De Novo Genome Assembly of the Sea Star Patiria pectinifera (Muller & Troschel, 1842) Using Oxford Nanopore Technology and Illumina Platforms

Abstract

The sea star Patiria pectinifera (Asteroidea; Asterinidae; homotypic synonym: Asterina pectinifera; Muller & Troschel, 1842) is widely distributed in the coastal regions of the Seas of East Asia and the northern Pacific Ocean. Here, a de novo genome sequence of P. pectinifera as a reference for fundamental and applied research was constructed by employing a combination of long-read Oxford Nanopore Technology (ONT) PromethION, short-read Illumina platforms, and 10 × Genomics. The draft genome of P. pectinifera, containing 13,848,344 and 156,878,348 contigs from ONT and Illumina platforms, respectively, was obtained. Assembly with CANU resulted in 2262 contigs with an N50 length of 367 kb. Finally, ARCS + LINKS assembly combined these contigs into 328 scaffolds, totaling 499 Mb with an N50 length of 2 Mbp. The estimated genome size by GenomeScope analysis was 461 Mb. BUSCO analysis indicated that 930 (97.5%) of the expected genes were found in the assembly, with 889 (93.2%) being single-copy and 41 (4.3%) duplicated after searching against the metazoan database. Annotation, utilizing sequences obtained from Illumina RNA-Seq and Pacific Biosciences Iso-Seq, led to the identification of 22,367 protein-coding genes. When examining the orthologous relationship of P. pectinifera against the scaffolds of the common sea star Patiria miniata, high contiguity was observed. Annotation of repeat elements highlighted an enrichment of 1,121,079 transposable elements, constituting 47% of the genome, suggesting their potential role in shaping the genome structure of P. pectinifera. This de novo genome assembly is expected to be a valuable resource for future studies, providing insight into the developmental, environmental, and ecological aspects of P. pectinifera biology.