Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA.
G3 (Bethesda). 2021 Dec 8;11(12). doi: 10.1093/g3journal/jkab306.
The fish order Syngnathiformes has been referred to as a collection of misfit fishes, comprising commercially important fish such as red mullets as well as the highly diverse seahorses, pipefishes, and seadragons-the well-known family Syngnathidae, with their unique adaptations including male pregnancy. Another ornate member of this order is the species mandarinfish. No less than two types of chromatophores have been discovered in the spectacularly colored mandarinfish: the cyanophore (producing blue color) and the dichromatic cyano-erythrophore (producing blue and red). The phylogenetic position of mandarinfish in Syngnathiformes, and their promise of additional genetic discoveries beyond the chromatophores, made mandarinfish an appealing target for whole-genome sequencing. We used linked sequences to create synthetic long reads, producing a highly contiguous genome assembly for the mandarinfish. The genome assembly comprises 483 Mbp (longest scaffold 29 Mbp), has an N50 of 12 Mbp, and an L50 of 14 scaffolds. The assembly completeness is also high, with 92.6% complete, 4.4% fragmented, and 2.9% missing out of 4584 BUSCO genes found in ray-finned fishes. Outside the family Syngnathidae, the mandarinfish represents one of the most contiguous syngnathiform genome assemblies to date. The mandarinfish genomic resource will likely serve as a high-quality outgroup to syngnathid fish, and furthermore for research on the genomic underpinnings of the evolution of novel pigmentation.
鲈形目鱼类被称为一群不匹配的鱼类，包括商业上重要的鱼类，如红鲻鱼，以及高度多样化的海马、海龙和海龙科，它们具有独特的适应性，包括雄性怀孕。这个目还有一个华丽的成员是mandarinfish（苏眉鱼）。在色彩斑斓的苏眉鱼中发现了不少于两种类型的色素细胞：蓝素细胞（产生蓝色）和双色氰基-红细胞素（产生蓝色和红色）。苏眉鱼在鲈形目中的系统发育位置，以及它们在色素细胞之外的潜在遗传发现，使得苏眉鱼成为全基因组测序的一个有吸引力的目标。我们使用连锁序列来创建合成长读长，为苏眉鱼产生了一个高度连续的基因组组装。基因组组装包含 4.83 亿个碱基对（最长支架 2900 万个碱基对），N50 为 1200 万个碱基对，L50 为 14 个支架。组装的完整性也很高，在 4584 个发现于硬骨鱼类的 BUSCO 基因中，有 92.6%完整，4.4%碎片化，2.9%缺失。在海龙科之外，苏眉鱼是迄今为止最连续的鲈形目基因组组装之一。苏眉鱼的基因组资源可能成为海龙鱼类的高质量外群，并且进一步研究新颖色素形成的基因组基础。
