title: Analysis of the Mitochondrial Genome in Hypomyces aurantius Reveals a Novel Twintron Complex in Fungi.
abstract: 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.
authors.affiliation: Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China. dengyoujin1980@163.com.|Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China. dengyoujin1980@163.com.
authors.forename: Youjin
authors.initials: Y
authors.lastname: Deng
authors.affiliation: Gutian Edible Fungal Research and Development Center, Ningde 352200, China. zz23161@163.com.
authors.forename: Qihui
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Gutian Edible Fungal Research and Development Center, Ningde 352200, China. rming@life.illinois.edu.
authors.forename: Ray
authors.initials: R
authors.lastname: Ming
authors.affiliation: Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China. llj_739@yahoo.com.
authors.forename: Longji
authors.initials: L
authors.lastname: Lin
authors.affiliation: Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China. lxz0217xz@yahoo.com.
authors.forename: Xiangzhi
authors.initials: X
authors.lastname: Lin
authors.affiliation: Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China. yy130816@yahoo.com.
authors.forename: Yiying
authors.initials: Y
authors.lastname: Lin
authors.affiliation: Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China. nevereverveer123@126.com.
authors.forename: Xiao
authors.initials: X
authors.lastname: Li
authors.affiliation: Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China. mrcfafu@163.com.
authors.forename: Baogui
authors.initials: B
authors.lastname: Xie
authors.affiliation: Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China. zwenfafu@163.com.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Wen
mesh_terms: D054629:Genome, Mitochondrial; D006999:Hypocreales / Q000235:genetics*; D007438:Introns; D008928:Mitochondria / Q000235:genetics; D024101:Mitochondrial Proteins / Q000145:classification / Q000378:metabolism; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D010802:Phylogeny; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D024101:Mitochondrial Proteins; D012343:RNA, Transfer
keywords: ORF; cobweb disease; homing endonuclease; intron