Deng Youjin, Zhang Qihui, Ming Ray, Lin Longji, Lin Xiangzhi, Lin Yiying, Li Xiao, Xie Baogui, Wen Zhiqiang
Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
Int J Mol Sci. 2016 Jun 30;17(7):1049. doi: 10.3390/ijms17071049.
Hypomyces aurantius is a mycoparasite that causes cobweb disease, a most serious disease of cultivated mushrooms. Intra-species identification is vital for disease control, however the lack of genomic data makes development of molecular markers challenging. Small size, high copy number, and high mutation rate of fungal mitochondrial genome makes it a good candidate for intra and inter species differentiation. In this study, the mitochondrial genome of H. H.a0001 was determined from genomic DNA using Illumina sequencing. The roughly 72 kb genome shows all major features found in other Hypocreales: 14 common protein genes, large and small subunit rRNAs genes and 27 tRNAs genes. Gene arrangement comparison showed conserved gene orders in Hypocreales mitochondria are relatively conserved, with the exception of Acremonium chrysogenum and Acremonium implicatum. Mitochondrial genome comparison also revealed that intron length primarily contributes to mitogenome size variation. Seventeen introns were detected in six conserved genes: five in cox1, four in rnl, three in cob, two each in atp6 and cox3, and one in cox2. Four introns were found to contain two introns or open reading frames: cox3-i2 is a twintron containing two group IA type introns; cox2-i1 is a group IB intron encoding two homing endonucleases; and cox1-i4 and cox1-i3 both contain two open reading frame (ORFs). Analyses combining secondary intronic structures, insertion sites, and similarities of homing endonuclease genes reveal two group IA introns arranged side by side within cox3-i2. Mitochondrial data for H. aurantius provides the basis for further studies relating to population genetics and species identification.
橙黄被毛孢是一种可引发蛛网病的真菌寄生菌，蛛网病是栽培蘑菇最严重的病害之一。种内鉴定对于病害防治至关重要，然而缺乏基因组数据使得分子标记的开发具有挑战性。真菌线粒体基因组体积小、拷贝数高且突变率高，使其成为种内和种间分化的良好候选对象。在本研究中，利用Illumina测序从基因组DNA中确定了橙黄被毛孢H. H.a0001的线粒体基因组。这个约72 kb的基因组展现出了在其他肉座菌目中发现的所有主要特征：14个常见蛋白质基因、大、小亚基rRNA基因以及27个tRNA基因。基因排列比较显示，除产黄顶孢和隐顶孢外，肉座菌目线粒体中的基因顺序相对保守。线粒体基因组比较还表明，内含子长度是导致有丝分裂基因组大小变化的主要因素。在6个保守基因中检测到17个内含子：cox1中有5个，rnl中有4个，cob中有3个，atp6和cox3中各有2个，cox2中有1个。发现4个内含子含有两个内含子或开放阅读框：cox3-i2是一个双内含子，包含两个IA型内含子；cox2-i1是一个IB型内含子，编码两种归巢内切酶；cox1-i4和cox1-i3都包含两个开放阅读框（ORF）。结合二级内含子结构、插入位点和归巢内切酶基因相似性的分析揭示，cox3-i2内有两个IA型内含子并排排列。橙黄被毛孢的线粒体数据为进一步开展群体遗传学和物种鉴定研究提供了基础。
