Fodor Erika, Okendo Javan, Szabó Nóra, Szabó Kata, Czimer Dávid, Tarján-Rácz Anita, Szeverényi Ildikó, Low Bi Wei, Liew Jia Huan, Koren Sergey, Rhie Arang, Orbán László, Miklósi Ádám, Varga Máté, Burgess Shawn M
Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary.
Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
bioRxiv. 2023 Aug 10:2023.08.10.552018. doi: 10.1101/2023.08.10.552018.
Over the decades, a small number of model species, each representative of a larger taxa, have dominated the field of biological research. Amongst fishes, zebrafish () has gained popularity over most other species and while their value as a model is well documented, their usefulness is limited in certain fields of research such as behavior. By embracing other, less conventional experimental organisms, opportunities arise to gain broader insights into evolution and development, as well as studying behavioral aspects not available in current popular model systems. The anabantoid paradise fish (), an "air-breather" species from Southeast Asia, has a highly complex behavioral repertoire and has been the subject of many ethological investigations, but lacks genomic resources. Here we report the reference genome assembly of using long-read sequences at 150-fold coverage. The final assembly consisted of ≈483 Mb on 152 contigs. Within the assembled genome we identified and annotated 20,157 protein coding genes and assigned ≈90% of them to orthogroups. Completeness analysis showed that 98.5% of the Actinopterygii core gene set (ODB10) was present as a complete ortholog in our reference genome with a further 1.2 % being present in a fragmented form. Additionally, we cloned multiple genes important during early development and using newly developed hybridization protocols, we showed that they have conserved expression patterns.
几十年来，少数几个模型物种主导了生物学研究领域，每个物种都代表一个更大的分类群。在鱼类中，斑马鱼（Danio rerio）比大多数其他物种更受欢迎，虽然它们作为模型的价值已有充分记录，但在某些研究领域，如行为学研究中，其用途有限。通过采用其他不太传统的实验生物，有机会更广泛地了解进化和发育，以及研究当前流行模型系统中无法获得的行为方面。攀鲈科斗鱼（Macropodus opercularis）是一种来自东南亚的“空气呼吸者”物种，具有高度复杂的行为模式，并且一直是许多行为学研究的对象，但缺乏基因组资源。在这里，我们报告了利用150倍覆盖度的长读长序列对攀鲈科斗鱼进行的参考基因组组装。最终组装结果由152个重叠群组成，约483 Mb。在组装好的基因组中，我们鉴定并注释了20157个蛋白质编码基因，并将其中约90%分配到直系同源组。完整性分析表明，在我们的参考基因组中，98.5%的辐鳍鱼核心基因集（ODB10）以完整的直系同源形式存在，另有1.2%以片段形式存在。此外，我们克隆了多个在早期发育过程中重要的基因，并使用新开发的原位杂交方案，表明它们具有保守的表达模式。
