Chromosome-level genome assembly of Hydractinia symbiolongicarpus

Abstract

Hydractinia symbiolongicarpus is a pioneering model organism for stem cell biology, being one of only a few animals with adult pluripotent stem cells (known as i-cells). However, the unavailability of a chromosome-level genome assembly has hindered a comprehensive understanding of global gene regulatory mechanisms underlying the function and evolution of i-cells. Here, we report the first chromosome-level genome assembly of H. symbiolongicarpus (HSymV2.0) using PacBio HiFi long-read sequencing and Hi-C scaffolding. The final assembly is 483 Mb in total length with 15 chromosomes representing 99.8% of the assembly. Repetitive sequences were found to account for 296 Mb (61%) of the total genome; we provide evidence for at least two periods of repeat expansion in the past. A total of 25,825 protein-coding genes were predicted in this assembly, which include 93.1% of the metazoan Benchmarking Universal Single-Copy Orthologs (BUSCO) gene set. 92.8% (23,971 genes) of the predicted proteins were functionally annotated. The H. symbiolongicarpus genome showed a high degree of macrosynteny conservation with the Hydra vulgaris genome. This chromosome-level genome assembly of H. symbiolongicarpus will be an invaluable resource for the research community that enhances broad biological studies on this unique model organism.

Keywords: Hydractinia; HSymV2.0; chromosome-level genome assembly; hydrozoa; stem cell.

Fig. 1.

Chromosome-level genome assembly of H. symbiolongicarpus (HSymV2.0). a) Colony of H. symbiolongicarpus male (Clone 291-10) attached to a glass microscope slide, showing mature feeding polyps (∼5 mm height), polyp buds, and shared stolon network (sexual polyps not pictured as they develop later). b) Hi-C contact map showing the 15 chromosome-level scaffolds and the unplaced sequences (Un). Scaffolds are ordered by length and assigned numbers.

Fig. 2.

Collinearity between the Hi-C scaffolds of the present study and the genetic linkage maps (Chen et al. 2023). a) Sequence alignments between the Hi-C scaffolds and pseudochromosomes based on the maternal genetic linkage map. b) Sequence alignments between the Hi-C scaffolds and pseudochromosomes based on the paternal genetic linkage map.

Fig. 3.

Interspersed repeat landscape of the H. symbiolongicarpus genome and H. vulgaris genome. a) Interspersed repeat landscape of H. symbiolongicarpus. b) Interspersed repeat landscape of H. vulgaris. The x-axis represents the level of Kimura substitution for repeat elements from the consensus sequences (relative age). The y-axis represents the relative abundance of each repeat family in the genome. Ancient active repeats are placed on the right side of the graph, and recently active repeats are on the left.

Fig. 4.

Gene annotation of the HSymV2.0 assembly. a) BLAST search results of the total 25,825 predicted protein-coding genes against the NCBI-nr database. Total 20,985 gene hits were identified in the NCBI-nr database. Top 20 species origins of the BLAST hits are shown as a bar plot. The inset pie chart represents the summary of species origins. The color scheme of the bar plot corresponds to that of the inset pie chart. b) Venn diagram showing functional annotations of the predicted protein-coding genes of the HSymV2.0 assembly. c) Gene structure of Piwi1 on the chromosome 13. d) Gene structure of Tfap2 on the chromosome 5.

Fig. 5.

Oxford dot plot of orthologs between H. symbiolongicarpus and H. vulgaris. a) Oxford dot plot using the 8,974 orthologs. For both species, orthologs are sequentially numbered according to their genomic positions. Each dot represents the orthologs. b) Oxford dot plot using orthologs on scaffold 5 and 15 of H. symbiolongicarpus genome assembly and those on the HVAEP3 and HVAEP5 of the H. vulgaris genome assembly. c) Oxford dot plot using orthologs on the scaffold 2 and 14 of H. symbiolongicarpus genome assembly and those on the HVAEP7 and HVAEP14 of the H. vulgaris genome assembly.