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Complete genome sequence of Moesziomyces antarcticus KMA5 isolated from rice in Korea
Korean J. Microbiol. 2023;59(4):340-342
Published online December 31, 2023
© 2023 The Microbiological Society of Korea.

Eunji Jeong, Jae Yun Lim, and Jeong-Ah Seo*

School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
Correspondence to: *E-mail: sja815@ssu.ac.kr; Tel.: +82-2-820-0449; Fax: +82-2-824-4383
Received September 14, 2023; Revised October 12, 2023; Accepted October 13, 2023.
Abstract
Moesziomyces antarcticus is a commercial strain that produces mannosylerythritol lipid that can be used as a microbial surfactant, in addition to lipase and xylan hydrolase. In this study, M. antarcticus KMA5 was isolated from rice sample collected in Chuncheon, South Korea. The genome sequence of M. antarcticus KMA5 was assembled into 26 chromosomes using the PacBio Sequel II platform. Moesziomyces antarcticus KMA5 contained 6,614 protein-coding genes and 207 CAZyme-related genes. In this study, the genome sequence of M. antarcticus was assembled at the chromosome level for the first time. The complete genome sequence of M. antarcticus KMA5 provides meaningful information of the genome of industrially important strain M. antarcticus.
Keywords : Moesziomyces antarcticus, chromosome level assembly, complete genome sequence, PacBio Sequel II, rice
Body

The basidiomycetous yeast Moesziomyces antarcticus, previously identified as Pseudozyma antarctica (Wang et al., 2015), is employed in the production of mannosylerythritol lipid (MEL), which is a well-known type of microbial biosurfactant (Nascimento et al., 2022). Also, M. antarcticus exhibits the ability to synthesize lipase and xylanolytic enzymes in various industrial biotechnology processes (Faria et al., 2019). In this study, M. antarcticus KMA5 was obtained from rice from Chuncheon province in Korea. Moesziomyces antarcticus KMA5 showed MEL producing ability (0.9 g/L) by liquid fermentation (Nascimento et al., 2022) and hydrolytic enzyme activity, including protease and lipase, by using screening plates (Jeong and Seo, 2023) (Unpublished data).

Moesziomyces antarcticus KMA5 was grown on 5 ml of complete media (Seo et al., 2006) at 25°C with 180 rpm shaking for 4 days to obtain hyphal mass. The genomic DNA was extracted from freeze-dried hyphae using modified CTAB method (Cota-Sánchez et al., 2006). The whole genome sequencing was performed using PacBio Sequel II platform by NICEM in Seoul National University. The 154,249 HiFi reads were generated (123-fold coverage) and de novo assembly using HiCanu assembler (Nurk et al., 2020) yielded 61 contigs with a 19.6 Mb. Out of the 61 contigs, 35 contigs were eliminated due to their association with ribosomal DNA repeat clusters, mitochondrial DNA, or overlap. The remaining contigs were assembled to 26 telomere-to-telomere chromosomes with telomeric repeat sequences in both terminal regions (Genome size, 18.7 Mb; GC content, 60.8%; N50, 7.4 Mb) (Table 1).

Genome feature of Moesziomyces antarcticus KMA5 and ATCC 34888
Features Moesziomyces antarcticus
KMA5 ATCC 34888T
Genome size, bp 18,696,573 18,376,790
GC content, % 60.8 60.8
Number of scaffolds 26 39
N50, bp 739,915 730,676
Number of protein-coding genes 6,614 5,911
Number of InterPro 5,460 5,111
Number of CAZyme-related genes 207 202
Number of protease genes 220 213
Number of secondary metabolite gene clusters 12 10
BUSCO completeness, % 99.3 95.1
GenBank accession number GCA_031214725.1 GCA_900322835.1
Reference This study Wang et al. (2015)

Note: The genome sequence of ATCC 34888, the type strain of Moesziomyces antarcticus, was obtained from GenBank.



The average nucleotide identity (ANI) values between the genome sequence of M. antarcticus KMA5 and eight genome sequences of Moesziomyces accessible in the NCBI database was calculated using OrthoANI (Lee et al., 2016). An ANI-based phylogenetic tree was generated using the hclust function in R program (Fig. 1). The ANI-based phylogenetic tree revealed that the genome of M. antarcticus KMA5 shared 98.9% similarity with three M. antarcticus strains, except for M. antarcticus T-34. Moesziomyces antarcticus T-34 shared more sequence similarity with Moesziomyces aphidis (97.6%) than the other four M. antarcticus strains (around 90.8%).

Fig. 1. Average nucleotide identity (ANI)-based phylogenetic tree of M. antarcticus KMA5.
Phylogenetic tree was constructed using hclust function in R package based on the ANI values of M. antarcticus KMA5 and other 8 strains of Moesziomyces. Whole genome sequences of 8 strains of Moesziomyces were obtained from GenBank. ANI values between nine genomes were calculated using OrthoANI.

Gene annotation was carried out using Funannotate pipeline v1.8.9 (Palmer and Stajich, 2020), and the quality of the assembly and annotation was evaluated using BUSCO v.5.2.1 (Simão et al., 2015). The BUSCO completeness score of assembly of M. antarcticus KMA5 is 99.3%. Moesziomyces antarcticus KMA5 had 6,614 protein-coding genes and 207 CAZyme-related genes (Table 1). CAZyme-related genes of M. antarcticus KMA5 included 103 Glycoside Hydrolases (44 families), 47 Glycosyl Transferases (22 families), 2 Polysaccharide Lyases (2 families), 31 Carbohydrate Esterases (8 families), and 24 Auxiliary Activities (7 families). The MEL biosynthetic gene cluster was found on chromosome 6 of M. antarcticus KMA5 with a size of 44 Kb.

This is the first report of the M. antarcticus genome assembled at the chromosome level. This complete genome sequence of M. antarcticus KMA5 provides important information of the genome sequence of M. antarcticus, a key commercial strain used to produce microbial biosurfactant and useful enzymes (Faria et al., 2019; Nascimento et al., 2022). Also, the genetic resources related to the MEL and hydrolytic enzymes, including the CAZyme and protease, found in M. antarcticus KMA5 might be useful in understanding enzymatic activities of M. antarcticus.

Strain and nucleotide sequence accession number

Moesziomyces antarcticus KMA5 has been deposited in the Korean Collection for Type Cultures (KCTC) under the number KCTC 56815. The complete genome sequence of M. antarcticus KMA5 has been deposited at the NCBI GenBank database under the accession number CP080177 – CP080202. Genome sequence of M. antarcticus KMA5 was also deposited to the National Agricultural Biotechnology Information Center (NABIC) under accession number NG-1546-000001–NG-1546-000026.

적 요

Moesziomyces antarcticus는 미생물 계면활성제로 사용할 수 있는 당지질인 mannosylerythritol lipid 생산과 바이오산업에서 리파아제와 자일란 가수분해효소 생산에 활용되는 주요한 산업 균주이다. 본 연구에서 대한민국 춘천에서 확보한 벼 시료로부터 M. antarcticus KMA5를 분리하고 전장 유전체 분석을 수행하였다. PacBio Sequel II 플랫폼을 사용하여 해독된 M. antarcticus KMA5의 전장 유전체는 총 크기가 18.7 Mb인 26개의 염색체로 조립되었다. 유전자 주석 분석 결과 M. antarcticus KMA5는 6,614개의 단백질 코딩 유전자와 207개의 CAZyme 관련 유전자를 가지고 있었다. 본 연구에서는 최초로 M. antarcticus의 유전체를 염색체 수준으로 조립하였다. Moesziomyces antarcticus KMA5의 전장 유전체 서열은 산업적으로 중요한 균주인 M. antarcticus의 유전체에 대한 유의미한 정보를 제공하고 있다.

Acknowledgments

This work was carried out with the support of “Cooperative Research Program for Agriculture Science and Technology Development (RS-2023-00230782)” Rural Development Administration, Republic of Korea, and the support of the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through the Crop Viruses and Pests Response Industry Technology Development Program (Grant Number: 320036-5), which is funded by the Ministry of Agriculture.

Conflict of Interest

The authors declare that there is no conflict of interest.

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