Abstract
Paracondylactis sinensis is a burrowing sea anemone inhabiting soft sediments along the Chinese coast, representing an ecologically and economically important actiniarian species. Despite its unique adaptations to hypoxia and sediment-associated stressors, genomic resources for burrowing sea anemones have been lacking. Here, we report a high-quality, chromosome-level genome assembly of P. sinensis. With PacBio HiFi long reads (39.77 × coverage), Illumina short reads, and Hi-C data, a 210.63 Mb genome with a contig N50 of 8.70 Mb and a scaffold N50 of 9.41 Mb was generated. A total of 93.44% of the assembly was anchored to 19 pseudo-chromosomes. BUSCO analysis indicated 95.91% completeness, confirming high assembly quality. Comprehensive annotation identified 19,420 protein-coding genes, of which 91.35% were functionally annotated. Repetitive elements accounted for 26.43% of the genome, with transposable elements representing 20.47%. This genome provides a crucial reference for understanding the genetic basis of environmental adaptation in P. sinensis and supports future efforts in its conservation, aquaculture, and bioactive compound exploration.
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Data availability
The raw sequencing data are available in the NCBI Sequence Read Archive (SRA) database (https://identifiers.org/ncbi/insdc.sra:SRP627585), the genome assembly is available in NCBI GenBank (https://identifiers.org/ncbi/insdc.gca:GCA_054491775.1), and the genome and annotation files are available via Figshare (https://doi.org/10.6084/m9.figshare.30209509.v1).
Code availability
Genome survey:
(1) Trimmomatic: parameter: ILLUMINACLIP:TruSeq. 3-PE-2.fa:2:30:10 LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:40.
(2) FastUniq: parameter: -t q -c 1.
(3) Jellyfish:
count: parameter: -G 2 -m 17 -C.
histo: all parameters were set as default.
stats: all parameters were set as default.
(4) GenomeScope: parameter: -p 2 -k 17 -m 10000.
Contamination screen:
(1) FCS-GX: parameter: --tax-id 1 --div None --split-fasta true --action-report true.
Genome assembly:
(1) Hifiasm: parameter: -l 3.
(2) Chromap: parameter: --preset hic --remove-pcr-duplicates.
(3) Yahs: all parameters were set as default.
(4) Juicer: all parameters were set as default.
(5) Samtools: all parameters were set as default.
Genome annotation:
(1) RepeatModeler: parameter: BuildDatabase -name, -LTRStruct.
(2) RepeatMasker: parameter: -e rmblast -gff -s -a -nolow.
(3) Hisat2: all parameters were set as default.
(4) Trinity: parameter: --genome_guided_bam --genome_guided_max_intron 20000.
(5) BRAKER3: all parameters were set as default.
(6) PASA: parameter:
Launch_PASA_pipeline.pl -C -R --ALIGNERS minimap2.
Launch_PASA_pipeline.pl –A.
(7) AGAT: all parameters were set as default.
Completeness evaluation
(1) BUSCO (for genome assembly): parameter: -m genome -l metazoa_odb10.
(2) BUSCO (for translated protein sequence): parameter: -m prot -l metazoa_odb10.
(3) CEGMA: all parameters were set as default.
(4) Merqury: parameter: meryl count k = 21.
Read mapping:
(1) BWA:
short reads: all parameters were set as default.
PacBio HiFi reads: parameter: -x pacbio.
(2) Picard: all parameters were set as default.
(3) Samtools: all parameters were set as default.
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Acknowledgements
This work was supported by Shandong Provincial Natural Science Foundation (No. ZR2025MS656), the Taizhou Science and Technology Plan Project (No. 25nyb03), and National Natural Science Foundation of China (No. 32570619). Thanks are given to the Oceanographic Data Center, IOCAS, for providing computing power.
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Junyuan Li: Conceptualization, Data curation, Formal analysis, Methodology, Software, Validation, Visualization and Writing. Rongye Tang: Conceptualization, Investigation, Project administration, Resources, Supervision, and Validation. Juan Feng: Investigation, Resources and Validation. Tinghui Xie: Resources and Validation. Sitong Liu: Software. Yang Li: Conceptualization, Validation,Funding acquisition, Project administration, Resources, Supervision,Writing -review& editing.
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Li, J., Tang, R., Feng, J. et al. Chromosome-scale genome of the burrowing sea anemone Paracondylactis sinensis. Sci Data (2026). https://doi.org/10.1038/s41597-026-06838-8
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DOI: https://doi.org/10.1038/s41597-026-06838-8
