A first genome survey sequencing of alvinocaridid shrimp Shinkaicaris leurokolos in deep-sea hydrothermal vent environment

Abstract

Abstract The alvinocaridid shrimp Shinkaicaris leurokolos Kikuchi and Hashimoto, 2000, is an evolutionarily important deep-sea species in hydrothermal vents of north-western Pacific. A genome survey of S. leurokolos was carried out in order to provide a foundation for its whole-genome sequencing. A total of 599 Gb high-quality sequence data were obtained in the study, representing approximately 118× coverage of the S. leurokolos genome. According to the 17-mer distribution frequency, the estimated genome size was 5.08 Gb, and its heterozygosity ratio and percentage of repeated sequences were 2.85 and 87.03%, respectively, showing a complex genome. The final scaffold assembly accounted for a total size of 9.53 Gb (32,796,062 scaffolds, N50 = 597 bp). Repetitive elements nearly constituted 45% of the nuclear genome, among which the most ubiquitous were long interspersed nuclear elements, DNA transposons and long-terminal repeat elements. A total of 12,121,553 genomic simple sequence repeats were identified, with the most frequent repeat motif being di-nucleotide (70.27%), followed by tri-nucleotide and tetra-nucleotide. From the genome survey sequences, the mitochondrial genome of S. leurokolos was also constructed and 71 single nucleotide polymorphisms were identified by comparison with previous published reference. This is the first report of de novo whole-genome sequencing and assembly of S. leurokolos. These newly developed genomic data contribute to a better understanding of genomic characteristics of shrimps from deep-sea chemosynthetic ecosystems, and provides valuable resources for further molecular marker development.