The genome sequence of the orange-striped anemone, Diadumene lineata (Verrill, 1869)

Chromosome-level genome assembly of a deep-sea Venus flytrap sea anemone sheds light upon adaptations to an extremely oligotrophic environment

The Venus flytrap sea anemone Actinoscyphia liui inhabits the nutrient-limited deep ocean in the tropical western Pacific. Compared with most other sea anemones, it has undergone a distinct modification of body shape similar to that of the botanic flytrap. However, the molecular mechanism by which such a peculiar sea anemone adapts to a deep-sea oligotrophic environment is unknown. Here, we report the chromosomal-level genome of A. liui constructed from PacBio and Hi-C data. The assembled genome is 522 Mb in size and exhibits a continuous scaffold N50 of 58.4 Mb. Different from most other sea anemones, which typically possess 14-18 chromosomes per haplotype, A. liui has only 11. The reduced number of chromosomes is associated with chromosome fusion, which likely represents an adaptive strategy to economize energy in oligotrophic deep-sea environments. Comparative analysis with other deep-sea sea anemones revealed adaptive evolution in genes related to cellular autophagy (TMBIM6, SESN1, SCOCB and RPTOR) and mitochondrial energy metabolism (MDH1B and KAD2), which may aid in A. liui coping with severe food scarcity. Meanwhile, the genome has undergone at least two rounds of expansion in gene families associated with fast synaptic transmission, facilitating rapid responses to water currents and prey. Positive selection was detected on putative phosphorylation sites of muscle contraction-related proteins, possibly further improving feeding efficiency. Overall, the present study provides insights into the molecular adaptation to deep-sea oligotrophic environments and sheds light upon potential effects of a novel morphology on the evolution of Cnidaria.

Topological structures and syntenic conservation in sea anemone genomes

There is currently little information about the evolution of gene clusters, genome architectures and karyotypes in early branching animals. Slowly evolving anthozoan cnidarians can be particularly informative about the evolution of these genome features. Here we report chromosome-level genome assemblies of two related anthozoans, the sea anemones Nematostella vectensis and Scolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence between the two species. Both genomes show chromosomal conservation, allowing us to reconstruct ancestral cnidarian and metazoan chromosomal blocks, consisting of at least 19 and 16 ancestral linkage groups, respectively. We show that, in contrast to Bilateria, the Hox and NK clusters of investigated cnidarians are largely disintegrated, despite the presence of staggered hox/gbx expression in Nematostella. This loss of microsynteny conservation may be facilitated by shorter distances between cis-regulatory sequences and their cognate transcriptional start sites. We find no clear evidence for topologically associated domains, suggesting fundamental differences in long-range gene regulation compared to vertebrates. These data suggest that large sets of ancestral metazoan genes have been retained in ancestral linkage groups of some extant lineages; yet, higher order gene regulation with associated 3D architecture may have evolved only after the cnidarian-bilaterian split.

De novo reconstruction of satellite repeat units from sequence data

Satellite DNA are long tandemly repeating sequences in a genome and may be organized as high-order repeats (HORs). They are enriched in centromeres and are challenging to assemble. Existing algorithms for identifying satellite repeats either require the complete assembly of satellites or only work for simple repeat structures without HORs. Here we describe Satellite Repeat Finder (SRF), a new algorithm for reconstructing satellite repeat units and HORs from accurate reads or assemblies without prior knowledge on repeat structures. Applying SRF to real sequence data, we show that SRF could reconstruct known satellites in human and well-studied model organisms. We also find satellite repeats are pervasive in various other species, accounting for up to 12% of their genome contents but are often underrepresented in assemblies. With the rapid progress in genome sequencing, SRF will help the annotation of new genomes and the study of satellite DNA evolution even if such repeats are not fully assembled.

Mitochondrial and nuclear gene sequencing confirms the presence of the invasive sea anemone Diadumene lineata (Verrill, 1869) (Cnidaria: Actiniaria) in Argentina

Background

Diadumene lineata is one of the most widespread sea anemone species worldwide. Although this species has been reported a few times on the Argentine coast since 2004, its identification has traditionally been based on external morphological characteristics, and in most cases no voucher specimens are available to support previous records.

Methods

In this study, we obtained DNA sequences of two mitochondrial markers (12S and 16S) and two nuclear markers (18S and 28S) from specimens of D. lineata collected in two locations on the Argentine coast separated by almost 800 km. Additionally, we conducted an analysis of the morphology, as well as the types and size ranges of cnidae, using specimens collected at three different locations along the Argentine coast. Furthermore, since introduced populations of D. lineata are presumably ephemeral and only reproduce asexually outside their native range, we examined the internal anatomy of representatives from the Argentine coast for gametogenic tissue as an indication of whether they might be capable of sexual reproduction.

Results

DNA data support our morphological identification, including cnidae analyses, of the specimens as D. lineata. Furthermore, all specimens examined were determined to be sterile.

Discussion

Genetic sequence comparisons, phylogenetic reconstruction, and cnidae data support the identification of individuals of D. lineata from Mar Chiquita and Garipe Beach, confirming the presence of the species on the Argentine coast using both morphological and molecular tools. The absence of fertile specimens suggests that each sampled population is likely reproducing only by asexual reproduction and possibly composed of clones. The presence of an additional category of longer p-mastigophores B2a in the actinopharynx and filaments, as well as holotrichs in the column, is also reported.

Conclusions

For the first time, we have confirmed the presence of D. lineata in Argentina through molecular data. Additionally, our findings indicate that the analyzed specimens are sterile, suggesting that this species is not engaging in sexual reproduction in the studied localities. It is crucial to continue monitoring the populations of D. lineata along the Argentine coast to assess whether they establish sexual reproduction, expand their distribution range or disappear, or potentially cause any harm to local species or alterations in benthic communities.

De novo reconstruction of satellite repeat units from sequence data

Satellite DNA are long tandemly repeating sequences in a genome and may be organized as high-order repeats (HORs). They are enriched in centromeres and are challenging to assemble. Existing algorithms for identifying satellite repeats either require the complete assembly of satellites or only work for simple repeat structures without HORs. Here we describe Satellite Repeat Finder (SRF), a new algorithm for reconstructing satellite repeat units and HORs from accurate reads or assemblies without prior knowledge on repeat structures. Applying SRF to real sequence data, we showed that SRF could reconstruct known satellites in human and well-studied model organisms. We also found satellite repeats are pervasive in various other species, accounting for up to 12% of their genome contents but are often underrepresented in assemblies. With the rapid progress on genome sequencing, SRF will help the annotation of new genomes and the study of satellite DNA evolution even if such repeats are not fully assembled.