title: Analysis of the complete mitochondrial genome of Pochonia chlamydosporia suggests a close relationship to the invertebrate-pathogenic fungi in Hypocreales.
abstract: BACKGROUND
  The fungus Pochonia chlamydosporia parasitizes nematode eggs and has become one of the most promising biological control agents (BCAs) for plant-parasitic nematodes, which are major agricultural pests that cause tremendous economic losses worldwide. The complete mitochondrial (mt) genome is expected to open new avenues for understanding the phylogenetic relationships and evolution of the invertebrate-pathogenic fungi in Hypocreales.
  
  
  RESULTS
  The complete mitogenome sequence of P. chlamydosporia is 25,615 bp in size, containing the 14 typical protein-coding genes, two ribosomal RNA genes, an intronic ORF coding for a putative ribosomal protein (rps3) and a set of 23 transfer RNA genes (trn) which recognize codons for all amino acids. Sequence similarity studies and syntenic gene analyses show that 87.02% and 58.72% of P. chlamydosporia mitogenome sequences match 90.50% of Metarhizium anisopliae sequences and 61.33% of Lecanicillium muscarium sequences with 92.38% and 86.04% identities, respectively. A phylogenetic tree inferred from 14 mt proteins in Pezizomycotina fungi supports that P. chlamydosporia is most closely related to the entomopathogenic fungus M. anisopliae. The invertebrate-pathogenic fungi in Hypocreales cluster together and clearly separate from a cluster comprising plant-pathogenic fungi (Fusarium spp.) and Hypocrea jecorina. A comparison of mitogenome sizes shows that the length of the intergenic regions or the intronic regions is the major size contributor in most of mitogenomes in Sordariomycetes. Evolutionary analysis shows that rps3 is under positive selection, leading to the display of unique evolutionary characteristics in Hypocreales. Moreover, the variability of trn distribution has a clear impact on gene order in mitogenomes. Gene rearrangement analysis shows that operation of transposition drives the rearrangement events in Pezizomycotina, and most events involve in trn position changes, but no rearrangement was found in Clavicipitaceae.
  
  
  CONCLUSIONS
  We present the complete annotated mitogenome sequence of P. chlamydosporia. Based on evolutionary and phylogenetic analyses, we have determined the relationships between the invertebrate-pathogenic fungi in Hypocreales. The invertebrate-pathogenic fungi in Hypocreales referred to in this paper form a monophyletic group sharing a most recent common ancestor. Our rps3 and trn gene order results also establish a foundation for further exploration of the evolutionary trajectory of the fungi in Hypocreales.
authors: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. linrm2010@gmail.com.
authors: Runmao
authors: R
authors: Lin
authors: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. chichuanliu@hotmail.com.
authors: Chichuan
authors: C
authors: Liu
authors: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. baobao8759@163.com.|College of Plant Protection, Hunan Agricultural University, Changsha, Hunan Province, 410128, China. baobao8759@163.com.
authors: Baoming
authors: B
authors: Shen
authors: Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, Hunan Province, 410128, China. baimiao2010@gmail.com.
authors: Miao
authors: M
authors: Bai
authors: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. lingjian2005@126.com.
authors: Jian
authors: J
authors: Ling
authors: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. chenguohua01@caas.cn.
authors: Guohua
authors: G
authors: Chen
authors: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. maozhenchuan@caas.cn.
authors: Zhenchuan
authors: Z
authors: Mao
authors: College of Life Sciences, Beijing Normal University, Beijing, 100875, China. chengxy@bnu.edu.cn.
authors: Xinyue
authors: X
authors: Cheng
authors: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. xiebingyan@caas.cn.
authors: Bingyan
authors: B
authors: Xie
mesh_terms: D016000:Cluster Analysis; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics*; D023061:Gene Order; D005800:Genes, Fungal; D054629:Genome, Mitochondrial; D006999:Hypocreales / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D026801:Synteny
chemical_list: D004271:DNA, Fungal; D004272:DNA, Mitochondrial
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