Chromosome-level genome assembly of the shuttles hoppfish, Periophthalmus modestus

Background The shuttles hoppfish (mudskipper), Periophthalmus modestus, is one of the mudskippers, which are the largest group of amphibious teleost fishes, which are uniquely adapted to live on mudflats. Because mudskippers can survive on land for extended periods by breathing through their skin and through the lining of the mouth and throat, they were evaluated as a model for the evolutionary sea-land transition of Devonian protoamphibians, ancestors of all present tetrapods. Results A total of 39.6, 80.2, 52.9, and 33.3 Gb of Illumina, Pacific Biosciences, 10X linked, and Hi-C data, respectively, was assembled into 1,419 scaffolds with an N50 length of 33 Mb and BUSCO score of 96.6%. The assembly covered 117% of the estimated genome size (729 Mb) and included 23 pseudo-chromosomes anchored by a Hi-C contact map, which corresponded to the top 23 longest scaffolds above 20 Mb and close to the estimated one. Of the genome, 43.8% were various repetitive elements such as DNAs, tandem repeats, long interspersed nuclear elements, and simple repeats. Ab initio and homology-based gene prediction identified 30,505 genes, of which 94% had homology to the 14 Actinopterygii transcriptomes and 89% and 85% to Pfam familes and InterPro domains, respectively. Comparative genomics with 15 Actinopterygii species identified 59,448 gene families of which 12% were only in P. modestus. Conclusions We present the high quality of the first genome assembly and gene annotation of the shuttles hoppfish. It will provide a valuable resource for further studies on sea-land transition, bimodal respiration, nitrogen excretion, osmoregulation, thermoregulation, vision, and mechanoreception.

Monodopsis and Vischeria genomes elucidate the biology of eustigmatophyte algae

Members of eustigmatophyte algae, especially Nannochloropsis, have been tapped for biofuel production owing to their exceptionally high lipid content. While extensive genomic, transcriptomic, and synthetic biology toolkits have been made available for Nannochloropsis, very little is known about other eustigmatophytes. Here we present three near-chromosomal and gapless genome assemblies of Monodopsis (60 Mb) and Vischeria (106 Mb), which are the sister groups to Nannochloropsis. These genomes contain unusually high percentages of simple repeats, ranging from 12% to 21% of the total assembly size. Unlike Nannochloropsis, LINE repeats are abundant in Monodopsis and Vischeria and might constitute the centromeric regions. We found that both mevalonate and non-mevalonate pathways for terpenoid biosynthesis are present in Monodopsis and Vischeria, which is different from Nannochloropsis that has only the latter. Our analysis further revealed extensive spliced leader trans-splicing in Monodopsis and Vischeria at 36-61% of genes. Altogether, the high-quality genomes of Monodopsis and Vischeria not only serve as the much-needed outgroups to advance Nannochloropsis research, but also shed new light on the biology and evolution of eustigmatophyte algae.

Copy number evolution in simple and complex tandem repeats across the C57BL/6 and C57BL/10 inbred mouse lines

Simple sequence tandem repeats are among the most rapidly evolving compartments of the genome. Some repeat expansions are associated with mammalian disease or meiotic segregation distortion, yet the rates of copy number change across generations are not well known. Here, we use 14 distinct sub-lineages of the C57BL/6 and C57BL/10 inbred mouse strains, which have been evolving independently over about 300 generations, to estimate the rates of copy number changes in genome-wide tandem repeats. Rates of change varied across repeats and across lines. Notably, CAG, whose expansions in coding regions are associated with many neurological and genetic disorders, was highly stable in copy number, likely indicating stabilizing selection. Rates of change were positively correlated with copy number, but the direction and magnitude of changes varied across lines. Some mouse lines experienced consistent losses or gains across most simple repeats, but this did not correlate with copy number changes in complex repeats. Rates of copy number change were similar between simple repeats and the more abundant complex repeats after normalization by copy number. Finally, the Y-specific centromeric repeat had a 4-fold higher rate of change than the homologous centromeric repeat on other chromosomes. Structural differences in satellite complexity, or restriction to the Y chromosome and elevated mutation rates of the male germline, may explain the higher rate of change. Overall, our work underscores the mutational fluidity of long tandem arrays of repeats, and the correlations and constraints between genome-wide tandem repeats which suggest that turnover is not a completely neutral process.

Comparative Analysis of Complete Chloroplast Genome Sequences in Edgeworthia (Thymelaeaceae) and New Insights Into Phylogenetic Relationships

The complete chloroplast genomes of three species of Edgeworthia namely, Edgeworthia albiflora, Edgeworthia chrysantha, and Edgeworthia gardneri (Thymelaeaceae), are reported and characterized. The chloroplast genomes displayed a typical quadripartite structure with conserved genome arrangement and specific divergence. The genomes ranged in length from 172,708 to 173,621 bp and displayed similar GC content of 36.5–36.7%. A total of 138–139 genes were predicted, including 92–93 protein-coding, 38 tRNAs and eight rRNAs genes. Variation in the number of short simple repeats and inverted region boundaries of the three cp genomes were observed. A mutational hotspot was detected along the nucleotide sequence from the ndhF to the trnL-UAG genes. The chloroplast genome-based and internal transcribed spacer (ITS)-based phylogenetic analyses using maximum-likelihood (ML) and Bayesian inference (BI) revealed that E. albiflora diverged before E. chrysantha and E. gardneri and placed the Edgeworthia clade at the base of the Eurasian Daphne group with strong bootstrap support. With an effective taxonomic treatment of the species of Edgeworthia, further molecular analyses of their intra- and interspecific genetic variation are inclined to support the treatment of E. albiflora and E. gardneri as two natural groups. The genetic information obtained from this study will provide valuable genomic resources for the identification of additional species and for deducing the phylogenetic evolution of Edgeworthia.

Copy number evolution in simple and complex tandem repeats across the C57BL/6 and C57BL/10 inbred mouse lines

Simple sequence tandem repeats are among the most rapidly evolving compartments of the genome. Some repeat expansions are associated with mammalian disease or meiotic segregation distortion, yet the rates of copy number change across generations are not well known. Here, we use 14 distinct sub-lineages of the C57BL/6 and C57BL/10 inbred mouse strains, which have been evolving independently over about 300 generations, to estimate the rates of copy number changes in genome-wide tandem repeats. Rates of change varied across simple repeats and across lines. Notably, CAG, whose expansions in coding regions are associated with many neurological and other genetic disorders, was highly stable in copy number, likely indicating purifying selection. Rates of change were generally positively correlated with copy number, but the direction and magnitude of changes varied across lines. Some mouse lines experienced consistent losses or gains across most genome-wide simple repeats, but this did not correlate with copy number changes in complex repeats. Rates of copy number change were similar between simple repeats and the much more abundant complex repeats once they were normalized by copy number. Finally, the Y-specific centromeric repeat had a 4-fold higher rate of change than the homologous centromeric repeat on other chromosomes. Structural differences in satellite complexity, or restriction to the Y chromosome and the elevated mutation rate of the male germline, may explain the higher rate of change. Overall, our work underscores the mutational fluidity of long tandem arrays of repeats, and the correlations and constraints between genome-wide tandem repeats which suggest that turnover is not a completely neutral process.

Characterization of New Molecular Markers of Three Botflies Parasitizing Cervid Hosts

Specific identification of oestrid larvae is usually problematic not only when using morphobiometric features, but also when applying molecular criteria, since very few molecular markers have been described for this group of flies. New molecular markers for oestrid are needed for more reliable species identification, diagnostic purposes, and epidemiological surveys; moreover, they can help in phylogenetic reconstruction. Here, we report the characterization of COI, 28S rDNA, ITS1, and ITS2 in Cephenemyia stimulator from roe deer and in Cephenemyia auribarbis and Pharyngomyia picta from red deer. The COI and 28S rDNA are very uniform in length, while the ITSs sequences are highly variable at both intraspecific and interspecific levels. The described ITSs sequences were longer than those described for other dipteran species by the presence of simple repeats and tandem repeat sequences. In C. auribarbis both ITS1 and ITS2 appeared as two variants, one short and the other long. In general, the analyzed markers present low intraspecific genetic variation and high interspecific variation. ITSs showed the greatest amount of intraspecific and interspecific variation. Phylogenetic analysis demonstrated that the characterized sequences differentiate the species and genera of Oestridae.

Association analysis of repetitive elements and R-loop formation across species

Background Although recent studies have revealed the genome-wide distribution of R-loops, our understanding of R-loop formation is still limited. Genomes are known to have a large number of repetitive elements. Emerging evidence suggests that these sequences may play an important regulatory role. However, few studies have investigated the effect of repetitive elements on R-loop formation. Results We found different repetitive elements related to R-loop formation in various species. By controlling length and genomic distributions, we observed that satellite, long interspersed nuclear elements (LINEs), and DNA transposons were each specifically enriched for R-loops in humans, fruit flies, and Arabidopsis thaliana, respectively. R-loops also tended to arise in regions of low-complexity or simple repeats across species. We also found that the repetitive elements associated with R-loop formation differ according to developmental stage. For instance, LINEs and long terminal repeat retrotransposons (LTRs) are more likely to contain R-loops in embryos (fruit fly) and then turn out to be low-complexity and simple repeats in post-developmental S2 cells. Conclusions Our results indicate that repetitive elements may have species-specific or development-specific regulatory effects on R-loop formation. This work advances our understanding of repetitive elements and R-loop biology.

Assessment of genetic diversity in Moroccan sesame (Sesamum indicum) using ISSR molecular markers

There is a need for sesame (Sesamum indicum L.) breeding in Morocco to release performant and adapted varieties, which requires a large genetic variability in the germplasm to be used. In this context, genetic diversity of sesame populations from different locations in Tadla area was investigated using ISSR (Inter Sequence Simple Repeats) markers as a simple method to reveal polymorphism among them. A total of 130 individuals representing 31 populations were sampled. Twenty-four ISSR primers were used for analysis of individuals representing the 31 different sesame populations grown in different agroclimatic zones of Tadla, accounting for 90% of sesame cultivation area in Morocco. Indeed, seven primers showed legible and reproducible genomic profiles with an interesting number of bands. A total of 57 bands were obtained with ISSR primers, of which 47 were polymorphic. PIC (Polymorphic Information Content) ranged from 0.002 to 0.350, showing that ISSR markers are informative and relevant for discriminating the populations evaluated. The similarity coefficient of ISSR data ranged from 0.509 to 1, with an average of 0.870. The results obtained showed that Moroccan sesame populations are characterized by a low genetic diversity, suggesting a genetic proximity among them. Therefore, new germplasm should be either introduced from diverse geographical origins or created through mutagenesis breeding in order to broaden the existing genetic variability.

The number of Z-repeats and super-repeats in nebulin greatly varies across vertebrates and scales with animal size

Nebulin is a skeletal muscle protein that associates with the sarcomeric thin filaments and has functions in regulating the length of the thin filament and the structure of the Z-disk. Here we investigated the nebulin gene in 53 species of birds, fish, amphibians, reptiles, and mammals. In all species, nebulin has a similar domain composition that mostly consists of ∼30-residue modules (or simple repeats), each containing an actin-binding site. All species have a large region where simple repeats are organized into seven-module super-repeats, each containing a tropomyosin binding site. The number of super-repeats shows high interspecies variation, ranging from 21 (zebrafish, hummingbird) to 31 (camel, chimpanzee), and, importantly, scales with body size. The higher number of super-repeats in large animals was shown to increase thin filament length, which is expected to increase the sarcomere length for optimal force production, increase the energy efficiency of isometric force production, and lower the shortening velocity of muscle. It has been known since the work of A.V. Hill in 1950 that as species increase in size, the shortening velocity of their muscle is reduced, and the present work shows that nebulin contributes to the mechanistic basis. Finally, we analyzed the differentially spliced simple repeats in nebulin's C terminus, whose inclusion correlates with the width of the Z-disk. The number of Z-repeats greatly varies (from 5 to 18) and correlates with the number of super-repeats. We propose that the resulting increase in the width of the Z-disk in large animals increases the number of contacts between nebulin and structural Z-disk proteins when the Z-disk is stressed for long durations.

Association analysis of repetitive elements and R-loop formation across species

ABSTRACTGenomes are known to have a large number of repetitive elements. Emerging evidence suggests that these non-coding elements may play an important regulatory role. However, few studies have investigated the effect of repetitive elements on R-loop formation. In this study, we found different repetitive elements related to R-loop formation in various species. By controlling length and genomic distributions, we observed that satellites, long interspersed nuclear elements (LINEs), and DNAs were each specifically enriched for R-loops in humans, fruit flies, and Arabidopsis thaliana, respectively. R-loops also tended to arise in regions of low-complexity or simple repeats across species. We also found that the repetitive elements associated with R-loop formation differ according to developmental stage. For instance, LINEs and long terminal repeats (LTRs) are more likely to contain R-loops in embryos (fruit fly) and then turn out to be low-complexity and simple repeats in post-developmental S2 cells. Our results indicate that repetitive elements may have species-specific or development-specific regulatory effects on R-loop formation. This work advances our understanding of repetitive elements and R-loop biology.