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Sci Rep. 2019 Jan 29;9(1):898. doi: 10.1038/s41598-018-38021-4.

Study of the whole genome, methylome and transcriptome of Cordyceps militaris.

Chen Y1,2,3,4,5, Wu Y1,3,4,5,6, Liu L3,5, Feng J3, Zhang T3, Qin S7, Zhao X7, Wang C3, Li D3, Han W3, Shao M3, Zhao P1, Xue J3, Liu X2,4, Li H2, Zhao E2,4, Zhao W3, Guo X7, Jin Y8, Cao Y9, Cui L3,10, Zhou Z11, Xia Q6, Rao Z12, Zhang Y13,14,15,16,17,18.

Author information

1
Human Genome Research Center, Tianjin University, Tianjin, 300309, China.
2
Zheng-Yuan-Tang (Tianjin) Biotechnology Co. Ltd, Tianjin, 300457, China.
3
Tianjin Lakeside Powergene Science Development Co. Ltd, Tianjin, 300309, China.
4
Zhejiang Chinagene Biomedicine Co. Ltd, Jiaxing, 314400, China.
5
Guizhou Gui'an Academy of Precision Medicine Co. Ltd, Gui'an, 561113, China.
6
State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China.
7
College of Life Sciences, Jiangsu University of Science and Technology, Zhenjiang, 212000, China.
8
College of Life Science, Zhejiang University, Hangzhou, 310058, China.
9
Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, 110001, China.
10
Department of Entomology, Penn State University, PA, 16802, USA.
11
Dynamiker Biotechnology (Tianjin) Co., Ltd, Tianjin, 300467, China.
12
Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, China. raozh@nankai.edu.cn.
13
Human Genome Research Center, Tianjin University, Tianjin, 300309, China. zhangyaozhou88@126.com.
14
Zheng-Yuan-Tang (Tianjin) Biotechnology Co. Ltd, Tianjin, 300457, China. zhangyaozhou88@126.com.
15
Tianjin Lakeside Powergene Science Development Co. Ltd, Tianjin, 300309, China. zhangyaozhou88@126.com.
16
Zhejiang Chinagene Biomedicine Co. Ltd, Jiaxing, 314400, China. zhangyaozhou88@126.com.
17
Guizhou Gui'an Academy of Precision Medicine Co. Ltd, Gui'an, 561113, China. zhangyaozhou88@126.com.
18
Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, China. zhangyaozhou88@126.com.

Abstract

The complete genome of Cordyceps militaris was sequenced using single-molecule real-time (SMRT) sequencing technology at a coverage over 300×. The genome size was 32.57 Mb, and 14 contigs ranging from 0.35 to 4.58 Mb with an N50 of 2.86 Mb were assembled, including 4 contigs with telomeric sequences on both ends and an additional 8 contigs with telomeric sequences on either the 5' or 3' end. A methylome database of the genome was constructed using SMRT and m4C and m6A methylated nucleotides, and many unknown modification types were identified. The major m6A methylation motif is GA and GGAG, and the major m4C methylation motif is GC or CG/GC. In the C. militaris genome DNA, there were four types of methylated nucleotides that we confirmed using high-resolution LCMS-IT-TOF. Using PacBio Iso-Seq, a total of 31,133 complete cDNA sequences were obtained in the fruiting body. The conserved domains of the nontranscribed regions of the genome include TATA boxes, which are the initial regions of genome replication. There were 406 structural variants between the HN and CM01 strains, and there were 1,114 structural variants between the HN and ATCC strains.

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