Academic literature on the topic 'Harbinger transposons'

Harbinger elements are DNA transposons that are widespread from plants to vertebrates but absent from mammalian genomes. Among vertebrates, teleost fish are the clade presenting not only the largest number of species but also the highest diversity of transposable elements, both quantitatively and qualitatively, making them a very attractive group to investigate the evolution of mobile sequences. We studied Harbinger DNA transposons and the distantly related ISL2EU elements in fish, focusing on representative teleost species compared to the spotted gar, the coelacanth, the elephant shark and the amphioxus. We observed high variability in the genomic composition of Harbinger-like sequences in teleost fish, as they covered 0.002–0.14% of the genome, when present. While Harbinger transposons might have been present in a common ancestor of all the fish species studied here, with secondary loss in elephant shark, our results suggests that ISL2EU elements were gained by horizontal transfer at the base of teleost fish 200–300 million years ago, and that there was secondary loss in a common ancestor of pufferfishes and stickleback. Harbinger transposons code for a transposase and a Myb-like protein. We reconstructed and compared molecular phylogenies of both proteins to get insights into the evolution of Harbinger transposons in fish. Transposase and Myb-like protein phylogenies showed global congruent evolution, indicating unique origin of the association between both genes and suggesting rare recombination between transposon sublineages. Finally, we report one case of Harbinger horizontal transfer between divergent fish species and the transcriptional activity of both Harbinger and ISL2EU transposons in teleost fish. There was male-biased expression in the gonads of the medaka fish.

How asexual reproduction shapes transposable element (TE) content and diversity in eukaryotic genomes remains debated. We performed an initial survey of TE load and diversity in the putative ancient asexual ostracod Darwinula stevensoni. We examined long contiguous stretches of DNA in clones from a genomic fosmid library, totaling about 2.5 Mb, and supplemented these data with results on TE abundance and diversity from an Illumina draft genome. In contrast to other TE studies in putatively ancient asexuals, which revealed relatively low TE content, we found that at least 19% of the fosmid dataset and 26% of the genome assembly corresponded to known transposons. We observed a high diversity of transposon families, including LINE, gypsy, PLE, mariner/Tc, hAT, CMC, Sola2, Ginger, Merlin, Harbinger, MITEs and helitrons, with the prevalence of DNA transposons. The predominantly low levels of sequence diversity indicate that many TEs are or have recently been active. In the fosmid data, no correlation was found between telomeric repeats and non-LTR retrotransposons, which are present near telomeres in other taxa. Most TEs in the fosmid data were located outside of introns and almost none were found in exons. We also report an N-terminal Myb/SANT-like DNA-binding domain in site-specific R4/Dong non-LTR retrotransposons. Although initial results on transposable loads need to be verified with high quality draft genomes, this study provides important first insights into TE dynamics in putative ancient asexual ostracods.

From its tropical origin in southwestern Mexico, maize spread over a wide latitudinal cline in the Americas. This feat defies the rule that crops are inhibited from spreading easily across latitudes. How the widespread latitudinal adaptation of maize was accomplished is largely unknown. Through positional cloning and association mapping, we resolved a flowering-time quantitative trait locus to a Harbinger-like transposable element positioned 57 kb upstream of a CCT transcription factor (ZmCCT9). The Harbinger-like element acts in cis to repress ZmCCT9 expression to promote flowering under long days. Knockout of ZmCCT9 by CRISPR/Cas9 causes early flowering under long days. ZmCCT9 is diurnally regulated and negatively regulates the expression of the florigen ZCN8, thereby resulting in late flowering under long days. Population genetics analyses revealed that the Harbinger-like transposon insertion at ZmCCT9 and the CACTA-like transposon insertion at another CCT paralog, ZmCCT10, arose sequentially following domestication and were targeted by selection for maize adaptation to higher latitudes. Our findings help explain how the dynamic maize genome with abundant transposon activity enabled maize to adapt over 90° of latitude during the pre-Columbian era.

Transposable elements (TEs) are self-replicating genetic sequences and are often described as important ‘drivers of evolution’. This driving force is because TEs promote genomic novelty by enabling rearrangement, and through exaptation as coding and regulatory elements. However, most TE insertions potentially lead to neutral or harmful outcomes, therefore host genomes have evolved machinery to suppress TE expansion. Through horizontal transposon transfer (HTT) TEs can colonize new genomes, and since new hosts may not be able to regulate subsequent replication, these TEs may proliferate rapidly. Here, we describe HTT of the Harbinger-Snek DNA transposon into sea kraits ( Laticauda ), and its subsequent explosive expansion within Laticauda genomes. This HTT occurred following the divergence of Laticauda from terrestrial Australian elapids approximately 15–25 Mya. This has resulted in numerous insertions into introns and regulatory regions, with some insertions into exons which appear to have altered UTRs or added sequence to coding exons. Harbinger-Snek has rapidly expanded to make up 8–12% of Laticauda spp. genomes; this is the fastest known expansion of TEs in amniotes following HTT. Genomic changes caused by this rapid expansion may have contributed to adaptation to the amphibious-marine habitat.

Abstract In this mini-review we present insight to the non-nuclear transposable elements and in silico analysis of miniature inverted transposable elements (MITEs) in the grapevine mitochondrial genome. Here we report the identification of 17 truncated sequences in grapevine (Vitis vinifera L.) mitochondrial genome which expectedly belongs to the four ancient transposon families (hAT, Tc1Mariner, Mutator and PIF/Harbinger). Some sequences with a high rate of homology in chloroplast and nuclear genomes were also identified. Thus, it suggests the intercellular gene transfer between these three organelles. These partial sequences showed a high level of similitude with full MITE sequences, and they were found in their inner region, supporting their MITE origin. Further analysis revealed these sequences in other life kingdoms (including eubacteria and archaea), which indicates their ancient origin. Further research showed that 13 out of the 17 sequences are conserved domains of the genes where they are located, suggesting their contribution to gene evolution. Therefore, we suppose that more studies of nature, origin and functional meaning of these sequences and their fusion with genes are necessary. In the light of our observations it will be useful for further studies of V. vinifera genome organizing and systematics, as well as for other species.

Abstract The formation of new genes is a major source of organism evolutionary innovation. Beyond their mutational effects, transposable elements can be co-opted by host genomes to form different types of sequences including novel genes, through a mechanism named molecular domestication. We report the formation of four genes through molecular domestication of Harbinger transposons, three in a common ancestor of jawed vertebrates about 500 million years ago and one in sarcopterygians approx. 430 million years ago. Additionally, one processed pseudogene arose approx. 60 million years ago in simians. In zebrafish, Harbinger-derived genes are expressed during early development but also in adult tissues, and predominantly co-expressed in male brain. In human, expression was detected in multiple organs, with major expression in the brain particularly during fetal development. We used CRISPR/Cas9 with direct gene knock-out in the F0 generation and the morpholino antisense oligonucleotide knock-down technique to study in zebrafish the function of one of these genes called MSANTD2, which has been suggested to be associated to neuro-developmental diseases such as autism spectrum disorders and schizophrenia in human. MSANTD2 inactivation led to developmental delays including tail and nervous system malformation at one day post fertilization. Affected embryos showed dead cell accumulation, major anatomical defects characterized by impaired brain ventricle formation and alterations in expression of some characteristic genes involved in vertebrate nervous system development. Hence, the characterization of MSANTD2 and other Harbinger-derived genes might contribute to a better understanding of the genetic innovations having driven the early evolution of the vertebrate nervous system.

Abstract Loss of seed shattering was a key step during cereal domestication, and greatly facilitated seed harvest of the staple cereal foxtail millet (Setaria italica) because the cereal has very small seeds. However, the genetic basis for this loss has been largely unknown. Here we combined comparative and association mapping to identify an 855-bp Harbinger transposable element insertion in the second exon of the foxtail millet gene shattering1 (sh1) that was responsible for loss of seed shattering. The sh1 gene encodes zinc finger and YABBY domains. The insert prevents transcription of the second exon, causing partial loss of the zinc finger domain and then loss of natural seed shattering. Specifically, sh1 functions as a transcription repressor and represses the transcription of genes associated with lignin synthesis in the abscission zone, including CAD2. The diversity of sh1 is highly reduced in foxtail millet, consistent with either a severe domestication bottleneck and/or a selective sweep. Phylogenetic analysis of sh1 further revealed a single origin of foxtail millet in China. Our results support the theories that transposons were the most active factors in genome evolution driving loss of natural seed shattering during foxtail millet domestication and that sh1 underwent parallel selection during domestication across different cereal species.

La formation de nouveaux gènes est une source majeure d’innovation pour les organismes. Au-delà de leurs effets mutagènes, les éléments transposables peuvent être source de nouveaux gènes. Lors de cette thèse, j’ai étudié les transposons à ADN Harbinger, que j’ai pu caractériser chez les poissons téléostéens. J’ai de plus identifié chez les vertébrés par criblage bioinformatique quatre nouveaux gènes dérivés de transposons Harbinger, trois formés à la base des vertébrés à mâchoires il y a environ 500 millions d’années et un chez les sarcoptérygiens il y a environ 430 millions d’années. Chez le poisson-zèbre, ces gènes sont exprimés pendant le développement précoce et dans les tissus adultes, avec une co-expression dans le cerveau mâle. Ils sont également activés dans le cerveau humain, en particulier pendant le développement fœtal. Afin d’étudier la fonction des gènes dérivés de transposons Harbinger, leur inactivation a été réalisée par CRISPR/Cas9 et oligonucléotides antisense de type morpholino. L’inactivation du gène MSANTD2, qui a été associé à des maladies neurodéveloppementales comme les troubles du spectre de l’autisme et la schizophrénie, produit des embryons présentant des retards de développement et des malformations de la queue et du système nerveux, en particulier des défauts de formation des ventricules du cerveau et de patterns neuronaux. Ainsi, cette thèse a permis de mettre en évidence des domestications moléculaires récurrentes de transposons Harbinger qui ont abouti à la formation d’une nouvelle famille de gènes chez les vertébrés. L’étude d’un des membres, MSANTD2, contribue à une meilleure compréhension des innovations génétiques qui ont déterminé l’évolution précoce du système nerveux des vertébrés
New gene formation is one of the major sources of evolutionary innovations for organisms. Beyond their mutational effects, transposable elements can be source of new genes. During my thesis, I have studied Harbinger DNA transposons, which I have characterized in teleost fish genomes. Moreover, I have identified four new genes derived from Harbinger transposons in vertebrates by bioinformatical screening. Three of them were formed at the base of jawed vertebrates around 500 million years ago, and another at the base of sarcopterygians around 430 million years ago. Using the zebrafish model, we have observed that these genes are expressed during early development and in adult tissues, with a co-expression in male brain. They are also activated in human brain, particularly during fetal development. In order to study Harbinger-derived genes function, their inactivation was performed using CRISPR/Cas9 and morpholino antisense oligonucleotide techniques. The inactivation of MSANTD2 gene, which has been associated with neurodevelopmental diseases such as autism spectrum disorder and schizophrenia, produced embryos with delayed development as well as tail and nervous system malformations, specifically with brain ventricles and neuronal pattern defects. Thus, this thesis has highlighted the recurrent and concomitant molecular domestications of Harbinger transposons, which have led to a new gene family in vertebrates. The study of one its member, MSANTD2, contributes to a better understanding of genetic innovations having driven the evolution of the nervous system in vertebrates