Chromosome-level Genome Assembly of the Northern Pacific Seastar Asterias Amurensis

Overview

Journal Sci Data

Specialty Science

Date 2023 Nov 5

PMID 37925473

Authors

Yanlin Wang

Yixin Wang

Yujia Yang

Gang Ni

Yulong Li

Muyan Chen

Affiliations

Soon will be listed here.

Abstract

Asterias amurensis has attracted widespread concern because of its population outbreaks, which has impacted fisheries and aquaculture, as well as disrupting local ecosystems. A high-quality reference genome is necessary to better investigate mechanisms of outbreak and adaptive changes. Combining PacBio HiFi and Hi-C sequencing data, we generated a chromosome-level A. amurensis genome with a size of 491.53 Mb. The contig N50 and scaffold N50 were 8.05 and 23.75 Mb, respectively. The result of BUSCO analysis revealed a completeness score of 98.85%. A total of 16,531 protein-coding genes were predicted in the genome, of which 94.63% were functionally annotated. The high-quality genome assembly resulting from this study will provide a valuable genetic resource for future research on the mechanism of population outbreaks and invasion ecology.

Citing Articles

Identification of a candidate sex determination region and sex-specific molecular markers based on whole-genome re‑sequencing in the sea star Asterias amurensis.

Wang Y, Yang H, Wang Y, Li Y, Ni G, Cummins S DNA Res. 2025; 32(1).

PMID: 39792457 PMC: 11757944. DOI: 10.1093/dnares/dsaf003.

Typical Marine Ecological Disasters in China Attributed to Marine Organisms and Their Significant Insights.

Yao L, He P, Xia Z, Li J, Liu J Biology (Basel). 2024; 13(9).

PMID: 39336105 PMC: 11429238. DOI: 10.3390/biology13090678.

Chromosome-level genome assembly of the northern Pacific seastar Asterias amurensis.

Wang Y, Wang Y, Yang Y, Ni G, Li Y, Chen M Sci Data. 2023; 10(1):767.

PMID: 37925473 PMC: 10625585. DOI: 10.1038/s41597-023-02688-w.

References

Ellis M, Clark Z, Treml E, Brown M, Matthews T, Pocklington J . Detecting marine pests using environmental DNA and biophysical models. Sci Total Environ. 2021; 816:151666. DOI: 10.1016/j.scitotenv.2021.151666. View

Blum M, Chang H, Chuguransky S, Grego T, Kandasaamy S, Mitchell A . The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 2020; 49(D1):D344-D354. PMC: 7778928. DOI: 10.1093/nar/gkaa977. View

Rhie A, Walenz B, Koren S, Phillippy A . Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020; 21(1):245. PMC: 7488777. DOI: 10.1186/s13059-020-02134-9. View

Manni M, Berkeley M, Seppey M, Simao F, Zdobnov E . BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol. 2021; 38(10):4647-4654. PMC: 8476166. DOI: 10.1093/molbev/msab199. View

Besemer J, Borodovsky M . GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 2005; 33(Web Server issue):W451-4. PMC: 1160247. DOI: 10.1093/nar/gki487. View

Flynn J, Hubley R, Goubert C, Rosen J, Clark A, Feschotte C . RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci U S A. 2020; 117(17):9451-9457. PMC: 7196820. DOI: 10.1073/pnas.1921046117. View

Parra G, Bradnam K, Korf I . CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007; 23(9):1061-7. DOI: 10.1093/bioinformatics/btm071. View

Bruna T, Hoff K, Lomsadze A, Stanke M, Borodovsky M . BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genom Bioinform. 2021; 3(1):lqaa108. PMC: 7787252. DOI: 10.1093/nargab/lqaa108. View

Richardson M, Sherman C, Lee R, Bott N, Hirst A . Multiple dispersal vectors drive range expansion in an invasive marine species. Mol Ecol. 2016; 25(20):5001-5014. DOI: 10.1111/mec.13817. View

10.

Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar G, Sonnhammer E . Pfam: The protein families database in 2021. Nucleic Acids Res. 2020; 49(D1):D412-D419. PMC: 7779014. DOI: 10.1093/nar/gkaa913. View

11.

Kim D, Langmead B, Salzberg S . HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015; 12(4):357-60. PMC: 4655817. DOI: 10.1038/nmeth.3317. View

12.

Haas B, Salzberg S, Zhu W, Pertea M, Allen J, Orvis J . Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008; 9(1):R7. PMC: 2395244. DOI: 10.1186/gb-2008-9-1-r7. View

13.

Emms D, Kelly S . OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015; 16:157. PMC: 4531804. DOI: 10.1186/s13059-015-0721-2. View

14.

Majoros W, Pertea M, Salzberg S . TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics. 2004; 20(16):2878-9. DOI: 10.1093/bioinformatics/bth315. View

15.

Saotome K, Komatsu M . Chromosomes of Japanese starfishes. Zoolog Sci. 2002; 19(10):1095-103. DOI: 10.2108/zsj.19.1095. View

16.

Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B . AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006; 34(Web Server issue):W435-9. PMC: 1538822. DOI: 10.1093/nar/gkl200. View

17.

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

18.

Galperin M, Wolf Y, Makarova K, Vera Alvarez R, Landsman D, Koonin E . COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res. 2020; 49(D1):D274-D281. PMC: 7778934. DOI: 10.1093/nar/gkaa1018. View

19.

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

20.

Dudchenko O, Batra S, Omer A, Nyquist S, Hoeger M, Durand N . De novo assembly of the genome using Hi-C yields chromosome-length scaffolds. Science. 2017; 356(6333):92-95. PMC: 5635820. DOI: 10.1126/science.aal3327. View