Characterization of the complete plastome of Ophrys aveyronensis , a Euro-Mediterranean orchid with an intriguing disjunct geographic distribution

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The m 6 A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants

International audienceGlobal, segmental, and gene duplication-related processes are driving genome size and complexity in plants. Despite their evolutionary potentials, those processes can also have adverse effects on genome regulation, thus implying the existence of specialized corrective mechanisms. Here, we report that an N6-methyladenosine (m 6 A)-assisted polyadenylation (m-ASP) pathway ensures tran-scriptome integrity in Arabidopsis thaliana. Efficient m-ASP pathway activity requires the m 6 A methyltransferase-associated factor FIP37 and CPSF30L, an m 6 A reader corresponding to an YT512-B Homology Domain-containing protein (YTHDC)-type domain containing isoform of the 30-kD subunit of cleavage and polyadenylation specificity factor. Targets of the m-ASP pathway are enriched in recently rearranged gene pairs, displayed an atypical chromatin signature, and showed transcriptional readthrough and mRNA chimera formation in FIP37-and CPSF30L-deficient plants. Furthermore, we showed that the m-ASP pathway can also restrict the formation of chimeric gene/transposable-element transcript, suggesting a possible implication of this pathway in the control of transposable elements at specific locus. Taken together, our results point to selective recognition of 39-UTR m 6 A as a safeguard mechanism ensuring transcriptome integrity at rearranged genomic loci in plants

Whole plastid genome-based phylogenomics supports an inner placement of the O. insectifera group rather than a basal position in the rapidly diversifying Ophrys genus (Orchidaceae)

International audienceWhole plastid genome-based phylogenomics supports an inner placement of the O. insectifera group rather than a basal position in the rapidly diversifying Ophrys genus (Orchidaceae) Some lineages of the Orchid genus Ophrys exhibit among the highest diversification rates reported so far. As a consequence of a such intense and rapid evolution, the systematics and the taxonomy of this genus remains unclear. A hybrid assembly approach based-on long-and short-read genomic data allowed us to outperform classical methods to successfully assemble whole plastid genomes for two new Ophrys species: O. aymoninii and O. lutea. Along with three other previously Ophrys plastid genome sequences, we then reconstructed the first whole plastome-based molecular phylogeny including representatives of the three mains recognized Ophrys lineages. Our results support the placement of the O. insectifera clade as sister group of 'non-basal Ophrys' rather than a basal position. Our findings corroborate recent results obtained from genomic data (RAD-seq and transcriptomes) but contrast with previous ones. These results therefore confirm that molecular phylogenetic hypotheses based on a limited number of loci (e.g. nrITS, matK, rbcL) may have provided a biased picture of phylogenetic relationships within Ophrys and possibly other plant taxa

Detection of active transposable elements in Arabidopsis thaliana using Oxford Nanopore Sequencing technology

International audienceBackground: Transposables elements (TEs) contribute to both structural and functional dynamics of most eukaryotic genomes. Because of their propensity to densely populate plant and animal genomes, the precise estimation of the impact of transposition on genomic diversity has been considered as one of the main challenges of today's genomics. The recent development of NGS (next generation sequencing) technologies has open new perspectives in population genomics by providing new methods for high throughput detection of Transposable Elements-associated Structural Variants (TEASV). However, these have relied on Illumina platform that generates short reads (up to 350 nucleotides). This limitation in size of sequence reads can cause high false discovery rate (FDR) and therefore limit the power of detection of TEASVs, especially in the case of large, complex genomes. The newest sequencing technologies, such as Oxford Nanopore Technologies (ONT) can generate kilobases-long reads thus representing a promising tool for TEASV detection in plant and animals.Results: We present the results of a pilot experiment for TEASV detection on the model plant species Arabidopsisthaliana using ONT sequencing and show that it can be used efficiently to detect TE movements. We generated a~0.8X genome coverage of a met1-derived epigenetic recombinant inbred line (epiRIL) using a MinIon device withR7 chemistry. We were able to detect nine new copies of the LTR-retrotransposon Evadé (EVD). We also evidencedthe activity of the DNA transposon CACTA, CAC1.Conclusions: Even at a low sequence coverage (0.8X), ONT sequencing allowed us to reliably detect several TEinsertions in Arabidopsis thaliana genome. The long read length allowed a precise and un-ambiguous mapping ofthe structural variations caused by the activity of TEs. This suggests that the trade-off between read length andgenome coverage for TEASV detection may be in favor of the former. Should the technology be further improvedboth in terms of lower error rate and operation costs, it could be efficiently used in diversity studies at populationlevel

Characterization Of Interspecific Gene Flows at The Genome-wide Level in a Natural Ecosystem The Massane Forest Reveals New Insights Into Horizontal Transfer In plants

Abstract Horizontal transfer (HT) refers to the exchange of genetic material between divergent species by mechanisms other than reproduction. In recent years, several studies have demonstrated HTs in eukaryotes, particularly in the context of parasitic relationships and in model species. However, very little is known about HT in natural ecosystems, especially those involving non-parasitic wild species, and the nature of the ecological relationships that promote these HTs. In this work, we conducted a pilot study investigating HTs by sequencing the genomes of 17 wild non-model species from a natural ecosystem, the Massane forest, located in southern France. To this end, we developed a new computational pipeline called INTERCHANGE that is able to characterize HTs at the whole genome level without prior annotation and directly in the raw sequencing reads. Using this pipeline, we identified 12 HT events, half of which occurred between lianas and trees. We found that only LTRs-retrotransposons and predominantly those from the Copia superfamily were transferred between these wild species. This study revealed a possible new route for HTs between non-parasitic plants and provides new insights into the genomic characteristics of horizontally transferred DNA in plant genomes

Genome-wide analysis of horizontal transfer in non-model wild species from a natural ecosystem reveals new insights into genetic exchange in plants

International audienceHorizontal transfer (HT) refers to the exchange of genetic material between divergent species by mechanisms other than reproduction. In recent years, several studies have demonstrated HTs in eukaryotes, particularly in the context of parasitic relationships and in model species. However, very little is known about HT in natural ecosystems, especially those involving non-parasitic wild species, and the nature of the ecological relationships that promote these HTs. In this work, we conducted a pilot study investigating HTs by sequencing the genomes of 17 wild non-model species from a natural ecosystem, the Massane forest, located in southern France. To this end, we developed a new computational pipeline called INTERCHANGE that is able to characterize HTs at the whole genome level without prior annotation and directly in the raw sequencing reads. Using this pipeline, we identified 12 HT events, half of which occurred between lianas and trees. We found that mainly low copy number LTR-retrotransposons from the Copia superfamily were transferred between these wild plant species, especially those of the Ivana and Ale lineages. This study revealed a possible new route for HTs between non-parasitic plants and provides new insights into the genomic characteristics of horizontally transferred DNA in plant genomes

Characterization of the complete plastome of Delphinium montanum, a polyploid, endemic and endangered Pyrenean Larkspur

Delphinium montanum DC. 1815, is an endangered larkspur endemic to the Eastern Pyrenees. For biogeographic and conservation purpose, a hybrid assembly approach based on long- and short-read genomic data allowed us to successfully assemble whole plastid genome of Delphinium montanum. The complete plastome is 154,185 bp in length, consisting of a pair of inverted repeats (IRs) of 26,559 bp, a large single-copy (LSC) region and a small single-copy region (SSC) of 84,746 and 16,320 bp, respectively. It was found to contain 136 genes, including 84 protein-coding genes, 44 trRNA genes and 8 rRNA genes. The overall GC content of the plastid genome is 38.3%. Phylogenetic inference supports the polyphyly of the Delphinium genus

Retrotranspositional landscape of Asian rice revealed by 3000 genomes

International audienceThe recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACK-POSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events

Additional file 2 of Detection of active transposable elements in Arabidopsis thaliana using Oxford Nanopore Sequencing technology

S3 text file. Genomic sequences of 10 unique loci used to estimate the genome coverage of sequence data. Sequences are given in fasta format. (TXT 40 kb