. This indirectly affects host genomes by maintaining active and diverse SINE lineages, whose insertions may impact (either positively or negatively) on the evolution of the genome.

High genetic variation and recombination events in the vicinity of non-autonomous transposable elements from ‘Candidatus Liberibacter asiaticus’

Two miniature inverted-repeat transposable elements (MITEs), MCLas-A and MCLas-B, were recently identified from ‘Candidatus Liberibacter asiaticus’ known to be associated with citrus Huanglongbing (HLB, yellow shoot disease). MCLas-A was suggested as an active MITE because of its mobility. The immediate upstream gene of the two MITEs was predicted to be a putative transposase. The goal of this study is to analyze the sequence variation in the upstream putative transposase of MITEs and explore the possible correlation between sequence variation of transposase gene and MITE activity. PCR and sequence analysis showed that 12 sequence types were found in six major amplicon types from 43 representative ‘Ca. L. asiaticus’ isolates from China, the United States and Brazil. Out of the 12 sequence types, three (T4, T5-2, T6) were reported for the first time. Recombination events were found in the two unique sequence types (T5-2 and T6) which were detected in all Brazilian isolates. Notably, no sequence variation or recombination events were detected in the upstream putative transposase gene of MCLas-A, suggesting the conservation of the transposase gene might be closely related with the MITE activity. Phylogenetic analysis demonstrated two well supported clades including five subclades were identified, clearly reflecting the geographical origins of isolates, especially that of Ruili isolates, São Paulo isolates and a few Florida isolates.