Characterization of the complete mitochondrial genome of Mucor indicus Lendn. 1930 (Mucorales: Mucoraceae), isolated from the wine fermentation system

Figures & data

Figure 1. Isolation of Mucor indicus mycelia from a wine fermentation system. A photo of the species was taken by Qiang Li.

Figure 2. The circular mitochondrial genome map of Mucor indicus. Colored blocks outside each ring indicate that the genes are on the direct strand, while colored blocks within the ring indicate that the genes are located on the reverse strand. The inner grayscale bar graph shows the GC content of the mitochondrial sequences. The circle inside the GC content graph marks the 50% threshold.

Figure 3. Bayesian inference (a) and maximum likelihood (b) tree generated using 14 concatenated mitochondrial protein-coding genes (atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6) from Mucor indicus and 25 other fungal species. The support values are Bayesian posterior probabilities (BPPs) and bootstrap values (BSs). Apiotrichum gracile was used as the outgroup. The accession number information of the sequence is as follows: Linnemannia amoeboidea (MZ411570) (Yang et al. 2022), Glomus cerebriforme (KC164356) (Beaudet et al. 2013), Mucor piriformis (OW971873), Rhizophagus fasciculatus (KM586389), Rhizophagus clarus (LC506577) (Kobayashi et al. 2018), Lichtheimia hongkongensis (KJ561171) (Leung et al. 2014), Gigaspora rosea (JQ693395) (Nadimi et al. 2012), Sanchytrium tribonematis (CM032193) (Galindo et al. 2021), Apiotrichum gracile (MZ439918) (Li et al. 2023), Mucor indicus (OR664024), Glomus intraradices (FJ648425) (Lee and Young 2009), Phycomyces blakesleeanus (KR809878), Entomortierella parvispora (LC659289) (Herlambang et al. 2022), Mortierella verticillata (AY863211) (Seif et al. 2005), Podila verticillata (CM046764) (Morales et al. 2022), Absidia glauca (NC_036158) (Ellenberger et al. 2016), Apophysomyces elegans (MT047458), Rhizopus oryzae (CM022358), Zancudomyces culisetae (CM007644) (Nie et al. 2019), Parasitella parasitica (KM382275) (Ellenberger et al. 2014), Paramicrosporidium saccamoebae (CM008827) (Quandt et al. 2017), Mucor circinelloides f. lusitanicus (KR809877), Amoeboradix gromovi (CM032194) (Galindo et al. 2021), Rhizophagus irregularis (JQ514224) (Formey et al. 2012), Rhizopus oryzae (CM022329), and Gigaspora margarita (MN857242) (Venice et al. 2020).

Yang Y, Liu XY, Huang B. 2022. The complete mitochondrial genome of Linnemannia amoeboidea (W. Gams) Vandepol & Bonito (Mortierellales: mortierellaceae. Mitochondrial DNA B Resour. 7(2):374–376.) doi:10.1080/23802359.2022.2039080.

 PubMed Web of Science ®Google Scholar

Beaudet D, Terrat Y, Halary S, de la Providencia IE, Hijri M. 2013. Mitochondrial genome rearrangements in glomus species triggered by homologous recombination between distinct mtDNA haplotypes. Genome Biol Evol. 5(9):1628–1643. doi:10.1093/gbe/evt120.

 PubMed Web of Science ®Google Scholar

Kobayashi Y, Maeda T, Yamaguchi K, Kameoka H, Tanaka S, Ezawa T, Shigenobu S, Kawaguchi M. 2018. The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi. BMC Genomics. 19(1):465. doi:10.1186/s12864-018-4853-0.

 PubMedGoogle Scholar

Leung SY, Huang Y, Lau SK, Woo PC. 2014. Complete Mitochondrial Genome Sequence of Lichtheimia ramosa (syn. Lichtheimia hongkongensis. Genome Announc. 2(4):e00644-14. doi:10.1128/genomeA.00644-14.

 Google Scholar

Nadimi M, Beaudet D, Forget L, Hijri M, Lang BF. 2012. Group I intron-mediated trans-splicing in mitochondria of Gigaspora rosea and a robust phylogenetic affiliation of arbuscular mycorrhizal fungi with Mortierellales. Mol Biol Evol. 29(9):2199–2210. doi:10.1093/molbev/mss088.

 PubMed Web of Science ®Google Scholar

Galindo LJ, López-García P, Torruella G, Karpov S, Moreira D. 2021. Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota. Nat Commun. 12(1):4973. doi:10.1038/s41467-021-25308-w.

 PubMed Web of Science ®Google Scholar

Li Q, Xiao W, Wu P, Zhang T, Xiang P, Wu Q, Zou L, Gui M. 2023. The first two mitochondrial genomes from Apiotrichum reveal mitochondrial evolution and different taxonomic assignment of Trichosporonales. IMA Fungus. 14(1):7. doi:10.1186/s43008-023-00112-x.

 PubMed Web of Science ®Google Scholar

Lee J, Young JPW. 2009. The mitochondrial genome sequence of the arbuscular mycorrhizal fungus Glomus intraradices isolate 494 and implications for the phylogenetic placement of Glomus. New Phytol. 183(1):200–211. doi:10.1111/j.1469-8137.2009.02834.x.

 PubMed Web of Science ®Google Scholar

Herlambang A, Guo Y, Takashima Y, Narisawa K, Ohta H, Nishizawa T. 2022. Whole-genome sequence of Entomortierella parvispora E1425, a mucoromycotan fungus associated with burkholderiaceae-related endosymbiotic bacteria. Microbiol Resour Announc. 11(1):e0110121. doi:10.1128/mra.01101-21.

 PubMed Web of Science ®Google Scholar

Seif E, Leigh J, Liu Y, Roewer I, Forget L, Lang BF. 2005. Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms. Nucleic Acids Res. 33(2):734–744. doi:10.1093/nar/gki199.

 PubMed Web of Science ®Google Scholar

Morales DP, Robinson AJ, Pawlowski AC, Ark C, Kelliher JM, Junier P, Werner JH, Chain PSG. 2022. Advances and challenges in fluorescence in situ hybridization for visualizing fungal endobacteria. Front Microbiol. 13:892227. doi:10.3389/fmicb.2022.892227.

 PubMed Web of Science ®Google Scholar

Ellenberger S, Burmester A, Wöstemeyer J. 2016. Complete mitochondrial DNA sequence of the mucoralean fungus Absidia glauca, a model for studying host-parasite interactions. Genome Announc. 4(2):e00153-16. doi:10.1128/genomeA.00153-16.

 PubMedGoogle Scholar

Nie Y, Wang L, Cai Y, Tao W, Zhang YJ, Huang B. 2019. Mitochondrial genome of the entomophthoroid fungus Conidiobolus heterosporus provides insights into evolution of basal fungi. Appl Microbiol Biotechnol. 103(3):1379–1391. doi:10.1007/s00253-018-9549-5.

 PubMed Web of Science ®Google Scholar

Ellenberger S, Burmester A, Wöstemeyer J. 2014. Complete mitochondrial DNA sequence of the mucoralean fusion parasite Parasitella parasitica. Genome Announc. 2(6):e00912-14. doi:10.1128/genomeA.00912-14.

 PubMedGoogle Scholar

Quandt CA, Beaudet D, Corsaro D, Walochnik J, Michel R, Corradi N, James TY. 2017. The genome of an intranuclear parasite, Paramicrosporidium saccamoebae, reveals alternative adaptations to obligate intracellular parasitism. Elife. 6:e29594. doi:10.7554/eLife.29594.

 PubMed Web of Science ®Google Scholar

Formey D, Molès M, Haouy A, Savelli B, Bouchez O, Bécard G, Roux C. 2012. Comparative analysis of mitochondrial genomes of Rhizophagus irregularis: syn. Glomus irregulare: reveals a polymorphism induced by variability generating elements. New Phytol. 196(4):1217–1227. doi:10.1111/j.1469-8137.2012.04283.x.

 PubMed Web of Science ®Google Scholar

Venice F, Ghignone S, Salvioli di Fossalunga A, Amselem J, Novero M, Xianan X, Sędzielewska Toro K, Morin E, Lipzen A, Grigoriev IV, et al. 2020. At the nexus of three kingdoms: the genome of the mycorrhizal fungus Gigaspora margarita provides insights into plant, endobacterial and fungal interactions. Environ Microbiol. 22(1):122–141. doi:10.1111/1462-2920.14827.

 PubMed Web of Science ®Google Scholar

Data availability statement

The genome sequence data that support the findings of this study are openly available in the NCBI GenBank at https://www.ncbi.nlm.nih.gov/under accession no. OR664024. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA1025866, SRR26320847 and SAMN37723662, respectively.