食线虫真菌洛斯里被毛孢线粒体基因组的再分析

Reanalysis of the mitochondrial genome of the nematophagous fungus Hirsutella rhossiliensis

摘要:

[目的]鉴定洛斯里被毛孢OWVT-1菌株的线粒体基因组，验证公布的USA-87-5菌株线粒体基因组中的错误，对洛斯里被毛孢正确的线粒体基因组序列进行注释并开展不同被毛孢物种间的比较线粒体基因组学分析。[方法]借助DNA高通量测序数据并通过必要的Sanger测序组装OWVT-1的线粒体基因组。通过PCR验证OWVT-1与公布的USA-87-5线粒体基因组序列差异的真实性。利用多种生物信息方法分析和注释洛斯里被毛孢的线粒体基因组。[结果]公布的洛斯里被毛孢USA-87-5菌株的线粒体基因组存在几处序列错误，包括3处长片段的插入缺失和多处短片段的插入缺失。实际上，洛斯里被毛孢USA-87-5与OWVT-1菌株的线粒体基因组序列完全相同。该菌的线粒体基因组全长62949 bp，在7个基因中共插入13个内含子，部分内含子和基因间区显现出序列退化的特征。洛斯里被毛孢、明尼苏达被毛孢、线虫被毛孢的线粒体基因组具有较强的共线性关系。除一些独立的ORF外，核心蛋白编码基因、rRNA基因和tRNA基因的排列顺序非常保守。基因间区的长短是影响3种被毛孢线粒体基因组大小最主要的因素。[结论]公布的洛斯里被毛孢USA-87-5菌株线粒体基因组中存在序列错误。本文新报道了OWVT-1菌株的线粒体基因组，并进行注释和比较线粒体基因组学分析。

Abstract:

[Objective] To identify the mitochondrial genome (mitogenome) of Hirsutella rhossiliensis OWVT-1 strain, verify erroneous sequences present in the published USA-87-5 mitogenome, and perform comparative mitogenomic analyses of three Hirsutella species.[Methods] The OWVT-1 mitogenome was assembled based on high-throughput DNA sequencing data and Sanger sequencing. PCR assays were performed to verify 3 long varying regions observed during alignment between the published USA-87-5 mitogenome and OWVT-1 mitogenome assembled in this study. Bioinformatics analyses were used to annotate the mitogenome sequence of OWVT-1.[Results] We detected several sequence errors in the published USA-87-5 mitogenome, including long sequence insertions/deletions and small indels. The mitogenomes of OWVT-1 and USA-87-5 were identical without any nucleotide difference. The complete mitogenome of H. rhossiliensis was 62949 bp in length, with 13 introns in seven genes. Several introns and intergenic regions seemed to have degenerated. The mitogenomes of H. rhossiliensis, H. vermicola, and H. minnesotensis showed a high synteny. Except free-standing ORFs, the gene order of core protein-encoding genes, rRNA genes, and tRNA genes were highly conserved among the three Hirsutella mitogenomes. The length at intergenic regions was a main factor affecting mitogenome sizes of different Hirsutella species.[Conclusion] There were erroneous sequences in the published USA-87-5 mitogenome. We reported the authentic mitogenome sequence of H. rhossiliensis using the highly virulent strain OWVT-1.