Near-Chromosomal-Level Genome Assembly of the Sea Urchin Echinometra lucunter, a Model for Speciation in the Sea

Wed, 07 Jun 2023 00:00:00 GMT

Echinometra 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.

A High Frequency of Chromosomal Duplications in Unicellular Algae Is Compensated by Translational Regulation

Tue, 23 May 2023 00:00:00 GMT

Although 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.

T Residues Preceded by Runs of G Are Hotspots of T→G Mutation in Bacteria

Mon, 22 May 2023 00:00:00 GMT

The 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.

Genome-Wide Discovery of Structural Variants Reveals Distinct Variant Dynamics for Two Closely Related Monilinia Species

Mon, 22 May 2023 00:00:00 GMT

Structural 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.

The First Genome of the Cold-Water Octocoral, the Pink Sea Fan, Eunicella verrucosa

Sat, 20 May 2023 00:00:00 GMT

Cold-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.