Complete mitochondrial genome sequence of the food fermentation fungus, Aspergillus luchuensis

Abstract

Aspergillus luchuensis is a filamentous fungus used for food and alcohol fermentation in many Asian countries. Here, we reported the complete mitochondrial genome sequence of A. luchuensis isolated from fermented soybean brick, called as Meju, in Korea. Its mitochondrial genome was successfully assembled from raw reads sequenced using MiSeq by Velvet and GapCloser. Total length of the mitochondrial genome is 31,228 bp and encoded 44 genes (16 protein-coding genes, two rRNAs, and 26 tRNAs). Nucleotide sequence of coding region takes over 25.6%, and overall GC content is 26.4%. Phylogenetic tree of mitochondrial genomes presented A. luchuensis and Aspergillus kawachii are clustered in one clade. This mitochondrial genome can be used for further analyses of Aspergillus mitochondrial comparative genomics to improve understanding of diverse Aspergillus species.

Keywords:

• Aspergillus luchuensis
• mitochondrial genome
• Ascomycota

Aspergillus luchuensis is a filamentous fungus that belongs to Aspergillus section Nigri (Samson et al. 2011) and is an important species for food fermentations in East Asia (Hong et al. 2013). For example, A. luchuensis has been widely used for producing distilled alcoholic beverages, such as awamori and shoju in Japan, and makgeolli in Korea (Inui 1901a, 1901b; Yu et al. 2004; Hong et al. 2014).

The hyphae of A. luchuensis were collected from fermented soybean brick, Meju, in South Korea and its DNA was extracted by using a DNeasy Plant Mini kit (QIAGEN, Hilden, Germany). Raw data generated by MISeq were subject to de novo assembly done by Velvet 1.2.10 (Zerbino and Birney 2008) and gap filling with SOAPGapCloser 1.12 (Zhao et al. 2011) to get complete mitochondrial genome. All assembled sequences were confirmed by alignment results generated by BWA 0.7.17 (Li 2013) and SAMtools 1.9 (Li et al. 2009). Geneious R11 11.0.5 (Biomatters Ltd, Auckland, New Zealand) was used to annotate its mitochondrial genome by comparing with that of Aspergillus kawachii (AP012272; Futagami et al. 2011). Voucher sample was deposited into Korean Agricultural Culture Collection (KACC) with accession number KACC-46490.

The length of A. luchuensis mitochondrial genome (GenBank accession is MK061298) is 31,228 bp, which is median length in comparison to eight available Aspergillus mitochondrial genomes (Futagami et al. 2011; Joardar et al. 2012; Xu et al. 2018); while average length of eight mitochondrial genomes is 34,446.38 bp, which is higher by 5.2 kb due to extremely large size of Aspergillus egyptiacus mitochondrial genome (Xu et al. 2018). A. luchuensis mitochondrial genome encoded 44 genes consisting of 16 protein-coding genes, two rRNAs, and 26 tRNAs. Nucleotide sequence of coding region takes over 25.6%, and overall GC content is 26.4%, which are similar to those of A. kawachii mitochondrial genome (Futagami et al. 2011).

Sequence alignment of nine Aspergillus mitochondrial genomes and one Penicillium mitochondrial genome as an outgroup was conducted by MAFFT 7.388 (Katoh and Standley 2013). The neighbor joining tree was constructed using MEGA X with 10,000 bootstrap replicates (Kumar et al. 2018). Based on phylogenetic tree, A. luchuensis is located in the clade of section Nigri in Subgenus Circumdati and it is similar to A. kawachii (Futagami et al. 2011; Figure 1). Interestingly, based on the Aspergillus taxonomy (Houbraken and Samson 2011; Kocsubé et al. 2016), subgenus Circumdati is split into two clades: sections Nigri and Flavi (Figure 1). A. luchuensis mitochondrial genome can be used for further analyses of Aspergillus mitochondrial comparative genomics to improve understanding of Aspergillus taxonomy.

Figure 1. Neighbor joining phylogenetic tree (bootstrap repeat is 10,000) of eight Aspergillus mitochondrial genomes and one Penicillium mitochondrial genome:Aspergillus luchuensis (MK061298, this study), Aspergillus kawachii (AP012272), Aspergillus egyptiacus (MH041273), Aspergillus tubingensis (NC_007597), Aspergillus nidulans (NC_017896), Aspergillus flavus (NC_026920), Aspergillus niger (NC_007445), Aspergillus fumigatus (NC_017016), and Penicillium chrysogenum (JMSF01000018).

Disclosure statement

The authors declare that they have no competing interests.

Additional information

Funding

This study was carried out with the support of project no. PJ01354902 of the National Institute of Agricultural Science, Rural Development Administration, Republic of Korea to SBH and supported by the National Research Foundation of Korea (NRF) grant funded by the Korea Government (NRF-2017R1D1A3B06035312) to KHH.