The state of Medusozoa genomics: current evidence and future challenges

Abstract

Medusozoa is a widely distributed ancient lineage that harbors one-third of Cnidaria diversity divided into 4 classes. This clade is characterized by the succession of stages and modes of reproduction during metagenic lifecycles, and includes some of the most plastic body plans and life cycles among animals. The characterization of traditional genomic features, such as chromosome numbers and genome sizes, was rather overlooked in Medusozoa and many evolutionary questions still remain unanswered. Modern genomic DNA sequencing in this group started in 2010 with the publication of the Hydra vulgaris genome and has experienced an exponential increase in the past 3 years. Therefore, an update of the state of Medusozoa genomics is warranted. We reviewed different sources of evidence, including cytogenetic records and high-throughput sequencing projects. We focused on 4 main topics that would be relevant for the broad Cnidaria research community: (i) taxonomic coverage of genomic information; (ii) continuity, quality, and completeness of high-throughput sequencing datasets; (iii) overview of the Medusozoa specific research questions approached with genomics; and (iv) the accessibility of data and metadata. We highlight a lack of standardization in genomic projects and their reports, and reinforce a series of recommendations to enhance future collaborative research.

Keywords: annotation; assembly; chromosome number; collaborative genomics; completeness; genome size.

Figure 1:

Medusozoa diversity. Examples of different genera covered by this review belong to Hydrozoa (A, B), Staurozoa (C), Cubozoa (D, E), and Scyphozoa (FG). (A) Craspedacusta sowerbii, (B) Cladonema radiatum, (C) Haliclystus sanjuanensis, (D) Copula sivickisi, (E) Tamoya haplonema, (F) Cassiopea xamachana, (G) Aurelia aurita. Credits to Alvaro E. Migotto (A, B, E, D), Marta Chiodin (C) and Joseph F. Ryan (F, G). Photographs A, B, D, E were obtained from Cifonauta [27]. Photographs are not to scale.

Figure 2:

Phylogenetic distribution of genomic information in Medusozoa. (A) Number of described species and number of species with genomic data; (B) chromosome number (2n) range; (C) genome size (Mb) range taking into account flow cytometry and Feulgen densitometry estimations; (D) total number of available assemblies and number of species with assembled genomes. In (B) and (C) single values were also included when only 1 species was characterized. Tree topology is explained in the Methods section. Information used for this graph is available in Supplementary File S5 Table S2.

Figure 3:

Assembly and genome features. (A) (from left to right): mean assembly length per class, GC content (%) per class, number of contigs and scaffolds per assembly colored by class, contig, and scaffold N50 (in kb) per assembly coloured by class, and count of assemblies of each class corresponding to the different BGP-metric values, where X and Y correspond to contig and scaffold N50, respectively, and Z to chromosome assignment (see Methods section). (B) (from left to right): mean repeat length (Mb) in assembly per class, mean total number of genes per class, mean exon number (count per gene) per class, and mean gene, intron, and exon length (kb) per assembly colored by class. The yellow arrowhead indicates S. malayensis gene features (see Box). Within the dotplots, a data point is indicated for each species. When more than one species per class was available, vertical lines were added to barplots to indicate the value dispersion around the mean. All other keys are specified in the figure. Information used for this graph is available in Supplementary File S5 Tables S4–S6.

Figure 4:

BUSCO Metazoa gene distribution in Medusozoa assemblies. Each column corresponds to a gene and each row an assembly. Columns were ordered based on presence from left to right and the least present genes (n = 96) are shown in detail. Genes absent in all or almost all assemblies (>80% of absence) are indicated in red; genes also reported absent [20] are indicated in boldface; genes absent in specific lineages are indicated with yellow rectangles. Higher quality assemblies are indicated in orange (BGP-metric > 1.0.0). The assembly with the highest quality score for BGP-metric is indicated by an orange circle and corresponds to Rhopilema esculentum [47]. Information used for this graph and full BUSCO gene names are available in Supplementary File S5 Table S7.