DataSheet_1_Chromosome-level genome assembly of the yellow boxfish (Ostracion cubicus) provides insights into the evolution of bone plates and ostracitoxin secretion.docx

The Ostracion cubicus, commonly known as the yellow boxfish, is a remarkable species with a body encased in a bone plate and the ability to produce an ostracitoxin from their skin when under stress. However, the genetic basis of those effective defense traits is still largely unknown due to the lack of genomic resources. Here, we assembled the first chromosome-level genome of O. cubicus with 867.50 Mb in genome size and 34.86 Mb N50 scaffold length by HiFi and Hi-C sequencing. Twenty-five pseudo-chromosomes, numbered according to size, covered 94.13% of the total assembled sequences. A total of 23,224 protein-coding genes were predicted, with a BUSCO completeness of 98.6%. Positive selection or rapid evolution was observed in genes related to scale and bone development (acsl4a, casr, keap1a, tbx1), and up-regulation of transcription was found in the skin of boxfish (bmp1, bmp2k, bmp4, bmp7, smad5, suco, prelp, mitf), likely associated with the bone plates evolution in the yellow boxfish. An expansion of the solute carrier family 22, a cluster of genes in solute carrier (SLCs) family, transmembrane protein family (TMEMs), vesicle trafficking (SECs), ATP-binding cassette (ABCs) and apolipoproteins (APOs) were identified under positive selection, rapid evolution, or up-regulated in the skin of boxfish, likely associated with the ostracitoxin secretion in the yellow boxfish. Our study not only presents a high-quality boxfish genome but also provides insights into bone plates evolution and ostracitoxin secretion of O. cubicus.

粒突箱鲀（Ostracion cubicus），俗称黄盒子鱼，是一类极具特色的物种：其躯体被骨板包裹，且在应激状态下可通过皮肤分泌箱鲀毒素（ostracitoxin）。然而，由于基因组研究资源的匮乏，这类高效防御性状的遗传基础目前仍在很大程度上尚不明确。本研究通过HiFi测序与Hi-C测序技术，组装获得了粒突箱鲀（O. cubicus）首个染色体级别的基因组，基因组大小为867.50 Mb，支架序列（scaffold）N50长度为34.86 Mb。研究共得到25条伪染色体，按长度排序后覆盖了总组装序列的94.13%。本研究共预测得到23224个蛋白质编码基因，经BUSCO评估的基因组完整度达98.6%。分析显示，与鳞片和骨发育相关的基因（acsl4a、casr、keap1a、tbx1）受到正选择或呈现快速进化特征；同时，黄盒子鱼皮肤中存在转录上调的基因（bmp1、bmp2k、bmp4、bmp7、smad5、suco、prelp、mitf），这类基因可能与粒突箱鲀的骨板演化密切相关。此外，本研究鉴定到溶质载体家族22、溶质载体（SLCs）家族基因簇、跨膜蛋白家族（TMEMs）、囊泡运输相关SEC家族（SECs）、ATP结合盒式蛋白家族（ABCs）以及载脂蛋白家族（APOs）的基因扩张事件；上述基因类群或受到正选择、或呈现快速进化特征，或在黄盒子鱼皮肤中存在转录上调，这可能与粒突箱鲀的箱鲀毒素分泌过程紧密相关。本研究不仅获得了高质量的黄盒子鱼基因组，同时为解析粒突箱鲀的骨板演化与箱鲀毒素分泌机制提供了关键见解。