The Importance of Complete and High-quality Genome Sequences in Research

Overview

Journal Front Fungal Biol

Specialty Biology

Date 2023 Sep 25

PMID 37746178

Authors

Valeria Ellena

Matthias G Steiger

Affiliations

Soon will be listed here.

Abstract

The possibility to sequence the entire genome of an organism revolutionized the fields of biology and biotechnology. The first genome sequence of the important filamentous fungus was obtained in 2007, 11 years after the release of the first eukaryotic genome sequence. From that moment, genomics of has seen major progresses, facilitated by the advances in the sequencing technologies and in the methodologies for gene function prediction. However, there are still challenges to face when trying to obtain complete genomes, equipped with all the repetitive sequences that they contain and without omitting the mitochondrial sequences. The aim of this perspective article is to discuss the current status of genomics and draw attention to the open challenges that the fungal community should address to move research of this important fungus forward.

Citing Articles

The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics.

Wang Z, Kim W, Wang Y, Yakubovich E, Dong C, Trail F Front Fungal Biol. 2023; 4:1214537.

PMID: 37746130 PMC: 10512317. DOI: 10.3389/ffunb.2023.1214537.

References

Cairns T, Nai C, Meyer V . How a fungus shapes biotechnology: 100 years of research. Fungal Biol Biotechnol. 2018; 5:13. PMC: 5966904. DOI: 10.1186/s40694-018-0054-5. View

Juhasz A, Laday M, Gacser A, Kucsera J, Pfeiffer I, Kevei F . Mitochondrial DNA organisation of the mtDNA type 2b of Aspergillus tubingensis compared to the Aspergillus niger mtDNA type 1a. FEMS Microbiol Lett. 2004; 241(1):119-26. DOI: 10.1016/j.femsle.2004.10.025. View

Niedzwiecka K, Tisi R, Penna S, Lichocka M, Plochocka D, Kucharczyk R . Two mutations in mitochondrial ATP6 gene of ATP synthase, related to human cancer, affect ROS, calcium homeostasis and mitochondrial permeability transition in yeast. Biochim Biophys Acta Mol Cell Res. 2017; 1865(1):117-131. DOI: 10.1016/j.bbamcr.2017.10.003. View

Romsdahl J, Blachowicz A, Chiang A, Singh N, Stajich J, Kalkum M . Characterization of Aspergillus niger Isolated from the International Space Station. mSystems. 2018; 3(5). PMC: 6143729. DOI: 10.1128/mSystems.00112-18. View

Grigoriev I, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R . MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res. 2013; 42(Database issue):D699-704. PMC: 3965089. DOI: 10.1093/nar/gkt1183. View

Gong W, Cheng Z, Zhang H, Liu L, Gao P, Wang L . Draft Genome Sequence of Aspergillus niger Strain An76. Genome Announc. 2016; 4(1). PMC: 4759068. DOI: 10.1128/genomeA.01700-15. View

Hazkani-Covo E, Zeller R, Martin W . Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet. 2010; 6(2):e1000834. PMC: 2820518. DOI: 10.1371/journal.pgen.1000834. View

Fang Q, Du M, Chen J, Liu T, Zheng Y, Liao Z . Degradation and Detoxification of Aflatoxin B1 by Tea-Derived RAF106. Toxins (Basel). 2020; 12(12). PMC: 7762301. DOI: 10.3390/toxins12120777. View

Sichtig H, Minogue T, Yan Y, Stefan C, Hall A, Tallon L . FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. Nat Commun. 2019; 10(1):3313. PMC: 6658474. DOI: 10.1038/s41467-019-11306-6. View

10.

Smith D . The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs?. Brief Funct Genomics. 2015; 15(1):47-54. PMC: 4812591. DOI: 10.1093/bfgp/elv027. View

11.

Hugaboom M, Beck M, Carrubba K, Chennupati D, Gupta A, Liu Q . Complete Mitochondrial Genome Sequences of Nine Aspergillus flavus Strains. Microbiol Resour Announc. 2021; 10(45):e0097121. PMC: 8582314. DOI: 10.1128/MRA.00971-21. View

12.

Wang L, Zhang J, Cao Z, Wang Y, Gao Q, Zhang J . Inhibition of oxidative phosphorylation for enhancing citric acid production by Aspergillus niger. Microb Cell Fact. 2015; 14:7. PMC: 4320542. DOI: 10.1186/s12934-015-0190-z. View

13.

Laothanachareon T, Tamayo-Ramos J, Nijsse B, Schaap P . Forward Genetics by Genome Sequencing Uncovers the Central Role of the Locus in Hydrogen Peroxide Induced Glucose Oxidase Expression. Front Microbiol. 2018; 9:2269. PMC: 6165874. DOI: 10.3389/fmicb.2018.02269. View

14.

Basenko E, Pulman J, Shanmugasundram A, Harb O, Crouch K, Starns D . FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. J Fungi (Basel). 2018; 4(1). PMC: 5872342. DOI: 10.3390/jof4010039. View

15.

Paul S, Ludena Y, Villena G, Yu F, Sherman D, Gutierrez-Correa M . High-quality draft genome sequence of a biofilm forming lignocellulolytic strain ATCC 10864. Stand Genomic Sci. 2017; 12:37. PMC: 5514509. DOI: 10.1186/s40793-017-0254-2. View

16.

Friedman S, Freitag M . Centrochromatin of Fungi. Prog Mol Subcell Biol. 2017; 56:85-109. DOI: 10.1007/978-3-319-58592-5_4. View

17.

Wang B, Lv Y, Li X, Lin Y, Deng H, Pan L . Profiling of secondary metabolite gene clusters regulated by LaeA in Aspergillus niger FGSC A1279 based on genome sequencing and transcriptome analysis. Res Microbiol. 2017; 169(2):67-77. DOI: 10.1016/j.resmic.2017.10.002. View

18.

Yin X, Shin H, Li J, Du G, Liu L, Chen J . Comparative genomics and transcriptome analysis of Aspergillus niger and metabolic engineering for citrate production. Sci Rep. 2017; 7:41040. PMC: 5247736. DOI: 10.1038/srep41040. View

19.

Sui Y, Ouyang L, Schutze T, Cheng S, Meyer V, Zhuang Y . Comparative genomics of the aconidial Aspergillus niger strain LDM3 predicts genes associated with its high protein secretion capacity. Appl Microbiol Biotechnol. 2020; 104(6):2623-2637. DOI: 10.1007/s00253-020-10398-1. View

20.

Hou L, Liu L, Zhang H, Zhang L, Zhang L, Zhang J . Functional analysis of the mitochondrial alternative oxidase gene (aox1) from Aspergillus niger CGMCC 10142 and its effects on citric acid production. Appl Microbiol Biotechnol. 2018; 102(18):7981-7995. DOI: 10.1007/s00253-018-9197-9. View