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Transposons make up the bulk of eukaryotic genomes, but are difficult to annotate because they evolve rapidly. Most of the unannotated portion of sequenced genomes is probably made up of various divergent transposons that have yet to be categorized. Helitrons are unusual rolling circle eukaryotic transposons that often capture gene sequences, making them of considerable evolutionary importance. Unlike other DNA transposons, Helitrons do not end in inverted repeats or create target site duplications, so they are particularly challenging to identify. Here we present HelitronScanner, a two-layered local combinational variable (LCV) tool for generalized Helitron identification that represents a major improvement over previous identification programs based on DNA sequence or structure. HelitronScanner identified 64,654 Helitrons from a wide range of plant genomes in a highly automated way. We tested HelitronScanner’s predictive ability in maize, a species with highly heterogeneous Helitron elements. LCV scores for the 5′ and 3′ termini of the predicted Helitrons provide a primary confidence level and element copy number provides a secondary one. Newly identified Helitrons were validated by PCR assays or by in silico comparative analysis of insertion site polymorphism among multiple accessions. Many new Helitrons were identified in model species, such as maize, rice, and Arabidopsis , and in a variety of organisms where Helitrons had not been reported previously to our knowledge, leading to a major upward reassessment of their abundance in plant genomes. HelitronScanner promises to be a valuable tool in future comparative and evolutionary studies of this major transposon superfamily.

This study presents the first genome and transcriptome analyses for Fusarium oxysporum f. sp. lactucae (Fola) which causes Fusarium wilt disease of lettuce. Long-read genome sequencing of three race 1 (Fola1) and three race 4 (Fola4) isolates revealed key differences in putative effector complement between races and with other F. oxysporum ff. spp. following mimp -based bioinformatic analyses. Notably, homologues of Secreted in Xylem ( SIX ) genes, also present in many other F. oxysporum ff. spp, were identified in Fola, with both SIX9 and SIX14 (multiple copies with sequence variants) present in both Fola1 and Fola4. All Fola4 isolates also contained an additional single copy of SIX8 . RNAseq of lettuce following infection with Fola1 and Fola4 isolates identified highly expressed effectors, some of which were homologues of those reported in other F. oxysporum ff. spp. including several in F. oxysporum f. sp. apii . Although SIX8 , SIX9 and SIX14 were all highly expressed in Fola4, of the two SIX genes present in Fola1, only SIX9 was expressed as further analysis revealed that SIX14 gene copies were disrupted by insertion of a transposable element. Two variants of Fola4 were also identified based on different genome and effector-based analyses. This included two different SIX8 sequence variants which were divergently transcribed from a shared promoter with either PSE1 or PSL1 respectively. In addition, there was evidence of two independent instances of HCT in the different Fola4 variants. The involvement of helitrons in Fola genome rearrangement and gene expression is discussed.

Genome size variation in eukaryotic species is largely influenced by repetitive DNA sequences such as transposable elements (TEs), simple repeats, and satellite DNAs (satDNAs), which do not necessarily correlate with organismal complexity. In insects, TEs are crucial to evolutionary processes and are correlated with variations in genome size. In this study, we describe, for the first time, the mobilome and satellitome of Drosophila amaguana, an Ecuadorian Neotropical species with a large, unexplored genome size, to assess the contribution of these repetitive DNA sequences to its genome composition. Using a draft genome assembly of approximately 455.5 Mb, generated from Illumina short-read sequences obtained from 10 wild specimens of D. amaguana collected at the Refugio de Vida Silvestre Pasochoa, we employed a de novo approach to create a manually curated TE library of 737 consensus sequences. We identified 716 novel TE families that had not been previously described, 20 TEs previously characterized in other Drosophila species, and one DNA transposon previously described in the Lepeophtheirus genus. The total TE content in the D. amaguana genome was 21.54%, distributed as follows: 6.35% Helitrons (1 superfamily), 5.13% LTR retrotransposons (5 superfamilies), 3.63% TIRs (9 superfamilies), 3.61% LINEs (7 superfamilies), 1.17% MITEs, 0.94% Maverick, 0.67% PLE, 0.02% SINEs, and 0.01% DIRS. We also identified 11.8% of simple repeats. Additionally, we estimated the satDNA content using Illumina raw reads and identified 16 satDNA families, all unique to the Drosophila genus, which comprise 4.90% of the genome. Overall, our results based on short-read data suggest that the large genome size of D. amaguana may not be the consequence of a high amount of TEs or satDNAs. Instead, its large genome size could be attributed to other factors (e.g., noncoding DNA occupying substantial portions of the genome or a high percentage of duplicated genes) that remain to be determined or explored in future studies using long-reads to overcome short-reads limitations. These findings may currently offer valuable insights into the adaptative and evolutionary processes of the mesophragmatica species group in the Andean forests.

In the absence of recombination, the number of transposable elements (TEs) increases due to less efficient selection, but the dynamics of such TE accumulations are not well characterized. Leveraging a dataset of 21 independent events of recombination cessation of different ages in mating-type chromosomes of Microbotryum fungi, we show that TEs rapidly accumulated in regions lacking recombination, but that TE content reached a plateau at ca. 50% of occupied base pairs by 1.5 million years following recombination suppression. The same TE superfamilies have expanded in independently evolved non-recombining regions, in particular rolling-circle replication elements ( Helitrons ). Long-terminal repeat (LTR) retrotransposons of the Copia and Ty3 superfamilies also expanded, through transposition bursts (distinguished from gene conversion based on LTR divergence), with both non-recombining regions and autosomes affected, suggesting that non-recombining regions constitute TE reservoirs. This study improves our knowledge of genome evolution by showing that TEs can accumulate through bursts, following non-linear decelerating dynamics. In the absence of recombination, the number of transposable elements (TEs) increases, but their accumulation dynamics are not well characterized. This study shows that TEs rapidly accumulated in non-recombining fungal mating-type chromosomes before reaching a plateau, possibly forming a TE reservoir.

Transposable elements (TEs) may contribute to evolutionary innovations through the rewiring of networks by supplying ready-to-use eis regulatory elements. Genes on the Drosophila X chromosome are coordinately regulated by the male specific lethal (MSL) complex to achieve dosage compensation in males. We show that the acquisition of dozens of MSL binding sites on evolutionarily new X chromosomes was facilitated by the independent co-option of a mutant helitron TE that attracts the MSL complex (TE domestication). The recently formed neo-X recruits helitrons that provide dozens of functional, but suboptimal, MSL binding sites, whereas the older XR chromosome has ceased acquisition and appears to have fine-tuned the binding affinities of more ancient elements for the MSL complex. Thus, TE-mediated rewiring of regulatory networks through domestication and amplification may be followed by fine-tuning of the cis-regulatory element supplied by the TE and erosion of nonfunctional regions.

DnaJ, or heat shock protein 40 (HSP40), is a conserved protein that functions as a molecular chaperone with a strong cytoprotective effect, participating in plant signal transduction, growth, development, and the response to heat stress and other adverse environmental conditions. Although functional characteristics of DnaJ/HSP40 have been described in several plant species, the underlying mechanisms are not completely understood. In this study, 99 putative maize (Zea mays L.) DnaJ genes (ZmDnaJ01–99) randomly distributed on 10 chromosomes were identified in the whole genome using bioinformatics approaches and classified into three groups according to protein structure. The conservation of the gene structure was closely related to the evolutionary tree. Collinearity analysis of DnaJ family genes among species revealed a close evolutionary relationship between maize and sorghum. Transposon analysis revealed helitrons inserted in 49 ZmDnaJs. Multiple stress-related cis-elements were found in the promoter regions of ZmDnaJ genes, suggesting a role in gene expression regulation in response to abiotic stress. The co-expression network screened 12 ZmDnaJ genes that could be induced by stress (drought, high temperature, and salt) and regulated by abscisic acid. ZmDnaJ96 overexpression increased antioxidant enzyme activity and reduced the damage caused by drought and high-temperature stress in Arabidopsis chloroplasts. Virus-induced silencing of ZmDnaJ96 reduced drought and heat tolerance in maize by reducing antioxidant enzyme activity. These results provide genetic resources for maize stress resistance molecular breeding, enhance knowledge of DnaJ gene function in maize, and offer a solid foundation for further in-depth study of the relationship between maize DnaJ/HSP40 members.

Helitrons are recently discovered eukaryotic transposons that are predicted to amplify by a rolling-circle mechanism. They are present in most plant and animal species investigated, but were previously overlooked partly because they lack terminal repeats and do not create target site duplications. Hetitrons are particularly abundant in flowering plants, where they frequently acquire, and sometimes express, 1 or more gene fragments. A structure-based search protocol was developed to find Helitrons and was used to analyze several plant and animal genomes, leading to the discovery of hundreds of new Helitrons. Analysis of these Helitrons has uncovered mechanisms of element evolution, including end creation and sequence acquisition. Preferential accumulation in genepoor regions and target site specificities were also identified. Overall, these studies provide insights into the transposition and evolution of Helitrons and their contributions to evolved gene content and genome structure.

Abstract Helitrons are the only group of rolling-circle transposons that encode a transposase with a helicase domain (Hel), which belongs to the Pif1 family. Because Pif1 helicases are important components of eukaryotic genomes, it has been suggested that Hel domains probably originated after a host eukaryotic Pif1 gene was captured by a Helitron ancestor. However, the few analyses exploring the evolution of Helitron transposases (RepHel) have focused on its Rep domain, which is also present in other mobile genetic elements. Here, we used phylogenetic and nonmetric multidimensional scaling analyses to investigate the relationship between Hel domains and Pif1-like helicases from a variety of organisms. Our results reveal that Hel domains are only distantly related to genomic helicases from eukaryotes and prokaryotes, and thus are unlikely to have originated from a captured Pif1 gene. Based on this evidence, and on recent studies indicating that Rep domains are more closely related to rolling-circle plasmids and phages, we suggest that Helitrons are descendants of a RepHel-encoding prokaryotic plasmid element that invaded eukaryotic genomes before the radiation of its major groups. We discuss how a Pif1-like helicase domain might have favored the transposition of Helitrons in eukaryotes beyond simply unwinding DNA intermediates. Finally, we demonstrate that some examples in the literature describing genomic helicases from eukaryotes actually consist of Hel domains from Helitrons, a finding that underscores how transposons can hamper the analysis of eukaryotic genes. This investigation also revealed that two groups of land plants appear to have lost genomic Pif1 helicases independently.

Rolling-circle (RC) transposons, or Helitrons, are a newly recognized group of eukaryotic transposable elements abundant in the genomes of plants, invertebrates, and zebrafish. We provide evidence for the colonization of a mammalian genome by Helitrons, which has not been reported previously. We identified and characterized two families of Helitrons in the little brown bat Myotis lucifugus. The consensus sequence for the first family, HeliBat1, displays the hallmarks of an autonomous Helitron, including coding capacity for an [almost equal to]1,500-aa protein with an RC replication motif and a region related to the SF1 superfamily of DNA helicases. The HeliBatN1 family is a nonautonomous Helitron family that is only distantly related to HeliBat1. The two HeliBat families have attained high copy numbers ([almost equal to]15,000 and > 100,000 copies, respectively) and make up at least [almost equal to]3% of the M. lucifugus genome. Sequence divergence and cross-species analyses indicate that both HeliBat families have amplified within the last [almost equal to]30-36 million years and are restricted to the lineage of vesper bats. We could not detect the presence of Helitrons in any other order of placental mammals, despite the broad representation of these taxa in the databases. We describe an instance of HeliBat-mediated transduction of a host gene fragment that was subsequently dispersed in [almost equal to]1,000 copies throughout the M. lucifugus genome. Given the demonstrated propensity of RC transposons to mediate the duplication and shuffling of host genes in bacteria and maize, it is tempting to speculate that the massive amplification of Helitrons in vesper bats has influenced the evolutionary trajectory of these mammals.

Nucleotide-binding domain leucine-rich repeat (NLR) proteins are a key component of the plant innate immune system. In plant genomes, NLRs exhibit considerable presence/absence variation and sequence diversity. Recent advances in sequencing technologies have made the generation of high-quality novel plant genome assemblies considerably more straightforward. Accurately identifying NLRs from these genomes is a prerequisite for improving our understanding of NLRs and identifying novel sources of disease resistance. While several tools have been developed to predict NLRs, they are hampered by low accuracy, speed, and availability. Here, the NLR annotation tool Resistify is presented. Resistify is an easy-to-use, rapid, and accurate tool to identify and classify NLRs from protein sequences. Applying Resistify to the RefPlantNLR database demonstrates that it can correctly identify NLRs from a diverse range of species. Applying Resistify in combination with tools to identify transposable elements to a panel of Solanaceae genomes reveals a previously undescribed association between NLRs and Helitron transposable elements.