This is a correction to: Shivam Bhardwaj and others, Sex Differences in 20-Hydroxyecdysone Hormone Levels Control Sexual Dimorphism in Bicyclus anynana Wing Patterns, Molecular Biology and Evolution, Volume 35, Issue 2, February 2018, Pages 465–472, https://doi.org/10.1093/molbev/msx301
AbstractSince the pioneering work of Dobzhansky in the 1930s and 1940s, many chromosomal inversions have been identified, but how they contribute to adaptation remains poorly understood. In Drosophila melanogaster, the widespread inversion polymorphism In(3R)Payne underpins latitudinal clines in fitness traits on multiple continents. Here, we use single-individual whole-genome sequencing, transcriptomics, and published sequencing data to study the population genomics of this inversion on four continents: in its ancestral African range and in derived populations in Europe, North America, and Australia. Our results confirm that this inversion originated in sub-Saharan Africa and subsequently became cosmopolitan; we observe marked monophyletic divergence of inverted and noninverted karyotypes, with some substructure among inverted chromosomes between continents. Despite divergent evolution of this inversion since its out-of-Africa migration, derived non-African populations exhibit similar patterns of long-range linkage disequilibrium between the inversion breakpoints and major peaks of divergence in its center, consistent with balancing selection and suggesting that the inversion harbors alleles that are maintained by selection on several continents. Using RNA-sequencing, we identify overlap between inversion-linked single-nucleotide polymorphisms and loci that are differentially expressed between inverted and noninverted chromosomes. Expression levels are higher for inverted chromosomes at low temperature, suggesting loss of buffering or compensatory plasticity and consistent with higher inversion frequency in warm climates. Our results suggest that this ancestrally tropical balanced polymorphism spread around the world and became latitudinally assorted along similar but independent climatic gradients, always being frequent in subtropical/tropical areas but rare or absent in temperate climates.
AbstractSex pheromones not only improve the reproductive success of the recipients, but also impose costs, such as a reduced life span. The underlying mechanisms largely remain to be elucidated. Here, we show that even a brief exposure to physiological amounts of the dominant Caenorhabditis elegans male pheromone, ascr#10, alters the expression of thousands of genes in hermaphrodites. The most dramatic effect on the transcriptome is the upregulation of genes expressed during oogenesis and the downregulation of genes associated with male gametogenesis. This result reveals a way in which social signals help to resolve the inherent conflict between spermatogenesis and oogenesis in a simultaneous hermaphrodite, presumably to optimally align reproductive function with the presence of potential mating partners. We also found that exposure to ascr#10 increased the risk of persistent intestinal infections in hermaphrodites due to pathological pharyngeal hypertrophy. Thus, our study reveals ways in which the male pheromone can not only have beneficial effects on the recipients’ reproduction, but also cause harmful consequences that reduce life span.
AbstractEchinometra lucunter, the rock-boring sea urchin, is a widely distributed echinoid and a model for ecological studies of reproduction, responses to climate change, and speciation. We present a near chromosome-level genome assembly of E. lucunter, including 21 scaffolds larger than 10 Mb predicted to represent each of the chromosomes of the species. The 760.4 Mb assembly includes a scaffold N50 of 30.0 Mb and BUSCO (benchmarking universal single-copy orthologue) single copy and a duplicated score of 95.8% and 1.4%, respectively. Ab-initio gene model prediction and annotation with transcriptomic data constructed 33,989 gene models composing 50.4% of the assembly, including 37,036 transcripts. Repetitive elements make up approximately 39.6% of the assembly, and unresolved gap sequences are estimated to be 0.65%. Whole genome alignment with Echinometra sp. EZ revealed high synteny and conservation between the two species, further bolstering Echinometra as an emerging genus for comparative genomics studies. This genome assembly represents a high-quality genomic resource for future evolutionary and developmental studies of this species and more broadly of echinoderms.
AbstractAlthough duplications have long been recognized as a fundamental process driving major evolutionary innovations, direct estimates of spontaneous chromosome duplication rates, leading to aneuploid karyotypes, are scarce. Here, from mutation accumulation (MA) experiments, we provide the first estimates of spontaneous chromosome duplication rates in six unicellular eukaryotic species, which range from 1 × 10−4 to 1 × 10−3 per genome per generation. Although this is ∼5 to ∼60 times less frequent than spontaneous point mutations per genome, chromosome duplication events can affect 1–7% of the total genome size. In duplicated chromosomes, mRNA levels reflected gene copy numbers, but the level of translation estimated by polysome profiling revealed that dosage compensation must be occurring. In particular, one duplicated chromosome showed a 2.1-fold increase of mRNA but translation rates were decreased to 0.7-fold. Altogether, our results support previous observations of chromosome-dependent dosage compensation effects, providing evidence that compensation occurs during translation. We hypothesize that an unknown posttranscriptional mechanism modulates the translation of hundreds of transcripts from genes located on duplicated regions in eukaryotes.
AbstractThe rate of mutation varies among positions in a genome. Local sequence context can affect the rate and has different effects on different types of mutation. Here, I report an effect of local context that operates to some extent in all bacteria examined: the rate of T→G mutation is greatly increased by preceding runs of three or more G residues. The strength of the effect increases with the length of the run. In Salmonella, in which the effect is strongest, a G run of length three 3 increases the rate by a factor of ∼26, a run of length 4 increases it by almost a factor of 100, and runs of length 5 or more increase it by a factor of more than 400 on average. The effect is much stronger when the T is on the leading rather than the lagging strand of DNA replication. Several observations eliminate the possibility that this effect is an artifact of sequencing error.
AbstractStructural variants (SVs) are variants with sizes bigger than 50 bp and capable of changing the size, copy number, location, orientation, and sequence content of genomic DNA. Although these variants have been proven to be extensive and involved in many evolutionary processes along the tree of life, there is still insufficient information on many fungal plant pathogens. In this study, the extent of SVs, as well as single-nucleotide polymorphisms (SNPs), has been determined for two prominent species of the Monilinia genus (the causal agents of brown rot disease in pome and stone fruits): Monilinia fructicola and Monilinia laxa for the first time. The genomes of M. fructicola were found to be more variant-rich in contrast to M. laxa based on the reference-based variant calling (with a total number of 266.618 and 190.599 SNPs and 1,540 and 918 SVs, respectively). The extent, as well as distribution of SVs, presented high conservation within the species and high diversity between the species. Investigation of potential functional effects of characterized variants revealed high potential relevance of SVs. Moreover, the detailed characterization of copy number variations (CNVs) for each isolate revealed that around 0.67% of M. fructicola genomes and 2.06% of M. laxa genomes are copy number variables. The variant catalog as well as distinct variant dynamics within and between the species presented in this study opens doors for many further research questions.
AbstractCold-water corals form an important part of temperate benthic ecosystems by increasing three-dimensionality and providing an important ecological substrate for other benthic fauna. However, the fragile three-dimensional structure and life-history characteristics of cold-water corals can leave populations vulnerable to anthropogenic disturbance. Meanwhile, the ability of temperate octocorals, particularly shallow-water species, to respond to adjustments in their environment linked to climate change has not been studied. This study reports the first genome assembly of the pink sea fan (Eunicella verrucosa), a temperate shallow-water octocoral species. We produced an assembly of 467 Mb, comprising 4,277 contigs and an N50 of 250,417 bp. In total, 213 Mb (45.96% of the genome) comprised repetitive sequences. Annotation of the genome using RNA-seq data derived from polyp tissue and gorgonin skeleton resulted in 36,099 protein-coding genes after 90% similarity clustering, capturing 92.2% of the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) ortholog benchmark genes. Functional annotation of the proteome using orthology inference identified 25,419 annotated genes. This genome adds to the very few genomic resources currently available in the octocoral community and represents a key step in allowing scientists to investigate the genomic and transcriptomic responses of octocorals to climate change.