Transcriptome mining is a powerful tool for gene discovery in plant sciences. Biosynthetic enzyme transcripts of specialized metabolites have been isolated using transcriptome datasets of non-model plants; however, this methodology has not been applied to fern metabolites. Herein, we attempted to isolate transcripts of squalene cyclases from the Lygodium japonicum transcriptome database. A BLAST search revealed the presence of four isotigs (12872, 12873, 33018, and 33763) annotated as squalene cyclase, two of which contained full-length open-reading frame sequences. However, both isotigs failed to be amplified; our investigation revealed them to be chimeric sequences due to incorrect assembly. We also revealed that part of isotigs 12873 and 33018 constituted a single gene, designated LJH. Conversely, homology-based PCR resulted in the isolation of a squalene cyclase homolog, LjSCx, distinct from the four isotigs. Biochemical characterization of LJH and LjSCx revealed that LJH is a hopene synthase gene and LjSCx is a pseudogene. These findings highlight the usefulness and limitations of transcriptome datasets, especially with respect to genes comprising a gene family.

转录组挖掘是植物科学中基因发现的强大工具。使用非模型植物的转录组数据集已经分离出了专门代谢物的生物合成酶转录本。但是，该方法尚未应用于蕨类代谢产物。在这里，我们试图从日本忍冬（Lygodium japonicum）转录组数据库中分离出角鲨烯环化酶的转录本。BLAST搜索显示存在四个标注为角鲨烯环化酶的异构体（12872、12873、33018和33763），其中两个包含全长开放阅读框序列。但是，两个isotig均未扩增。我们的调查显示，由于装配错误，它们是嵌合序列。我们还发现，isotigs 12873和33018的一部分构成了单个基因，称为LJH。相反，基于同源性PCR产生了角鲨烯环化酶同系物，的隔离LjSCx，从四个不同isotigs。LJH和LjSCx的生化特征表明LJH是一个希望合酶基因，而LjSCx是一个假基因。这些发现突出了转录组数据集的有用性和局限性，特别是对于包含基因家族的基因而言。