Hildahl Tami, Saillant Eric
School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, 39564, USA.
Mol Biol Rep. 2025 Jan 3;52(1):99. doi: 10.1007/s11033-024-10195-3.
The gray snapper (Lutjanus griseus) is a marine reef fish commonly found in coastal and shelf waters of the tropical and subtropical western Atlantic Ocean. In this work, a draft reference genome was developed to support population genomic studies of gray snapper needed to assist with conservation and fisheries management efforts.
Hybrid assembly of PacBio and Illumina sequencing reads yielded a 1,003,098,032 bp reference across 2039 scaffolds with N50 and L50 values of 1,691,591 bp and 163 scaffolds, respectively. A linkage map was generated by genotyping parents and 286 offspring of a single pair cross using the double digest Restriction Associated DNA (ddRAD) protocol. The map featured 10,965 informative markers that were assigned to 24 linkage groups and used to scaffold the assembly. The anchored assembly spanned 962,844,722 bp (N50 = 41,865,368 bp, L50 = 11 scaffolds) in 24 pseudo chromosomes and yielded a BUSCO score of 95.2%. Annotation of the final assembly in Augustus revealed 39,070 candidate genes. Gene ontology annotation was obtained for 48.8% of the predicted genes. Analysis of shared syntenic regions revealed that each gray snapper chromosome matched a unique Japanese medaka, Oryzias latipes, counterpart and the reference showed a high degree of synteny with the closely related Lutjanus erythropterus assembly.
This resource will greatly enhance genomic studies of conservation and management of natural populations as well as efforts to develop breeding programs for this species and other lutjanids.
灰笛鲷（Lutjanus griseus）是一种常见于热带和亚热带西大西洋沿海及陆架水域的海洋礁鱼。在本研究中，我们构建了一个参考基因组草图，以支持灰笛鲷种群基因组研究，为保护和渔业管理工作提供帮助。
通过对PacBio和Illumina测序读段进行混合组装，获得了一个长度为1,003,098,032 bp的参考基因组，分布在2039个支架上，N50和L50值分别为1,691,591 bp和163个支架。利用双酶切限制性内切酶相关DNA（ddRAD）方法对一对亲本及其286个后代进行基因分型，构建了一个连锁图谱。该图谱包含10,965个信息性标记，被分配到24个连锁群中，并用于支架组装。锚定组装后的基因组跨度为962,844,722 bp（N50 = 41,865,368 bp，L50 = 11个支架），分布在24条假染色体上，BUSCO评分为95.2%。利用Augustus对最终组装结果进行注释，共发现39,070个候选基因。48.8%的预测基因获得了基因本体注释。对共享同线性区域的分析表明，每条灰笛鲷染色体都与日本青鳉（Oryzias latipes）的一条独特对应染色体相匹配，且该参考基因组与近缘的红鳍笛鲷（Lutjanus erythropterus）组装结果显示出高度的同线性。
该资源将极大地促进对自然种群保护和管理的基因组研究，以及为该物种和其他笛鲷科鱼类制定育种计划的工作。
