Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats

Independent evolution of satellite DNA sequences in homologous sex chromosomes of Neotropical armored catfish (Harttia)

The Neotropical armored catfish Harttia is a valuable model for studying sex chromosome evolution, featuring two independently evolved male-heterogametic systems. This study examined satellitomes-sets of satellite DNAs-from four Amazonian species: H. duriventris (X1X2Y), H. rondoni (XY), H. punctata (X1X2Y), and H. villasboas (X1X2Y). These species share homologous sex chromosomes, with their satellitomes showing a high number of homologous satellite DNAs (satDNAs), primarily located on centromeres or telomeres, and varying by species. Each species revealed a distinct satDNA profile, with independent amplification and homogenization events occurring, suggesting an important role of these repetitive sequences in sex chromosome differentiation in a short evolutionary time, especially in recently originated sex chromosomes. Whole chromosome painting and bioinformatics revealed that in Harttia species without heteromorphic sex chromosomes, a specific satDNA (HviSat08-4011) is amplified in the same linkage group associated with sex chromosomes, suggesting an ancestral system. Such sequence (HviSat08-4011) has partial homology with the ZP4 gene responsible for the formation of the egg envelope, in which its role is discussed. This study indicates that these homologous sex chromosomes have diverged rapidly, recently, and independently in their satDNA content, with transposable elements playing a minor role when compared their roles on autosomal chromosome evolution.

Transcriptional dynamics and tissue-specific expression patterns of transposable elements in orthopteran insects

Transposable elements (TEs) are prevalent in the genomes of orthopteran insects, contributing significantly to their genome evolution and diversity. In light of the existing gap in our understanding of TEs transcript dynamics in orthopteran insects, we recognize the critical need to undertake comprehensive analyses in this area. Therefore, we have decided to delve into the characterization of TE transcripts, their abundance profiles, and the formation of chimeric transcripts using RNA-seq data and genome assemblies. The transcript analysis of TEs across various species revealed significant differences in TE abundance and expression patterns. In particular, Schistocerca americana exhibited twice the number of transcripts within the genus Schistocerca compared to the average of other species, while Gryllus bimaculatus displayed the lowest number of transcripts. Despite this, all Schistocerca species shared similar fractions of TE transcripts at the clade level, with DNA transposons (45%) being the most abundant, followed by LINE (19%) and LTR elements (18%). Interestingly, Acrida cinerea displayed different TE abundance patterns compared to Schistocerca species, particularly with an increased proportion of LTR transcripts, accounting for 31% of the total transcripts. Further analysis revealed tissue-specific transcriptional activity of TE clades, with notable differences between male and female specimens. In Gryllus bimaculatus, TEs were highly transcribed across ovaries and gut tissues in females compared to male testes and gut. Conversely, Gastrimargus marmoratus displayed higher TE transcription in male tissues compared to females, indicating species-specific expression patterns. A similar pattern has been observed in Acrida cinerea, except in female gonads, where 4618 TEs were transcribed compared to 3757 in male gonads. Despite these variations, no correlation was found between genome size and TE transcript abundance. Additionally, highly conserved TEs were involved in the formation of chimeric transcripts, indicating potential regulatory roles in gene expression. The expression quantification analysis of chimeric TEs and genes revealed tissue-specific expression patterns, and TEs do not control the overall expression of all genes except some, suggesting regulatory roles of TEs in gene expression. Overall, our study underscores tissue-specific variations in TE expression and transcript abundance among different species. Additionally, our findings suggest the involvement of highly conserved TEs in the formation of chimeric transcripts across different species.

Repetitive DNAs: the 'invisible' regulators of insect adaptation and speciation

Like other eukaryotes, insect genomes contain a large portion of repetitive sequences, particularly transposable elements and satellite DNAs. This review highlights key studies on repetitive DNAs and examines their structural, functional, and evolutionary impact on insect genomes. Repetitive sequences promote genetic diversification through mutations and large-scale rearrangements, playing a crucial role in shaping genomic architecture, aiding organismal adaptation, and driving speciation. We also explore the influence of repeats in genome size variation and species incompatibilities, along with their contribution to adaptive phenotypes and gene regulation. Studying repetitive DNA in insects not only provides insights into basic genomic features but also offers valuable information for conservation strategies, pest control, and advancements in genetics, ecology, and evolutionary biology.

Evolutionary dynamics of repetitive elements and their relationship with genome size in Acrididae

It is widely accepted that repetitive elements (REs) represent the primary mechanism driving genome size variation across eukaryotes. The observed genome sizes and REs of 59 species within the Acrididae were obtained and characterized. The genome sizes observed ranged from 6.60 pg to 19.35 pg, while the proportion of REs varied from 57.92 % to 83.58 %. The primary contributors were identified as LTR (2.34 % ∼ 20.98 %) and LINEs (6.70 % ∼ 16.33 %). The results of ancestral reconstruction indicated that the proportion of REs in ancestral nodes was 69.53 %, which suggests that they have undergone extensive genome expansion or contraction. A significant positive correlation was identified between the proportion of REs and genome size. Transposable elements were found to account for approximately 41 % of the observed variation in genome size. Moreover, the LTR was identified as the most significant RE type in relation to genome size expansion within the Acrididae.

The evolutionary dynamics of genome sizes and repetitive elements in Ensifera (Insecta: Orthoptera)

BACKGROUND

In evolutionary biology, identifying and quantifying inter-lineage genome size variation and elucidating the underlying causes of that variation have long been goals. Repetitive elements (REs) have been proposed and confirmed as being among the most important contributors to genome size variation. However, the evolutionary implications of genome size variation and RE dynamics are not well understood.

RESULTS

A total of 35 Ensifera insects were collected from different areas in China, including nine species of crickets and 26 species of katydids. The genome sizes of seven species were then determined using flow cytometry. The RepeatExplorer2 pipeline was employed to retrieve the repeated sequences for each species, based on low-coverage (0.1 X) high-throughput Illumina unassembled short reads. The genome sizes of the 35 Ensifera insects exhibited a considerable degree of variation, ranging from 1.00 to 18.34 pg. This variation was more than 18-fold. Similarly, the RE abundances exhibited considerable variation, ranging from 13.66 to 61.16%. In addition, the Tettigonioidea had larger genomes and contained significantly more REs than did the Grylloidea genomes. Analysis of the correlation between RE abundance and the genome size of 35 Ensifera insects revealed that the abundance of REs, transposable elements (TEs), long terminal repeats (LTRs), and long interspersed nuclear elements (LINEs) are significantly correlated with genome size. Notably, there is an inflection point in this correlation, where species with increasingly large genomes (e.g., > 5-10 pg) have repeats that contribute less to genome expansion than expected. Furthermore, this study revealed contrasting evolutionary directions between the Tettigonioidea and Grylloidea clades in terms of the expansion of REs. Tettigonioidea species exhibit a gradual increase in ancestral genome size and RE abundance as they diverge, while Grylloidea species experience sustained genome contraction.

CONCLUSIONS

This study reveals extensive variation in genome size and RE abundance in Ensifera insects, with distinct evolutionary patterns across two major groups, Tettigonioidea and Grylloidea. This provides valuable insights into the variation in genome size and RE abundance in Ensifera insects, offering a comprehensive understanding of their evolutionary history.

Chromosome-level genome assembly of the morabine grasshopper Vandiemenella viatica19

Morabine grasshoppers in the Vandiemenella viatica species group, which show karyotype diversity, have been studied for their ecological distribution and speciation in relation to their genetic and chromosomal diversity. They are good models for studying sex chromosome evolution as "old" and newly emerged sex chromosomes co-exist within the group. Here we present a reference genome for the viatica19 chromosomal race, that possesses the ancestral karyotype within the group. Using PacBio HiFi and Hi-C sequencing, we generated a chromosome-level assembly of 4.09 Gb in span, scaffold N50 of 429 Mb, and complete BUSCO score of 98.1%, containing 10 pseudo-chromosomes. We provide Illumina datasets of males and females, used to identify the X chromosome. The assembly contains 19,034 predicted protein-coding genes, and a total of 75.21% of repetitive DNA sequences. By leveraging HiFi reads, we mapped the genome-wide distribution of methylated bases (5mC and 6 mA). This comprehensive assembly offers a robust reference for morabine grasshoppers and supports further research into speciation and sex chromosome diversification within the group and its related species.

No single rescue recipe: genome complexities modulate insect response to climate change

Declines in insect populations have gained formidable attention. Given their crucial role in the ecosystem, the causes of declining insect populations must be investigated. However, the insect clade has been associated with low extinction and high diversification rates. It is unlikely that insects underwent mass extinctions in the past. However, the pace of current climate change could make insect populations vulnerable to extinction. We propose genome size (GS) and transposable elements (TEs) to be rough estimates to assess extinction risk. Larger GS and/or proliferating TEs have been associated with adaptation in rapid climate change scenarios. We speculate that unstable, stressful environmental conditions are strongly associated with GS and TE expansion, which could be further correlated with adaptations. Alternately, stressful conditions trigger TE bursts that are not purged in smaller populations. GS and TE loads could be indicators of small effective populations in the wild, likely experiencing bottlenecks or drastic climatic perturbations, which calls for an urgent assessment of extinction risk.

Evolutionary Dynamics of Satellite DNA Repeats across the Tettigoniidae Family: Insights from Genomic Analysis

Satellite DNA repeats are repetitive DNA sequences found in eukaryotic genomes, typically consisting of short DNA motifs repeated in tandem arrays. Despite the vast body of literature on satellite DNA repeats in other taxa, investigations specifically targeting Tettigoniidae remain conspicuously absent. Our study aims to fill a critical gap in our understanding of satellitome evolutionary processes shaping Tettigoniidae genomes. Repeatome analysis revealed that the Meconema thalassinum genome comprises 92%, and Phryganogryllacris superangulata had the lowest value of 34%, with an average of 67% in other Tettigoniidae species. The analysis reveals significant variation in the number of satellite DNA repeats across species of the Tettigoniidae family, with M. thalassinum exhibiting the highest count, 246, reported in insects to date and the lowest count, 10, in Pholidoptera griseoptera. Ruspolia dubia and Ruspolia yunnana, which are congeneric species, showcase distinct counts of 104 and 84 families, respectively. Satellite DNA repeats in R. dubia exhibit the highest abundance, constituting 17.2% of the total genome, while the lowest abundance was reported in P. griseoptera, at 5.65%. The genome size correlates weakly with the satellite DNA family count (rs = 0.42, p = 0.29), but a strong correlation exists between satellite abundance and family number (rs = 0.73, p = 0.03). Moreover, the analysis of satellite DNA gain and loss patterns provides insights into the amplification and homogenization of satellite DNA families within the genome, with species-specific repeats exhibiting a positive trend toward amplification. The chromosomal distribution in M. thalassinum displayed that the highest accumulation was observed on Chr12, Chr01, and Chr04, constituting 17.79%, 17.4%, and 17.22% of the total chromosome size, respectively. The chromosome-specific propagation of satellite DNA families was evident, with MthSat01 solely on chromosome 1 and MthSat170 on chromosome 2, sharing 1.64% and 2.33%. The observed conservation and variations in satellite DNA number and abundances, along with distinct patterns of gain and loss, indicate the influence of potentially diverse evolutionary processes shaping the genomic landscape of these insects, which requires further investigation. Furthermore, the differential accumulation of satellite DNA on specific chromosomes implies that potential chromosome-specific functions or structural features influence the retention and proliferation of satellite sequences.

Comprehensive analysis of the Xya riparia genome uncovers the dominance of DNA transposons, LTR/Gypsy elements, and their evolutionary dynamics

Transposable elements (TEs) are DNA sequences that can move or replicate within a genome, and their study has become increasingly important in understanding genome evolution and function. The Tridactylidae family, including Xya riparia (pygmy mole cricket), harbors a variety of transposable elements (TEs) that have been insufficiently investigated. Further research is required to fully understand their diversity and evolutionary characteristics. Hence, we conducted a comprehensive repeatome analysis of X. riparia species using the chromosome-level assembled genome. The study aimed to comprehensively analyze the abundance, distribution, and age of transposable elements (TEs) in the genome. The results indicated that the genome was 1.67 Gb, with 731.63 Mb of repetitive sequences, comprising 27% of Class II (443.25 Mb), 16% of Class I (268.45 Mb), and 1% of unknown TEs (19.92 Mb). The study found that DNA transposons dominate the genome, accounting for approximately 60% of the total repeat size, with retrotransposons and unknown elements accounting for 37% and 3% of the genome, respectively. The members of the Gypsy superfamily were the most abundant amongst retrotransposons, accounting for 63% of them. The transposable superfamilies (LTR/Gypsy, DNA/nMITE, DNA/hAT, and DNA/Helitron) collectively constituted almost 70% of the total repeat size of all six chromosomes. The study further unveiled a significant linear correlation (Pearson correlation: r = 0.99, p-value = 0.00003) between the size of the chromosomes and the repetitive sequences. The average age of DNA transposon and retrotransposon insertions ranges from 25 My (million years) to 5 My. The satellitome analysis discovered 13 satellite DNA families that comprise about 0.15% of the entire genome. In addition, the transcriptional analysis of TEs found that DNA transposons were more transcriptionally active than retrotransposons. Overall, the study suggests that the genome of X. riparia is complex, characterized by a substantial portion of repetitive elements. These findings not only enhance our understanding of TE evolution within the Tridactylidae family but also provide a foundation for future investigations into the genomic intricacies of related species.

Chromosomal Radiation: A model to explain karyotypic diversity in cryptic species

We present a concept that explains the pattern of occurrence of widely distributed organisms with large chromosomal diversity, large or small molecular divergence, and the insufficiency or absence of morphological identity. Our model is based on cytogenetic studies associated with molecular and biological data and can be applied to any lineage of sister species, chronospecies, or cryptic species. Through the evaluation of the karyotypic macrostructure, as the physical location of genes e satellites DNAs, in addition to phylogenetic reconstructions from mitochondrial and nuclear genes, per example, we have observed morphologically indistinguishable individuals presenting different locally fixed karyomorphs with phylogeographic discontinuity. The biological process behind this pattern is seen in many groups of cryptic species, in which variation lies mainly in the organization of their genomes but not necessarily in the ecosystems they inhabit or in their external morphology. It's similar to the processes behind other events observed in the distribution of lineages. In this work, we explore the hypothesis of a process analogous to ecological-evolutionary radiation, which we called Chromosomal Radiation. Chromosomal Radiation can be adaptive or non-adaptive and applied to different groups of organisms.

Abundance and Diversification of Repetitive Elements in Decapoda Genomes

Repetitive elements are a major component of DNA sequences due to their ability to propagate through the genome. Characterization of Metazoan repetitive profiles is improving; however, current pipelines fail to identify a significant proportion of divergent repeats in non-model organisms. The Decapoda order, for which repeat content analyses are largely lacking, is characterized by extremely variable genome sizes that suggest an important presence of repetitive elements. Here, we developed a new standardized pipeline to annotate repetitive elements in non-model organisms, which we applied to twenty Decapoda and six other Crustacea genomes. Using this new tool, we identified 10% more repetitive elements than standard pipelines. Repetitive elements were more abundant in Decapoda species than in other Crustacea, with a very large number of highly repeated satellite DNA families. Moreover, we demonstrated a high correlation between assembly size and transposable elements and different repeat dynamics between Dendrobranchiata and Reptantia. The patterns of repetitive elements largely reflect the phylogenetic relationships of Decapoda and the distinct evolutionary trajectories within Crustacea. In summary, our results highlight the impact of repetitive elements on genome evolution in Decapoda and the value of our novel annotation pipeline, which will provide a baseline for future comparative analyses.

Satellite DNAs-From Localized to Highly Dispersed Genome Components

According to the established classical view, satellite DNAs are defined as abundant non-coding DNA sequences repeated in tandem that build long arrays located in heterochromatin. Advances in sequencing methodologies and development of specialized bioinformatics tools enabled defining a collection of all repetitive DNAs and satellite DNAs in a genome, the repeatome and the satellitome, respectively, as well as their reliable annotation on sequenced genomes. Supported by various non-model species included in recent studies, the patterns of satellite DNAs and satellitomes as a whole showed much more diversity and complexity than initially thought. Differences are not only in number and abundance of satellite DNAs but also in their distribution across the genome, array length, interspersion patterns, association with transposable elements, localization in heterochromatin and/or in euchromatin. In this review, we compare characteristic organizational features of satellite DNAs and satellitomes across different animal and plant species in order to summarize organizational forms and evolutionary processes that may lead to satellitomes' diversity and revisit some basic notions regarding repetitive DNA landscapes in genomes.

New estimates of genome size in Orthoptera and their evolutionary implications

Animal genomes vary widely in size, and much of their architecture and content remains poorly understood. Even among related groups, such as orders of insects, genomes may vary in size by orders of magnitude-for reasons unknown. The largest known insect genomes were repeatedly found in Orthoptera, e.g., Podisma pedestris (1C = 16.93 pg), Stethophyma grossum (1C = 18.48 pg) and Bryodemella holdereri (1C = 18.64 pg). While all these species belong to the suborder of Caelifera, the ensiferan Deracantha onos (1C = 19.60 pg) was recently found to have the largest genome. Here, we present new genome size estimates of 50 further species of Ensifera (superfamilies Gryllidea, Tettigoniidea) and Caelifera (Acrididae, Tetrigidae) based on flow cytometric measurements. We found that Bryodemella tuberculata (Caelifera: Acrididae) has the so far largest measured genome of all insects with 1C = 21.96 pg (21.48 gBp). Species of Orthoptera with 2n = 16 and 2n = 22 chromosomes have significantly larger genomes than species with other chromosome counts. Gryllidea genomes vary between 1C = 0.95 and 2.88 pg, and Tetrigidae between 1C = 2.18 and 2.41, while the genomes of all other studied Orthoptera range in size from 1C = 1.37 to 21.96 pg. Reconstructing ancestral genome sizes based on a phylogenetic tree of mitochondrial genomic data, we found genome size values of >15.84 pg only for the nodes of Bryodemella holdereri / B. tuberculata and Chrysochraon dispar / Euthystira brachyptera. The predicted values of ancestral genome sizes are 6.19 pg for Orthoptera, 5.37 pg for Ensifera, and 7.28 pg for Caelifera. The reasons for the large genomes in Orthoptera remain largely unknown, but a duplication or polyploidization seems unlikely as chromosome numbers do not differ much. Sequence-based genomic studies may shed light on the underlying evolutionary mechanisms.

Combined CRISPR toolkits reveal the domestication landscape and function of the ultra-long and highly repetitive silk genes

Highly repetitive sequences play a major structural and function role in the genome. In the present study, we developed Cas9-assisted cloning and SMRT sequencing of long repetitive sequences (CACS) to sequence and manipulate highly repetitive genes from eukaryotic genomes. CACS combined Cas9-mediated cleavage of a target segment from an intact genome, Gibson assembly cloning, and PacBio SMRT sequencing. Applying CACS, we directly cloned and sequenced the complete sequences of fibroin heavy chain (FibH) genes from 17 domesticated (Bombyx mori) and 7 wild (Bombyx mandarina) silkworms. Our analysis revealed the unique fine structure organization, genetic variations, and domestication dynamics of FibH. We also demonstrated that the length of the repetitive regions determined the mechanical properties of silk fiber, which was further confirmed by Cas9 editing of FibH. CACS is a simple, robust, and efficient approach, providing affordable accessibility to highly repetitive regions of a genome. STATEMENT OF SIGNIFICANCE: Silkworm silk is the earliest and most widely used animal fiber, and its excellent performance mainly depends on the fibroin heavy chain (FibH) protein. The FibH gene is the main breakthrough in understanding the formation mechanism and improvement of silk fiber. In the study, we developed a CACS method for characterizing the fine structure and domestication landscape of 24 silkworm FibH genes. We used CRISPR/Cas9 to edit the repetitive sequence of FibH genes, revealing the relationship between FibH genes and mechanical properties of silkworm silk. Our study is helpful in modifying silk genes to manipulate other valuable highly repetitive sequences, and provides insight for silkworm breeding.

In Silico Identification and Characterization of Satellite DNAs in 23 Drosophila Species from the Montium Group

Satellite DNA (satDNA) is a class of tandemly repeated non-protein coding DNA sequences which can be found in abundance in eukaryotic genomes. They can be functional, impact the genomic architecture in many ways, and their rapid evolution has consequences for species diversification. We took advantage of the recent availability of sequenced genomes from 23 Drosophila species from the montium group to study their satDNA landscape. For this purpose, we used publicly available whole-genome sequencing Illumina reads and the TAREAN (tandem repeat analyzer) pipeline. We provide the characterization of 101 non-homologous satDNA families in this group, 93 of which are described here for the first time. Their repeat units vary in size from 4 bp to 1897 bp, but most satDNAs show repeat units < 100 bp long and, among them, repeats ≤ 10 bp are the most frequent ones. The genomic contribution of the satDNAs ranges from ~1.4% to 21.6%. There is no significant correlation between satDNA content and genome sizes in the 23 species. We also found that at least one satDNA originated from an expansion of the central tandem repeats (CTRs) present inside a Helitron transposon. Finally, some satDNAs may be useful as taxonomic markers for the identification of species or subgroups within the group.

Transposable element expansion and low-level piRNA silencing in grasshoppers may cause genome gigantism

Background

Transposable elements (TEs) have been likened to parasites in the genome that reproduce and move ceaselessly in the host, continuously enlarging the host genome. However, the Piwi-interacting RNA (piRNA) pathway defends animal genomes against the harmful consequences of TE invasion by imposing small-RNA-mediated silencing. Here we compare the TE activity of two grasshopper species with different genome sizes in Acrididae (Locusta migratoria manilensis♀1C = 6.60 pg, Angaracris rhodopa♀1C = 16.36 pg) to ascertain the influence of piRNAs.

Results

We discovered that repetitive sequences accounted for 74.56% of the genome in A. rhodopa, more than 56.83% in L. migratoria, and the large-genome grasshopper contained a higher TEs proportions. The comparative analysis revealed that 41 TEs (copy number > 500) were shared in both species. The two species exhibited distinct “landscapes” of TE divergence. The TEs outbreaks in the small-genome grasshopper occurred at more ancient times, while the large-genome grasshopper maintains active transposition events in the recent past. Evolutionary history studies on TEs suggest that TEs may be subject to different dynamics and resistances in these two species. We found that TE transcript abundance was higher in the large-genome grasshopper and the TE-derived piRNAs abundance was lower than in the small-genome grasshopper. In addition, we found that the piRNA methylase HENMT, which is underexpressed in the large-genome grasshopper, impedes the piRNA silencing to a lower level.

Conclusions

Our study revealed that the abundance of piRNAs is lower in the gigantic genome grasshopper than in the small genome grasshopper. In addition, the key gene HENMT in the piRNA biogenesis pathway (Ping-Pong cycle) in the gigantic genome grasshopper is underexpressed. We hypothesize that low-level piRNA silencing unbalances the original positive correlation between TEs and piRNAs, and triggers TEs to proliferate out of control, which may be one of the reasons for the gigantism of grasshopper genomes.

Transposons and non-coding regions drive the intrafamily differences of genome size in insects

Genome size (GS) can vary considerably between phylogenetically close species, but the landscape of GS changes in insects remain largely unclear. To better understand the specific evolutionary factors that determine GS in insects, we examined flow cytometry-based published GS data from 1,326 insect species, spanning 700 genera, 155 families, and 21 orders. Model fitting showed that GS generally followed an Ornstein-Uhlenbeck adaptive evolutionary model in Insecta overall. Ancestral reconstruction indicated a likely GS of 1,069 Mb, suggesting that most insect clades appeared to undergo massive genome expansions or contractions. Quantification of genomic components in 56 species from nine families in four insect orders revealed that the proliferation of transposable elements contributed to high variation in GS between close species, such as within Coleoptera. This study sheds lights on the pattern of GS variation in insects and provides a better understanding of insect GS evolution.

Satellitome of the Red Palm Weevil, Rhynchophorus ferrugineus (Coleoptera: Curculionidae), the Most Diverse Among Insects

The red palm weevil, Rhynchophorus ferrugineus, is the most harmful species among those pests affecting palm trees. Its impact causes important economic losses around the World. Nevertheless, the genetic information of Rh. ferrugineus is very scarce. Last year, the first genome assembly was published including a rough description of its repeatome. However, no information has been added about one of the main components of repeated DNA, the satellite DNA. Herein, we presented the characterization of the satellitome of this important species that includes 112 satellite DNA families, the largest number in an insect genome. These satellite DNA families made up around 25% of the genome while the most abundant family, RferSat01-169, alone represented 20.4%. Chromosomal location of most abundant satellite DNA families performed by fluorescence in situ hybridization showed that all of them are dispersed in the euchromatin on all chromosomes but some of them are also specifically accumulated either on the pericentromeric heterochromatic regions of all chromosomes or on specific chromosomes. Finally, the transcription of satellitome families was analyzed through Rh. ferrugineus development. It was found that 55 out of 112 satellite DNA families showed transcription, some families seemed to be transcribed across all stages while a few appeared to be stage-specific, indicating a possible role of those satellite DNA sequences in the development of this species.

The Singular Evolution of Olea Genome Structure

The current view of plant genome evolution proposes that genome size has mainly been determined by polyploidisation and amplification/loss of transposons, with a minor role played by other repeated sequences, such as tandem repeats. In cultivated olive (Olea europaea subsp. europaea var. europaea), available data suggest a singular model of genome evolution, in which a massive expansion of tandem-repeated sequences accompanied changes in nuclear architecture. This peculiar scenario highlights the importance of focusing on Olea genus evolution, to shed light on mechanisms that led to its present genomic structure. Next-generation sequencing technologies, bioinformatics and in situ hybridisation were applied to study the genomic structure of five related Olea taxa, which originated at different times from their last common ancestor. On average, repetitive DNA in the Olea taxa ranged from ~59% to ~73% of the total genome, showing remarkable differences in terms of composition. Among repeats, we identified 11 major families of tandem repeats, with different abundances in the analysed taxa, five of which were novel discoveries. Interestingly, overall tandem repeat abundance was inversely correlated to that of retrotransposons. This trend might imply a competition in the proliferation of these repeat classes. Indeed, O. paniculata, the species closest to the Olea common ancestor, showed very few tandem-repeated sequences, while it was rich in long terminal repeat retrotransposons, suggesting that the amplification of tandem repeats occurred after its divergence from the Olea ancestor. Furthermore, some tandem repeats were physically localised in closely related O. europaea subspecies (i.e., cultivated olive and O. europaea subsp. cuspidata), which showed a significant difference in tandem repeats abundance. For 4 tandem repeats families, a similar number of hybridisation signals were observed in both subspecies, apparently indicating that, after their dissemination throughout the olive genome, these tandem repeats families differentially amplified maintaining the same positions in each genome. Overall, our research identified the temporal dynamics shaping genome structure during Olea speciation, which represented a singular model of genome evolution in higher plants.

Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda

Spodoptera frugiperda (fall armyworm) is a member of the superfamily Noctuoidea that accounts for more than a third of all Lepidoptera and includes a considerable number of agricultural and forest pest species. Spodoptera frugiperda is a polyphagous species that is a significant agricultural pest worldwide, emphasizing its economic importance. Spodoptera frugiperda's genome size, assembly, phylogenetic classification, and transcriptome analysis have all been previously described. However, the different studies reported different compositions of repeated DNA sequences that occupied the whole assembled genome, and the Spodoptera frugiperda genome also lacks the comprehensive study of dynamic satellite DNA. We conducted a comparative analysis of repetitive DNA across geographically distant populations of Spodoptera frugiperda, particularly satellite DNA, using publicly accessible raw genome data from eight different geographical regions. Our results showed that most transposable elements (TEs) were commonly shared across all geographically distant samples, except for the Maverick and PIF/Harbinger elements, which have divergent repeat copies. The TEs age analysis revealed that most TEs families consist of young copies 1-15 million years old; however, PIF/Harbinger has some older/degenerated copies of 30-35 million years old. A total of seven satellite DNA families were discovered, accounting for approximately 0.65% of the entire genome of the Spodoptera frugiperda fall armyworm. The repeat profiling analysis of satellite DNA families revealed differential read depth coverage or copy numbers. The satellite DNA families range in size from the lowest 108 bp SfrSat06-108 families to the largest (1824 bp) SfrSat07-1824 family. We did not observe a statistically significant correlation between monomer length and K2P divergence, copy number, or abundance of each satellite family. Our findings suggest that the satellite DNA families identified in Spodoptera frugiperda account for a considerable proportion of the genome's repetitive fraction. The satellite DNA families' repeat profiling revealed a point mutation along the reference sequences. Limited TEs differentiation exists among geographically distant populations of Spodoptera frugiperda.

The transposable element-rich genome of the cereal pest Sitophilus oryzae

BACKGROUND

The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions.

RESULTS

We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis.

CONCLUSIONS

Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

Comparative Analysis of Transposable Elements in Genus Calliptamus Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation

Simple Summary

Calliptamus is a genus of grasshoppers belonging to the family Acrididae. The genus Calliptamus includes approximately 17 recognized species. Calliptamus abbreviatus, Calliptamus italicus, and Calliptamus barbarus are three species that are widely found in northern China. These species are polyphagous, feeding on a variety of wild plants as well as crops, particularly legumes. The genome sizes, phylogenetic position, and transcriptome analysis of the genus Calliptamus were already known previous to this research. The repeatome analysis of these species was missing, which is directly linked to the larger genome sizes of the grasshoppers. Here, we classified repetitive DNA sequences at the level of superfamilies and sub-families, and found that LINE, TcMar-Tc1 and Ty3-gypsy LTR retrotransposons dominated the repeatomes of all genomes, accounting for 16–34% of the total genomes of these species. Satellite DNA dynamic evolutionary changes in all three genomes played a role in genome size evolution. This study would be a valuable source for future genome assemblies.

Abstract

Transposable elements (TEs) play a significant role in both eukaryotes and prokaryotes genome size evolution, structural changes, duplication, and functional variabilities. However, the large number of different repetitive DNA has hindered the process of assembling reference genomes, and the genus level TEs diversification of the grasshopper massive genomes is still under investigation. The genus Calliptamus diverged from Peripolus around 17 mya and its species divergence dated back about 8.5 mya, but their genome size shows rather large differences. Here, we used low-coverage Illumina unassembled short reads to investigate the effects of evolutionary dynamics of satDNAs and TEs on genome size variations. The Repeatexplorer2 analysis with 0.5X data resulted in 52%, 56%, and 55% as repetitive elements in the genomes of Calliptamus barbarus, Calliptamus italicus, and Calliptamus abbreviatus, respectively. The LINE and Ty3-gypsy LTR retrotransposons and TcMar-Tc1 dominated the repeatomes of all genomes, accounting for 16–35% of the total genomes of these species. Comparative analysis unveiled that most of the transposable elements (TEs) except satDNAs were highly conserved across three genomes in the genus Calliptamus grasshoppers. Out of a total of 20 satDNA families, 17 satDNA families were commonly shared with minor variations in abundance and divergence between three genomes, and 3 were Calliptamus barbarus specific. Our findings suggest that there is a significant amplification or contraction of satDNAs at genus phylogeny which is the main cause that made genome size different.

Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution

The distinctive biology and unique evolutionary features of snakes make them fascinating model systems to elucidate how genomes evolve and how variation at the genomic level is interlinked with phenotypic-level evolution. Similar to other eukaryotic genomes, large proportions of snake genomes contain repetitive DNA, including transposable elements (TEs) and satellite repeats. The importance of repetitive DNA and its structural and functional role in the snake genome, remain unclear. This review highlights the major types of repeats and their proportions in snake genomes, reflecting the high diversity and composition of snake repeats. We present snakes as an emerging and important model system for the study of repetitive DNA under the impact of sex and microchromosome evolution. We assemble evidence to show that certain repetitive elements in snakes are transcriptionally active and demonstrate highly dynamic lineage-specific patterns as repeat sequences. We hypothesize that particular TEs can trigger different genomic mechanisms that might contribute to driving adaptive evolution in snakes. Finally, we review emerging approaches that may be used to study the expression of repetitive elements in complex genomes, such as snakes. The specific aspects presented here will stimulate further discussion on the role of genomic repeats in shaping snake evolution.

Cytogenomic analysis unveils mixed molecular evolution and recurrent chromosomal rearrangements shaping the multigene families on Schistocerca grasshopper genomes

Multigene families are essential components of eukaryotic genomes and play key roles either structurally and functionally. Their modes of evolution remain elusive even in the era of genomics, because multiple multigene family sequences coexist in genomes, particularly in large repetitive genomes. Here, we investigate how the multigene families 18S rDNA, U2 snDNA, and H3 histone evolved in 10 species of Schistocerca grasshoppers with very large and repeat-enriched genomes. Using sequenced genomes and fluorescence in situ hybridization mapping, we find substantial differences between species, including the number of chromosomal clusters, changes in sequence abundance and nucleotide composition, pseudogenization, and association with transposable elements (TEs). The intragenomic analysis of Schistocerca gregaria using long-read sequencing and genome assembly unveils conservation for H3 histone and recurrent pseudogenization for 18S rDNA and U2 snDNA, likely promoted by association with TEs and sequence truncation. Remarkably, TEs were frequently associated with truncated copies, were also among the most abundant in the genome, and revealed signatures of recent activity. Our findings suggest a combined effect of concerted and birth-and-death models driving the evolution of multigene families in Schistocerca over the last 8 million years, and the occurrence of intra- and interchromosomal rearrangements shaping their chromosomal distribution. Despite the conserved karyotype in Schistocerca, our analysis highlights the extensive reorganization of repetitive DNAs in Schistocerca, contributing to the advance of comparative genomics for this important grasshopper genus.

Satellitome Analysis of the Pacific Oyster Crassostrea gigas Reveals New Pattern of Satellite DNA Organization, Highly Scattered across the Genome

Several features already qualified the invasive bivalve species Crassostrea gigas as a valuable non-standard model organism in genome research. C. gigas is characterized by the low contribution of satellite DNAs (satDNAs) vs. mobile elements and has an extremely low amount of heterochromatin, predominantly built of DNA transposons. In this work, we have identified 52 satDNAs composing the satellitome of C. gigas and constituting about 6.33% of the genome. Satellitome analysis reveals unusual, highly scattered organization of relatively short satDNA arrays across the whole genome. However, peculiar chromosomal distribution and densities are specific for each satDNA. The inspection of the organizational forms of the 11 most abundant satDNAs shows association with constitutive parts of Helitron mobile elements. Nine of the inspected satDNAs are dominantly found in mobile element-associated form, two mostly appear standalone, and only one is present exclusively as Helitron-associated sequence. The Helitron-related satDNAs appear in more chromosomes than other satDNAs, indicating that these mobile elements could be leading satDNA propagation in C. gigas. No significant accumulation of satDNAs on certain chromosomal positions was detected in C. gigas, thus establishing a novel pattern of satDNA organization on the genome level.

Insights into the genomic evolution of insects from cricket genomes

Most of our knowledge of insect genomes comes from Holometabolous species, which undergo complete metamorphosis and have genomes typically under 2 Gb with little signs of DNA methylation. In contrast, Hemimetabolous insects undergo the presumed ancestral process of incomplete metamorphosis, and have larger genomes with high levels of DNA methylation. Hemimetabolous species from the Orthopteran order (grasshoppers and crickets) have some of the largest known insect genomes. What drives the evolution of these unusual insect genome sizes, remains unknown. Here we report the sequencing, assembly and annotation of the 1.66-Gb genome of the Mediterranean field cricket Gryllus bimaculatus, and the annotation of the 1.60-Gb genome of the Hawaiian cricket Laupala kohalensis. We compare these two cricket genomes with those of 14 additional insects and find evidence that hemimetabolous genomes expanded due to transposable element activity. Based on the ratio of observed to expected CpG sites, we find higher conservation and stronger purifying selection of methylated genes than non-methylated genes. Finally, our analysis suggests an expansion of the pickpocket class V gene family in crickets, which we speculate might play a role in the evolution of cricket courtship, including their characteristic chirping.

Ylla, Extavour et al. use genomic data from crickets to investigate the evolution of large genome sizes and DNA methylation events in insects. Their findings indicate that transposable element activity drove genome expansion in hemimetabolous insects, such as crickets and grasshoppers, and that DNA methylation is predominant in conserved genes.

An endangered flightless grasshopper with strong genetic structure maintains population genetic variation despite extensive habitat loss

Conservation research is dominated by vertebrate examples but the shorter generation times and high local population sizes of invertebrates may lead to very different management strategies, particularly for species with low movement rates. Here we investigate the genetic structure of an endangered flightless grasshopper, Keyacris scurra, which was used in classical evolutionary studies in the 1960s. It had a wide distribution across New South Wales (NSW) and Victoria in pre-European times but has now become threatened because of land clearing for agriculture and other activities. We revisited remnant sites of K. scurra, with populations now restricted to only one area in Victoria and a few small patches in NSW and the Australian Capital Territory (ACT). Using DArtseq to generate SNP markers as well as mtDNA sequence data, we show that the remaining Victorian populations in an isolated valley are genetically distinct from the NSW populations and that all populations tend to be genetically unique, with large F ST values up to 0.8 being detected for the SNP datasets. We also find that, with one notable exception, the NSW/ACT populations separate genetically into previously described chromosomal races (2n = 15 vs. 2n = 17). Isolation by distance was detected across both the SNP and mtDNA datasets, and there was substantial differentiation within chromosomal races. Genetic diversity as measured by heterozygosity was not correlated with the size of remaining habitat where the populations were found, with high variation present in some remnant cemetery sites. However, inbreeding correlated negatively with estimated habitat size at 25-500 m patch radius. These findings emphasize the importance of small habitat areas in conserving genetic variation in such species with low mobility, and they highlight populations suitable for future translocation efforts.

When and how do sex-linked regions become sex chromosomes?

The attention given to heteromorphism and genetic degeneration of "classical sex chromosomes" (Y chromosomes in XY systems, and the W in ZW systems that were studied first and are best described) has perhaps created the impression that the absence of recombination between sex chromosomes is inevitable. I here argue that continued recombination is often to be expected, that absence of recombination is surprising and demands further study, and that the involvement of selection in reduced recombination is not yet well understood. Despite a long history of investigations of sex chromosome pairs, there is a need for more quantitative approaches to studying sex-linked regions. I describe a scheme to help understand the relationships between different properties of sex-linked regions. Specifically, I focus on their sizes (differentiating between small regions and extensive fully sex-linked ones), the times when they evolved, and their differentiation, and review studies using DNA sequencing in nonmodel organisms that are providing information about the processes causing these properties.