Analyses of the Complete Mitochondrial Genome of Paraconiothyrium sp. and Gene Rearrangement Diversity in the Pleosporales

The Pleosporales is the most predominant order in the Dothideomycetes class, which contains over 4700 species that function in a variety of ways. The material used in this research was previously isolated from the Chinese white wax scale insect, and it was determined to be a Paraconiothyrium genus species that belonged to the Pleosporales order. For further molecular analysis, we assembled the complete mitochondrial genome of Paraconiothyrium sp. based on short reads of BGISEQ sequencing and subreads from Pacbio sequencing. The results showed that it was 42,734 bp in length and contained 8 open reading frames, 12 protein-coding genes and 31 non-coding genes. Phylogenetic analysis showed it was affiliated to the Pleosporales order and formed a sister relationship with Pithomyces chartarum. Compared to the seven other species in the Pleosporales order, Paraconiothyrium sp. has generally conserved gene content and structure, while the homologous blocks and gene order were shown to be significantly rearranged, in accordance with the species diversity in the Pleosporales order. In this study, we presented the first mitochondrial genome of Paraconiothyrium fungi to be reported, and we also showed gene order diversity in the Pleosporales order. These findings will lay the foundation for further species studies regarding molecular diversity and our understanding of species characteristics in the Paraconiothyrium genus.

[1]  Pu Yang,et al.  Two Cladosporium Fungi with Opposite Functions to the Chinese White Wax Scale Insect Have Different Genome Characters , 2022, Journal of fungi.

[2]  Pu Yang,et al.  Genomic Analyses of the Fungus Paraconiothyrium sp. Isolated from the Chinese White Wax Scale Insect Reveals Its Symbiotic Character , 2022, Genes.

[3]  Xiaojun Yan,et al.  Cytotoxic Polyketide Metabolites from a Marine Mesophotic Zone Chalinidae Sponge-Associated Fungus Pleosporales sp. NBUF144 , 2021, Marine drugs.

[4]  John-James Wilson,et al.  Evolution of tRNA gene rearrangement in the mitochondrial genome of ichneumonoid wasps (Hymenoptera: Ichneumonoidea). , 2020, International journal of biological macromolecules.

[5]  Jun Deng,et al.  The challenge of Coccidae (Hemiptera: Coccoidea) mitochondrial genomes: The case of Saissetia coffeae with novel truncated tRNAs and gene rearrangements. , 2020, International journal of biological macromolecules.

[6]  Fei Cao,et al.  Dipleosporalones A and B, Dimeric Azaphilones from a Marine-Derived Pleosporales sp. Fungus. , 2020, Journal of natural products.

[7]  Xiao-Long Yuan,et al.  Characterization of Nuclear and Mitochondrial Genomes of Two Tobacco Endophytic Fungi Leptosphaerulina chartarum and Curvularia trifolii and Their Contributions to Phylogenetic Implications in the Pleosporales , 2020, International journal of molecular sciences.

[8]  Q. Song,et al.  Genome sequence of the Chinese white wax scale insect Ericerus pela: the first draft genome for the Coccidae family of scale insects , 2019, GigaScience.

[9]  Akiko Okusu,et al.  Molecular phylogenetics of Aspidiotini armored scale insects (Hemiptera: Diaspididae) reveals rampant paraphyly, curious species radiations, and multiple origins of association with Melissotarsus ants (Hymenoptera: Formicidae). , 2018, Molecular phylogenetics and evolution.

[10]  J. Fletcher,et al.  Annotation and analysis of the mitochondrial genome of Coniothyrium glycines, causal agent of red leaf blotch of soybean, reveals an abundance of homing endonucleases , 2018, PloS one.

[11]  Xingzhong Liu,et al.  Hawaiienols A-D, Highly Oxygenated p-Terphenyls from an Insect-Associated Fungus, Paraconiothyrium hawaiiense. , 2018, Journal of natural products.

[12]  Pu Yang,et al.  A Lethal Fungus Infects the Chinese White Wax Scale Insect and Causes Dramatic Changes in the Host Microbiota , 2018, Scientific Reports.

[13]  Jian Wang,et al.  SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data , 2017, GigaScience.

[14]  Niranjan Nagarajan,et al.  Fast and accurate de novo genome assembly from long uncorrected reads. , 2017, Genome research.

[15]  S. Baker,et al.  The mitochondrial genome of the ethanol-metabolizing, wine cellar mold Zasmidium cellare is the smallest for a filamentous ascomycete. , 2016, Fungal biology.

[16]  Pu Yang,et al.  Identification and evaluation of reference genes in the Chinese white wax scale insect Ericerus pela , 2016, SpringerPlus.

[17]  G. Sung,et al.  Complete mitochondrial genome of the entomopathogenic fungus Beauveria pseudobassiana (Ascomycota, Cordycipitaceae) , 2015, Mitochondrial DNA.

[18]  L. Fan,et al.  Characterization and Phylogenetic Analysis of the Mitochondrial Genome of Shiraia bambusicola Reveals Special Features in the Order of Pleosporales , 2015, PloS one.

[19]  Pu Yang,et al.  Transcriptome Analysis of Sexually Dimorphic Chinese White Wax Scale Insects Reveals Key Differences in Developmental Programs and Transcription Factor Expression , 2015, Scientific Reports.

[20]  Lei Wang,et al.  Paraconfuranones A–H, eight new furanone analogs from the insect‐associated fungus Paraconiothyrium brasiliense MZ‐1 , 2015, Magnetic resonance in chemistry : MRC.

[21]  Pu Yang,et al.  Protein profiles of Chinese white wax scale, Ericerus pela, at the male pupal stage by high-throughput proteomics. , 2014, Archives of insect biochemistry and physiology.

[22]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[23]  Pu Yang,et al.  Transcriptome Analysis of the Chinese White Wax Scale Ericerus pela with Focus on Genes Involved in Wax Biosynthesis , 2012, PloS one.

[24]  P. Crous,et al.  Fungi associated with die-back symptoms of apple and pear trees, a possible inoculum source of grapevine trunk disease pathogens , 2011 .

[25]  K. Hyde,et al.  Pleosporales , 2011, Fungal Diversity.

[26]  Sunggil Kim,et al.  Identification of mitochondrial genome rearrangements unique to novel cytoplasmic male sterility in radish (Raphanus sativus L.) , 2009, Theoretical and Applied Genetics.

[27]  Luciano Digiampietri,et al.  The mitochondrial genome of the phytopathogenic basidiomycete Moniliophthora perniciosa is 109 kb in size and contains a stable integrated plasmid. , 2008, Mycological research.

[28]  C. Hon,et al.  The mitochondrial genome of the Basidiomycete fungus Pleurotus ostreatus (oyster mushroom). , 2008, FEMS microbiology letters.

[29]  Afshan Mohajeri,et al.  Detection and evaluation of hydrogen bond strength in nucleic acid base pairs. , 2008, The journal of physical chemistry. A.

[30]  S. LaGreca,et al.  New bottles for old wine: fruit body types, phylogeny, and classification. , 2007, Mycological research.

[31]  O. Eriksson,et al.  Phylogenetic relationships of coprophilous Pleosporales (Dothideomycetes, Ascomycota), and the classification of some bitunicate taxa of unknown position. , 2006, Mycological research.

[32]  A. Keszthelyi,et al.  Differences in Mitochondrial Genome Organization of Cryptococcus Neoformans Strains , 2005, Antonie van Leeuwenhoek.

[33]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[34]  N. O'neill,et al.  Molecular phylogeny of Leptosphaeria and Phaeosphaeria , 2002, Mycologia.

[35]  K. Hyde,et al.  Phylogenetic significance of the pseudoparaphyses in Loculoascomycete taxonomy. , 2000, Molecular phylogenetics and evolution.

[36]  Y. Zhang,et al.  Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation , 2009, Studies in mycology.

[37]  P. Kittakoop,et al.  Diketopiperazines and phthalides from a marine derived fungus of the order pleosporales. , 2008, Planta medica.