Simulation based estimation of branching models for LTR retrotransposons

Motivation: LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows to take into account both positions and degradations of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. Results: Various functions have been implemented in order to simulate their spread and visualization tools are proposed. Based on these simulation tools, we show that an accurate estimation of the parameters of this propagation model can be performed. We applied this method to the study of the spread of the transposable elements ROO, GYPSY, and DM412 on a chromosome of \textit{Drosophila melanogaster}. Availability: Our proposal has been implemented using Python software. Source code is freely available on the web at https://github.com/SergeMOULIN/retrotransposons-spread.Comment: 7 pages, 3 figures, 7 tables. Submit to "Bioiformatics" on March 1, 201

Evolutionary histories of legume genomes and mechanisms of genome remodeling

Evolutionary genomics analysis of plants aims to reveal and help us to understand the history of genome evolution that plants have undergone. So far, many specific topics and questions of genome evolution have been studied and answered. However, there are still a large number of questions to which the answers are unknown or not clear. In this dissertation, I focus on two specific topics of evolutionary genomics: (1) genome size evolution following genomic rearrangements in plants; (2) ancestral genome reconstruction in legumes. Using a model of two wild peanut relatives in which one genome experienced large rearrangements, we find that the main determinant in genome size reduction is a set of inversions which experienced subsequent net sequence removal in the inverted regions. We observe a general pattern in which sequence is lost more rapidly at newly distal (telomeric) regions than it is gained at newly proximal (pericentromeric) regions – resulting in net sequence loss in the inverted regions. The major driver of this process is recombination, determined by the chromosomal location. Any type of genomic rearrangement that exposes proximal regions to higher recombination rates can cause genome size reduction by this mechanism. Sequence loss in those regions was primarily due to removal of transposable elements. Illegitimate recombination is likely the major mechanism responsible for the sequence removal, rather than unequal intrastrand recombination. We also measure the relative rate of genome size reduction in these two Arachis diploids. We also test our model in other plant species and find that it applies in all cases examined, suggesting our model is widely applicable. Inversions occurring in tetraploid cultivated peanut after the polyploidization event provide us an excellent opportunity to examine the model of genome size reduction following genomic rearrangements in polyploidy. It is also a good opportunity to understand the genome size reduction process at its early stage, since the inversions are quite recent (likely younger than 10,000 years). We observe that the model of genome size reduction still holds in the recently-derived tetraploid peanut as it does in the much earlier-diverging diploid progenitors. We find that the genome size reduction process starts with differences in very long sequence deletions and then spreads to mid-length sequence deletions later. We measure the relative rate of size reduction of the inverted region in tetraploid peanut, finding that it is higher than the rates calculated in our previous study between Arachis diploids. We argue this is because the rate of size reduction is more rapid in the early generations after the inversion. We describe the reconstruction of a hypothetical ancestral genome for the papilionoid legumes, in order to help us better understand the evolutionary histories of these legumes. We use a novel method for identifying informative markers, to reconstruct the ancestral genomes for selected legume species, including Glycine max, which has a recent exclusive WGD event. We infer that the reconstructed most recent common ancestor of all selected legume species (all within the Papilionoideae) has 9 chromosomes. The model then predicts that chromosome numbers reduced to 8 in Medicago truncatula and Cicer arietinum separately, through two separate single fusion events. In Lotus japonicus, a series of rearrangement events is the major cause of the chromosome number reduction to 6. We infer that the chromosome number increased mostly independently in Cajanus cajan, Glycine max, Phaseolus vulgaris and Vigna radiata. In Arachis (A. duranensis and A. ipaensis), there was an increase in chromosome number prior to their divergence. The chromosome structural evolution described here is consistent with the phylogenetic distribution of a large collection of chromosome counts in the legumes

Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution

Background Transposable elements (TEs) can represent one of the major sources of genomic variation across eukaryotes, providing novel raw materials for species diversification and innovation. While considerable effort has been made to study their evolutionary dynamics across multiple animal clades, molluscs represent a substantially understudied phylum. Here, we take advantage of the recent increase in mollusc genomic resources and adopt an automated TE annotation pipeline combined with a phylogenetic tree-based classification, as well as extensive manual curation efforts, to characterize TE repertories across 27 bivalve genomes with a particular emphasis on DDE/D class II elements, long interspersed nuclear elements (LINEs), and their evolutionary dynamics.Results We found class I elements as highly dominant in bivalve genomes, with LINE elements, despite less represented in terms of copy number per genome, being the most common retroposon group covering up to 10% of their genome. We mined 86,488 reverse transcriptases (RVT) containing LINE coming from 12 clades distributed across all known superfamilies and 14,275 class II DDE/D-containing transposons coming from 16 distinct superfamilies. We uncovered a previously underestimated rich and diverse bivalve ancestral transposon complement that could be traced back to their most recent common ancestor that lived similar to 500 Mya. Moreover, we identified multiple instances of lineage-specific emergence and loss of different LINEs and DDE/D lineages with the interesting cases of CR1- Zenon, Proto2, RTE-X, and Academ elements that underwent a bivalve-specific amplification likely associated with their diversification. Finally, we found that this LINE diversity is maintained in extant species by an equally diverse set of long-living and potentially active elements, as suggested by their evolutionary history and transcription profiles in both male and female gonads.Conclusions We found that bivalves host an exceptional diversity of transposons compared to other molluscs. Their LINE complement could mainly follow a "stealth drivers" model of evolution where multiple and diversified families are able to survive and co-exist for a long period of time in the host genome, potentially shaping both recent and early phases of bivalve genome evolution and diversification. Overall, we provide not only the first comparative study of TE evolutionary dynamics in a large but understudied phylum such as Mollusca, but also a reference library for ORF-containing class II DDE/D and LINE elements, which represents an important genomic resource for their identification and characterization in novel genomes

A Chromosome-Scale Assembly of the Garden Orach (Atriplex hortensis L.) Genome Using Oxford Nanopore Sequencing

Atriplex hortensis (2n = 2x = 18, 1C genome size 1.1 gigabases), also known as garden orach and mountain-spinach, is a highly nutritious, broadleaf annual of the Amaranthaceae-Chenopodiaceae alliance (Chenopodiaceae sensu stricto, subfam. Chenopodioideae) that has spread in cultivation from its native primary domestication area in Eurasia to other temperate and subtropical regions worldwide. Atriplex L. is a highly complex but, as understood now, a monophyletic group of mainly halophytic and/or xerophytic plants, of which A. hortensis has been a vegetable of minor importance in some areas of Eurasia (from Central Asia to the Mediterranean) at least since antiquity. Nonetheless, it is a crop with tremendous nutritional potential due primarily to its exceptional leaf and seed protein quantities (approaching 30%) and quality (high levels of lysine). Although there is some literature describing the taxonomy and production of A. hortensis, there is a general lack of genetic and genomic data that would otherwise help elucidate the genetic variation, phylogenetic positioning, and future potential of the species. Here, we report the assembly of the first high-quality, chromosome-scale reference genome for A. hortensis cv. “Golden.” Long-read data from Oxford Nanopore’s MinION DNA sequencer was assembled with the program Canu and polished with Illumina short reads. Contigs were scaffolded to chromosome scale using chromatin-proximity maps (Hi-C) yielding a final assembly containing 1,325 scaffolds with a N50 of 98.9 Mb – with 94.7% of the assembly represented in the nine largest, chromosome-scale scaffolds. Sixty-six percent of the genome was classified as highly repetitive DNA, with the most common repetitive elements being Gypsy- (32%) and Copia-like (11%) long-terminal repeats. The annotation was completed using MAKER which identified 37,083 gene models and 2,555 tRNA genes. Completeness of the genome, assessed using the Benchmarking Universal Single Copy Orthologs (BUSCO) metric, identified 97.5% of the conserved orthologs as complete, with only 2.2% being duplicated, reflecting the diploid nature of A. hortensis. A resequencing panel of 21 wild, unimproved and cultivated A. hortensis accessions revealed three distinct populations with little variation within subpopulations. These resources provide vital information to better understand A. hortensis and facilitate future study

Fishing for Junk: investigating the genomic and evolutionary roles of transposable element expansion within neotropical catfish

Transposable elements (TEs) are short DNA sequences that possess the ability to replicate throughout a genome. They are found ubiquitously across the tree of life and can reach high genomic abundance. Understanding the evolutionary and genomic consequences of TE action is thus of great importance and is aided by a growing ability to annotate TEs within non-model organisms. Teleost genomes have the greatest diversity of TEs of any vertebrate and are therefore ideal study systems to better understand TE biology. This work presents the first detailed foray into the TE biology of the Corydoradinae, a species rich clade of Neotropical catfish with an evolutionary history characterised by rapid colour pattern change, polyploidy and TE proliferation. In-silico modelling was utilised to demonstrate that TE proliferations may be driven by both beneficial insertion effects and whole genome duplications. The latest ‘de-novo’ TE pipelines were utilised to create a Corydoradinae-specific TE library, with this process increasing estimated TE abundance, altering TE composition, and reducing approximate age of insertions. A significant phylogenetic shift in expressed TE content within the Corydoradinae is also found, though this is somewhat dependent on choice of TE library during annotation. Furthermore, TE insertions appear to accumulate in genic regions at a greater rate within polyploid versus non-polyploid species. For example, a Mariner TE with an amphibian origin has horizontally transferred and inserted within the bone developmental gene ‘mmp13’ of multiple polyploid Corydoradinae species, with potential impacts regarding facial shape diversification. Finally, despite many incidences of TE activity inducing changes to colour pattern phenotypes in other organisms, Corydoradinae pigmentation genes were not found to be enriched in TE insertions and evolve under stricter purifying selection pressure than other genes. In summary, this work furthers our understanding of the causes and consequences of TE activity within a non-model system

Sex and Repetitive Sequence Dynamics in Bacillus Stick Insects (Phasmida, Bacillidae)

Eukaryotic genomes are characterized by the wide occurrence of repetitive sequences; these play an important role in genome structure and variability and the reproductive biology of the host organism seems to affect their dynamics. The relationship between sex and the non-LTR retrotransposable element R2 is here studied in Bacillus stick insects. In this genus, in addition to gonochorism, reproduction is achieved through several non-canonical mechanisms. The analyses were performed in populations of the strictly gonochoric B. grandii, the facultative parthenogenetic B. rossius and the obligate parthenogenetic B. atticus, as well as in the offspring of either facultative (B. rossius) and obligate (B. atticus) parthenogenetic isolates or of crosses between gonochoric individuals of facultative parthenogenetic populations of B. rossius. Data here produced showed that R2 is present and active in all Bacillus species, irrespective of the reproductive strategy, counteracting Muller’s ratchet expectations. Moreover, the lowest values of R2 accumulation detected in the obligate unisexual B. atticus suggest that also mechanisms limiting R2 load are active. The higher R2 accumulations found in facultative parthenogenetics, with respect to the values scored in obligate ones, could be due to the different mechanism of parthenogenesis. Furthermore, models of parental-offspring inheritance evidenced that also recombination and selection appear to control R2 proliferation. These results highlighted the presence of unisexuals bearing transposable element (TE) insertions. Their survival may be allowed from mechanisms able to keep the TE load low which, in addition to the recombination and selection, could be represented from silencing mechanisms and selection of less virulent TEs. Muller’s ratchet predictions were counteracted also in the analysis conducted to determine the abundance of repetitive sequences in the genomes of B. grandii, B. rossius and B. atticus. In fact, in the latter TEs content was comparable to the one found in the other species

Transposable elements in arthropods genomes with non-canonical reproductive strategies.

Gli elementi trasponibili (TEs) sono componenti universali dei genomi di tutti gli esseri viventi. L'attività ed il movimento degli TEs hanno importanti effetti sul genoma ospite e per questo sono considerati dei fattori importanti nell'evoluzione del genoma. Le relazioni che intercorrono tra TEs e il loro genoma ospite sono ancora ampiamente dibattute. Hickey già nel 1982 suggerì che queste relazioni potevano essere influenzate dalla modalità di riproduzione del genoma ospite. Organismi bisessuali, attraverso i meccanismi propri della meiosi, riuscirebbero a contrastare la proliferazione degli TEs, al contrario negli organismi unisessuali, proprio a causa della mancanza di questi meccanismi, gli TEs tendono a proliferare ed accumulare all'interno del genoma. Al fine di valutare queste ipotesi, ho isolato e caratterizzato gli TEs in organismi con strategie riproduttive non canoniche. Ho condotto le mie analisi in due organismi: gli insetti stecco del genere Bacillus e nel fossile vivente Triops cancriformis. Entrambi presentano strategie riproduttive che vanno dal gonocorismo alla partenogenesi, rendendoli un eccellente modello per lo studio e la caratterizzazione degli TEs. Nel genere Bacillus mi sono focalizzata sullo studio del retrotransposone non-LTR R2. Ho isolato e caratterizzato sette elementi R2 completi; sia in specie gonocoriche che partenogenetiche. Ho trovato un elemento R2 degenerato presente nel genoma di B. rossius da almeno 5 milioni di anni. In oltre, le mie analisi suggeriscono per la prima volta che anche gli elementi R2 possono trasferirsi attraverso eventi di trasferimento orizzontale. I miei dati mostrano una panoramica della composizione di TEs nel genoma di una popolazione partenogenetica di Triops cancriformis. Dalle mie analisi si evince che il 20% della library di triops è composta da TEs.Transposable elements (TEs) are universal components of all living organisms. TEs activity and movement have profound effects on host genome and today many researchers agree to consider them as important actors in genome evolution. The relationships between TEs and their host genomes are still under debate. Different hypotheses were proposed to explain TEs dynamics in host genome; one of these propose that host reproductive strategies can influence TEs evolutionary dynamics (Hickey, 1982). In fact, bisexual organisms, through homologous chromosomes recombination and reassortment during meiosis and amphimixis, can control the spread and proliferation of mobile elements, while unisexual organisms would experience an increase of these elements density due to the inability to eliminate them through exclusive mechanisms of sexual reproduction. In order to evaluate these hypothesis, I isolated and characterized TEs in organisms with non-canonical reproductive strategies. I performed my analyses in two organisms: the stick insects of the Bacillus genus and in the tadpole shrimps T. cancriformis. In both instances reproductive strategies range from bisexual gonochoric reproduction, to unisexual parthenogenesis, making them an excellent model for the study and characterization of TEs. In the Bacillus genus I focused on the R2 non-LTR retrotranposon. I isolated and sequenced by primer walking seven R2 complete elements; both gonochoric and parthenogenetic Bacillus species. I found a R2 degenerate element present in the B. rossius genome since 5 Myr ago. In addition, my analyses for the first time suggest that also R2 retrotransposons can use horizontal transfer as a strategy to colonize a new genome. My data showed a TEs overview in a T. cancriformis parthenogenetic population. In contrast with the theoretical, my analyses highlighted that the 20% of the library is composed by TEs, in which both TEs classes are widely represented (class I, 11.4% and class II, 8.9%)

Independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae)

Phytochemical diversity is thought to result from coevolutionary cycles as specialization in herbivores imposes diversifying selection on plant chemical defenses. Plants in the speciose genus Erysimum (Brassicaceae) produce both ancestral glucosinolates and evolutionarily novel cardenolides as defenses. Here we test macroevolutionary hypotheses on co-expression, co-regulation, and diversification of these potentially redundant defenses across this genus. We sequenced and assembled the genome of E. cheiranthoides and foliar transcriptomes of 47 additional Erysimum species to construct a phylogeny from 9868 orthologous genes, revealing several geographic clades but also high levels of gene discordance. Concentrations, inducibility, and diversity of the two defenses varied independently among species, with no evidence for trade-offs. Closely related, geographically co-occurring species shared similar cardenolide traits, but not glucosinolate traits, likely as a result of specific selective pressures acting on each defense. Ancestral and novel chemical defenses in Erysimum thus appear to provide complementary rather than redundant functions.Austrian Science Fund (FWF) PZ00P3-161472National Science Foundation (NSF) 1811965 1645256Triad FoundationGerman Research Foundation (DFG) DFG-PE 2059/3-1Agencia Estatal de Investigacion CGL2017-86626-C2-2-PLOEWE Program Insect Biotechnology and BioresourcesJunta de Andalucía A-RNM505-UGR1