Supporting data for "Genome Assembly of the Roundjaw Bonefish (Albula glossodonta), a Vulnerable Circumtropical Sportfish"

Bonefishes are cryptic species indiscriminately targeted by subsistence and recreational fisheries worldwide. The roundjaw bonefish, <i>Albula glossodonta</i>, is the most widespread bonefish species in the Indo-Pacific and is listed as vulnerable to extinction by the IUCNs Red List due to anthropogenic activities. Whole-genome datasets allow for improved population and species delimitation, which - prior to this study - were lacking for <i>Albula</i> species. <br>We generated a high-quality genome assembly of an <i>A. glossodonta</i> individual from Hawaii, USA. The 1.05 Gbp contig-level assembly had an NG50 of 4.75 Mbp and a maximum length of 28.2 Mbp. Scaffolding yielded an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. Half the genome was contained in 20 scaffolds. The genome was comprised of 6.5% repetitive elements, and it was annotated with 28.3 K protein-coding genes. We then analyzed 66 <i>A. glossodonta</i> individuals and 38,355 SNP loci to evaluate population genetic connectivity between six atolls in Seychelles and Mauritius in the Western Indian Ocean. We observed genetic homogeneity between atolls in Seychelles and evidence of reduced gene flow between Seychelles and Mauritius. The South Equatorial Current could be one mechanism limiting gene flow of <i>A. glossodonta</i> populations between Seychelles and Mauritius. <br>Quantifying the spatial population structure of widespread fishery species such as bonefishes is necessary for effective transboundary management and conservation. This population genomic dataset mapped to a high-quality genome assembly allowed us to discern shallow population structure in a widespread species in the Western Indian Ocean. The genome assembly will be useful for addressing the taxonomic uncertainties of bonefishes globally.

北梭鱼属于隐存种，在全球范围内被自给性渔业与休闲渔业无差别捕捞。圆颌北梭鱼（*Albula glossodonta*）是印度-太平洋分布最广的北梭鱼物种，由于人为活动影响，被国际自然保护联盟（IUCN）红色名录列为易危物种。全基因组数据集有助于优化种群与物种界定，而在本研究开展前，北梭鱼属（*Albula*）物种的相关研究仍较为匮乏。
本研究对采自美国夏威夷的1尾圆颌北梭鱼个体进行了高质量基因组组装。该重叠群（contig）水平的基因组组装总长1.05吉碱基对（Gbp），NG50值为4.75兆碱基对（Mbp），最长重叠群长度达28.2 Mbp。经过支架构建（scaffolding）后，组装的NG50值提升至14.49 Mbp，最长支架长度达42.29 Mbp，仅20个支架即可覆盖基因组一半的序列。该基因组重复序列占比为6.5%，共注释得到28300个蛋白质编码基因。
随后，我们对66尾圆颌北梭鱼个体与38355个单核苷酸多态性（SNP）位点进行分析，以评估西印度洋塞舌尔与毛里求斯境内6座环礁间的种群遗传连通性。研究结果显示，塞舌尔境内各环礁间存在遗传同质性，而塞舌尔与毛里求斯种群间的基因流显著减弱。南赤道流可能是限制塞舌尔与毛里求斯圆颌北梭鱼种群间基因交流的潜在因素之一。
对北梭鱼这类广布渔业物种开展空间种群结构量化研究，是实现高效跨界管理与物种保护的必要前提。依托高质量基因组组装比对得到的种群基因组数据集，我们得以解析西印度洋该广布物种的微弱种群结构。该基因组组装结果将有助于解决全球范围内北梭鱼的分类学争议问题。