Mitochondrial Genomic Characteristics and Phylogenetic Analysis of a Brewing Fungus, Tiegh. 1875 (Mucorales: Rhizopodaceae)

Overview

Journal Mitochondrial DNA B Resour

Date 2024 May 22

PMID 38774188

Authors

Yue Deng

Guangjiu Chen

Xuedong Bao

Jie He

Qiang Li

Affiliations

Soon will be listed here.

Abstract

Tiegh. 1875 is widely used in a variety of industries, such as brewing, wine making, baking, and medicine production, as it has the capability to break down proteins and generate surface-active agents. To date, the mitochondrial genome features of early evolved fungi from the genus have not been extensively studied. Our research obtained a full mitochondrial genome of species, which was 43,837 bp in size and had a GC content of 24.93%. This genome contained 14 core protein-coding genes, 3 independent ORFs, 7 intronic ORFs, 24 tRNAs, and 2 rRNA genes. Through the use of the BI phylogenetic inference method, we were able to create phylogenetic trees for 25 early differentiation fungi which strongly supported the major clades; this indicated that is most closely related to .

References

Nguyen M, Kaul D, Muto C, Cheng S, Richter R, Bruno V . Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients. Microb Genom. 2020; 6(12). PMC: 8116672. DOI: 10.1099/mgen.0.000473. View

Lohse M, Drechsel O, Kahlau S, Bock R . OrganellarGenomeDRAW--a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 2013; 41(Web Server issue):W575-81. PMC: 3692101. DOI: 10.1093/nar/gkt289. View

Schubert M, Lindgreen S, Orlando L . AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes. 2016; 9:88. PMC: 4751634. DOI: 10.1186/s13104-016-1900-2. View

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

Celestino K, Cunha R, Felix C . Characterization of a beta-glucanase produced by Rhizopus microsporus var. microsporus, and its potential for application in the brewing industry. BMC Biochem. 2006; 7:23. PMC: 1712339. DOI: 10.1186/1471-2091-7-23. View

Li Q, Zhang T, Li L, Bao Z, Tu W, Xiang P . Comparative Mitogenomic Analysis Reveals Intraspecific, Interspecific Variations and Genetic Diversity of Medical Fungus . J Fungi (Basel). 2022; 8(8). PMC: 9394262. DOI: 10.3390/jof8080781. View

McBride H, Neuspiel M, Wasiak S . Mitochondria: more than just a powerhouse. Curr Biol. 2006; 16(14):R551-60. DOI: 10.1016/j.cub.2006.06.054. View

Ellenberger S, Burmester A, Wostemeyer J . Complete Mitochondrial DNA Sequence of the Mucoralean Fungus Absidia glauca, a Model for Studying Host-Parasite Interactions. Genome Announc. 2016; 4(2). PMC: 4807231. DOI: 10.1128/genomeA.00153-16. View

Li Q, Li L, Zhang T, Xiang P, Wu Q, Tu W . The first two mitochondrial genomes for the genus Ramaria reveal mitochondrial genome evolution of Ramaria and phylogeny of Basidiomycota. IMA Fungus. 2022; 13(1):16. PMC: 9469536. DOI: 10.1186/s43008-022-00100-7. View

10.

Zhang X, Chen H, Ni Y, Wu B, Li J, Burzynski A . Plant mitochondrial genome map (PMGmap): A software tool for the comprehensive visualization of coding, noncoding and genome features of plant mitochondrial genomes. Mol Ecol Resour. 2024; 24(5):e13952. DOI: 10.1111/1755-0998.13952. View

11.

Leung S, Huang Y, Lau S, Woo P . Complete Mitochondrial Genome Sequence of Lichtheimia ramosa (syn. Lichtheimia hongkongensis). Genome Announc. 2014; 2(4). PMC: 4081996. DOI: 10.1128/genomeA.00644-14. View

12.

Lanfear R, Frandsen P, Wright A, Senfeld T, Calcott B . PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses. Mol Biol Evol. 2016; 34(3):772-773. DOI: 10.1093/molbev/msw260. View

13.

Yao D, Xu L, Wu M, Wang X, Wang K, Li Z . Microbial Community Succession and Metabolite Changes During Fermentation of BS Sufu, the Fermented Black Soybean Curd by , , and . Front Microbiol. 2021; 12:665826. PMC: 8267895. DOI: 10.3389/fmicb.2021.665826. View

14.

Zhang S, Wang Y, Zhang N, Sun Z, Shi Y, Cao X . Purification and Characterisation of a Fibrinolytic Enzyme from var. . Food Technol Biotechnol. 2016; 53(2):243-248. PMC: 5068409. DOI: 10.17113/ftb.53.02.15.3874. View

15.

Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G . MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2012; 69(2):313-9. DOI: 10.1016/j.ympev.2012.08.023. View

16.

Zhang Y, Fan X, Li J, Zhang S . Mitochondrial genome of Cordyceps blackwelliae: organization, transcription, and evolutionary insights into Cordyceps. IMA Fungus. 2023; 14(1):13. PMC: 10327131. DOI: 10.1186/s43008-023-00118-5. View

17.

Slater G, Birney E . Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 2005; 6:31. PMC: 553969. DOI: 10.1186/1471-2105-6-31. View

18.

Chen C, Khaleel S, Huang H, Wu C . Software for pre-processing Illumina next-generation sequencing short read sequences. Source Code Biol Med. 2014; 9:8. PMC: 4064128. DOI: 10.1186/1751-0473-9-8. View

19.

Papp T, Palagyi Z, FERENCZY L, Vagvolgyi C . The mitochondrial genome of Mucor piriformis. FEMS Microbiol Lett. 1999; 171(1):67-72. DOI: 10.1111/j.1574-6968.1999.tb13413.x. View

20.

Gao W, Chen X, He J, Sha A, Luo Y, Xiao W . Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains. BMC Genomics. 2024; 25(1):456. PMC: 11084086. DOI: 10.1186/s12864-024-10374-3. View