- Email: [email protected]
Genome sequence of a laccase producing fungus Trametes sp. AH28-2
Accepted Manuscript Title: Genome sequence of a laccase producing fungus Trametes sp. AH28-2 Author: Jingjing Wang Yinliang Zhang Yong Xu Wei Fang Xiaotang Wang Zemin Fang Yazhong Xiao PII: DOI: Reference:
S0168-1656(15)30173-5 http://dx.doi.org/doi:10.1016/j.jbiotec.2015.11.001 BIOTEC 7294
To appear in:
Journal of Biotechnology
Received date: Accepted date:
28-10-2015 2-11-2015
Please cite this article as: Wang, Jingjing, Zhang, Yinliang, Xu, Yong, Fang, Wei, Wang, Xiaotang, Fang, Zemin, Xiao, Yazhong, Genome sequence of a laccase producing fungus Trametes sp.AH28-2.Journal of Biotechnology http://dx.doi.org/10.1016/j.jbiotec.2015.11.001 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
1
Title: Genome sequence of a laccase producing fungus Trametes sp. AH28-2
2
Authors: Jingjing Wanga,b,1, Yinliang Zhangc,1, Yong Xua,b, Wei Fanga,b, Xiaotang Wangd, Zemin Fanga,b*, Yazhong Xiaoa,b*
3 4
Address: a, School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
5
b, Anhui Provincial Engineering Technology Research Center of
6
Microorganisms and Biocatalysis, Hefei, Anhui 230601, China
7
c, School of Life Sciences, University of Science and Technology of China,
8
Hefei, Anhui 230027, China
9
d, Department of Chemistry & Biochemistry, Florida International University, Miami, Florida 33199, United States
10 11 12
1
13
* Correspondence
14
Phone/Fax: +86 551 63861861
15
E-mail: [email protected] (to FZ); yzxiao@ ahu.edu.cn (to XY
, these authors contributed equally to this work.
16 17 18
Highlights
19 20
Trametes sp. AH28-2, a white rot fungus which isolated from rotting wood in
21
China, can be induced by kraft lignin to secrete high levels of extracellular laccase,
22
and differentially express laccase genes upon addition of different phenolic 1
23 24 25
compounds. We present the whole genome sequence of Trametes sp. AH28-2 and its genetic basis for lignin degradation and phenolic xenobiotics metabolism.
26
Trametes sp. AH28-2, a white rot fungus which isolated from rotting wood in
27
China, can be induced by kraft lignin to secrete high levels of extracellular laccase,
28
and differentially express laccase genes upon addition of different phenolic
29
compounds.
30 31
We present the whole genome sequence of Trametes sp. AH28-2 and its genetic basis for lignin degradation and phenolic xenobiotics metabolism.
32
We present the genome of this strain, which consists of 502 contigs and resulting
33
in 306 scaffolds. We present the genome of this strain, which consists of 502 contigs
34
and resulting in 306 scaffolds.
2
35
ABSTRACT
36
Trametes sp. AH28-2 (CCTCC AF 2015027) is a white rot fungus isolated from
37
rotting wood in China. Primary study indicated that this strain can be induced by kraft
38
lignin to secrete high levels of extracellular laccase, and differentially express laccase
39
genes upon addition of different phenolic compounds. Here we report the complete
40
genome sequence of Trametes sp. AH28-2 and its genetic basis for lignin degradation
41
and phenolic xenobiotics metabolism.
42 43
Keywords:
44
Trametes sp. AH28-2, laccase producing fungus, whole genome.
45
3
46
White rot basidiomycete fungi have been known to possess a unique ability to break
47
down the recalcitrant lignin polymer to carbon dioxide and water, and an enormous
48
potential to biodegrade a wide range of toxic environmental pollutants including those
49
that are normally resistant to bacterial degradation (Syed and Yadav, 2012). They
50
were equipped with extraordinary enzyme machinery, including lignin peroxidases,
51
manganese peroxidases, versatile peroxidases, and laccases, for efficient metabolism
52
of a wide variety of chemicals and large biological macromolecules (Pollegioni et al.,
53
2015; Syed and Yadav, 2012). Trametes sp. has been one of the most extensively
54
studied members of this group. A large amount of information has been accumulated
55
on the biodegradation of lignocellulose and xenobiotics by Trametes sp. (Pollegioni et
56
al., 2015), as well as their lignin degrading enzyme production and regulation (Janusz
57
et al., 2013). Trametes sp. AH28-2 is a white-rot basidiomycete that was originally
58
isolated from rotting wood in China. Preliminary studies indicate that this
59
microorganism is able to degrade lignin when grown on wood and can be induced by
60
kraft lignin to secrete high levels of extracellular laccase (Xiao et al., 2001).
61
Furthermore, its laccase genes were differently expressed upon addition of different
62
phenolic compounds (Xiao et al., 2004) or a Trichoderma strain (Zhang et al., 2006).
63
To generate genomic insights into its ligninolytic degradation and laccase gene
64
regulation, we performed the whole-genome sequencing of Trametes sp. AH28-2.
65
Trametes sp. AH28-2 was deposited at China Center for Type Culture Collection
66
(CCTCC AF 2015027). The genome of Trametes sp. AH28-2 was sequenced using
67
Illumina Hiseq 2000 sequencing platform with three paired-end libraries (0.17, 0.5, 4
68
and 6-kb insert size) at Beijing Genomics Institute (Wuhan, China). Shotgun
69
sequencing of Trametes sp. AH28-2 genome produced 4,717 Mb clean data after
70
filtering low quality and adapter contamination reads. The short reads from the three
71
libraries were assembled by SOAPdenovo 1.05 (Li et al., 2010), with optimal
72
assembly acquired with the key parameter K=59. The assembly generated 502 contigs
73
with a N50 of 307,958 bp, and resulting in 306 scaffolds with a N50 of 580,701 bp.
74
Finally, a 38.9 Mb draft genome sequence with a 58.81% G+C content of Trametes sp.
75
AH28-2 was obtained (Table 1).
76
By combining several different gene predictors including Homology (genewise
77
software, version 2.2.0) (Birney et al., 2004), SNAP (version 2010-07-08) (Johnson et
78
al., 2008), Augustus (version 2.6.1) (Keller et al., 2011), and Genemarkes (version
79
2.3e) (Ter-Hovhannisyan et al., 2008), a number of 12,397 protein-coding gene
80
models were predicted, with an average sequence length of 1,963 bp. The genome
81
contains 326 tRNA, 1 rRNA and 34 snRNA, with a total length of 32,781 bp,
82
accounting for 0.08% of the genome. The length of all genes was up to 24,345,232 bp,
83
which contained 18,608,442 bp of exons and 5,736,790 bp of introns. The repetitive
84
sequences represented approximately 3.06% of the genome, and a total number of
85
1,191,235 bp repeat sequences were identified, the majority of which were LTR
86
(2.13% of the genome). No more large scale dispersed segmental duplication was
87
observed. Approximately 70% of the genes were annotated by similarity searches
88
against homologous sequences and protein domains.
89
A total of 30 Trametes sp. AH28-2 genes could be assigned to lignin-degrading 5
90
enzyme system, including 13 lignin peroxidases, 6 manganese peroxidases, 7 laccases,
91
and 4 versatile peroxidases. Additionally, genome annotation identified 173 P450
92
genes, 36 glutathione S-transferase genes, and 52 different ABC transporter genes,
93
indicating that Trametes sp. AH28-2 possesses a complicated system in lignin and
94
xenobiotics metabolism.
95 96
Nucleotide sequence accession number
97
This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank
98
under the accession LJJJ00000000. The version described in this paper is version
99
LJJJ01000000.
100 101
Acknowledgement
102
This work was supported by grants from the National Natural Sciences Foundation of
103
China (31170056, 30770058, 30470056), National Natural Science Foundation of
104
Anhui Province (1308085QC46), the Introduction Project of Academic and
105
Technology Leaders in Anhui University (32030066).
106 107
References
108
Birney, E., Clamp, M., Durbin, R., (2004) GeneWise and Genomewise. Genome Res.
109
14, 988-995.
110
Janusz, G., Kucharzyk, K.H., Pawlik, A., Staszczak, M., Paszczynski, A.J., (2013)
111
Fungal laccase, manganese peroxidase and lignin peroxidase: gene expression 6
112
and regulation. Enzyme Microb. Technol. 52, 1-12.
113
Johnson, A.D., Handsaker, R.E., Pulit, S.L., Nizzari, M.M., O'Donnell, C.J., de
114
Bakker, P.I.W., (2008) SNAP: a web-based tool for identification and annotation
115
of proxy SNPs using HapMap. Bioinformatics 24, 2938-2939.
116
Keller, O., Kollmar, M., Stanke, M., Waack, S., (2011) A novel hybrid gene prediction
117
method employing protein multiple sequence alignments. Bioinformatics 27,
118
757-763.
119
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G.,
120
Kristiansen, K., Li, S., Yang, H., Wang, J., Wang, J., (2010) De novo assembly of
121
human genomes with massively parallel short read sequencing. Genome Res. 20,
122
265-272.
123 124
Pollegioni, L., Tonin, F., Rosini, E., (2015) Lignin-degrading enzymes. FEBS J. 282, 1190-1213.
125
Syed, K., Yadav, J.S., (2012) P450 monooxygenases (P450ome) of the model white
126
rot fungus Phanerochaete chrysosporium. Crit. Rev. Microbiol. 38, 339-363.
127
Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y.O., Borodovsky, M., (2008) Gene
128
prediction in novel fungal genomes using an ab initio algorithm with
129
unsupervised training. Genome Res. 18, 1979-1990.
130
Xiao, Y., Zhang, M., Wu, J., Wang, Y., Hang, J., Zeng, W., Shi, Y., (2001) Factors of
131
laccase producing and fermentation conditions by a new white-rot fungus
132
AH28-2. Chinese Journal of Biotechnology 17, 579-583.
133
Xiao, Y.Z., Chen, Q., Hang, J., Shi, Y.Y., Xiao, Y.Z., Wu, J., Hong, Y.Z., Wang, Y.P., 7
134
(2004) Selective induction, purification and characterization of a laccase isozyme
135
from the basidiomycete Trametes sp. AH28-2. Mycologia 96, 26-35.
136
Zhang, H., Hong, Y.Z., Xiao, Y.Z., Yuan, J., Tu, X.M., Zhang, X.Q., (2006) Efficient
137
production of laccases by Trametes sp. AH28-2 in cocultivation with a
138
Trichoderma strain. Appl. Microbiol. Biotechnol. 73, 89-94.
139
8
140
Table 1 The characteristics of assembly scaffold and genome of Trametes sp. AH28-2 Scaffold
Contig
Total Number
306
502
Total Length (bp)
38,904,488
38,560,147
N50 (bp)
580,701
307,958
Max Length (bp)
1,776,945
1,776,945
GC Content (%)
58.81%
58.81%
Number of Gene
12,397
Number of Exons
79,191
Number of Intron
66,794
Length of Gene (bp)
24,345,232
Length of Exons (bp)
18,608,442
Average Length of Gene (bp)
1,963.80
Total Length of Repeat Size 1,191,235 (bp) tRNA Number
326
rRNA Number
1
ncRNA Number (#)
34
141
9
S0168-1656(15)30173-5 http://dx.doi.org/doi:10.1016/j.jbiotec.2015.11.001 BIOTEC 7294
To appear in:
Journal of Biotechnology
Received date: Accepted date:
28-10-2015 2-11-2015
Please cite this article as: Wang, Jingjing, Zhang, Yinliang, Xu, Yong, Fang, Wei, Wang, Xiaotang, Fang, Zemin, Xiao, Yazhong, Genome sequence of a laccase producing fungus Trametes sp.AH28-2.Journal of Biotechnology http://dx.doi.org/10.1016/j.jbiotec.2015.11.001 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
1
Title: Genome sequence of a laccase producing fungus Trametes sp. AH28-2
2
Authors: Jingjing Wanga,b,1, Yinliang Zhangc,1, Yong Xua,b, Wei Fanga,b, Xiaotang Wangd, Zemin Fanga,b*, Yazhong Xiaoa,b*
3 4
Address: a, School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
5
b, Anhui Provincial Engineering Technology Research Center of
6
Microorganisms and Biocatalysis, Hefei, Anhui 230601, China
7
c, School of Life Sciences, University of Science and Technology of China,
8
Hefei, Anhui 230027, China
9
d, Department of Chemistry & Biochemistry, Florida International University, Miami, Florida 33199, United States
10 11 12
1
13
* Correspondence
14
Phone/Fax: +86 551 63861861
15
E-mail: [email protected] (to FZ); yzxiao@ ahu.edu.cn (to XY
, these authors contributed equally to this work.
16 17 18
Highlights
19 20
Trametes sp. AH28-2, a white rot fungus which isolated from rotting wood in
21
China, can be induced by kraft lignin to secrete high levels of extracellular laccase,
22
and differentially express laccase genes upon addition of different phenolic 1
23 24 25
compounds. We present the whole genome sequence of Trametes sp. AH28-2 and its genetic basis for lignin degradation and phenolic xenobiotics metabolism.
26
Trametes sp. AH28-2, a white rot fungus which isolated from rotting wood in
27
China, can be induced by kraft lignin to secrete high levels of extracellular laccase,
28
and differentially express laccase genes upon addition of different phenolic
29
compounds.
30 31
We present the whole genome sequence of Trametes sp. AH28-2 and its genetic basis for lignin degradation and phenolic xenobiotics metabolism.
32
We present the genome of this strain, which consists of 502 contigs and resulting
33
in 306 scaffolds. We present the genome of this strain, which consists of 502 contigs
34
and resulting in 306 scaffolds.
2
35
ABSTRACT
36
Trametes sp. AH28-2 (CCTCC AF 2015027) is a white rot fungus isolated from
37
rotting wood in China. Primary study indicated that this strain can be induced by kraft
38
lignin to secrete high levels of extracellular laccase, and differentially express laccase
39
genes upon addition of different phenolic compounds. Here we report the complete
40
genome sequence of Trametes sp. AH28-2 and its genetic basis for lignin degradation
41
and phenolic xenobiotics metabolism.
42 43
Keywords:
44
Trametes sp. AH28-2, laccase producing fungus, whole genome.
45
3
46
White rot basidiomycete fungi have been known to possess a unique ability to break
47
down the recalcitrant lignin polymer to carbon dioxide and water, and an enormous
48
potential to biodegrade a wide range of toxic environmental pollutants including those
49
that are normally resistant to bacterial degradation (Syed and Yadav, 2012). They
50
were equipped with extraordinary enzyme machinery, including lignin peroxidases,
51
manganese peroxidases, versatile peroxidases, and laccases, for efficient metabolism
52
of a wide variety of chemicals and large biological macromolecules (Pollegioni et al.,
53
2015; Syed and Yadav, 2012). Trametes sp. has been one of the most extensively
54
studied members of this group. A large amount of information has been accumulated
55
on the biodegradation of lignocellulose and xenobiotics by Trametes sp. (Pollegioni et
56
al., 2015), as well as their lignin degrading enzyme production and regulation (Janusz
57
et al., 2013). Trametes sp. AH28-2 is a white-rot basidiomycete that was originally
58
isolated from rotting wood in China. Preliminary studies indicate that this
59
microorganism is able to degrade lignin when grown on wood and can be induced by
60
kraft lignin to secrete high levels of extracellular laccase (Xiao et al., 2001).
61
Furthermore, its laccase genes were differently expressed upon addition of different
62
phenolic compounds (Xiao et al., 2004) or a Trichoderma strain (Zhang et al., 2006).
63
To generate genomic insights into its ligninolytic degradation and laccase gene
64
regulation, we performed the whole-genome sequencing of Trametes sp. AH28-2.
65
Trametes sp. AH28-2 was deposited at China Center for Type Culture Collection
66
(CCTCC AF 2015027). The genome of Trametes sp. AH28-2 was sequenced using
67
Illumina Hiseq 2000 sequencing platform with three paired-end libraries (0.17, 0.5, 4
68
and 6-kb insert size) at Beijing Genomics Institute (Wuhan, China). Shotgun
69
sequencing of Trametes sp. AH28-2 genome produced 4,717 Mb clean data after
70
filtering low quality and adapter contamination reads. The short reads from the three
71
libraries were assembled by SOAPdenovo 1.05 (Li et al., 2010), with optimal
72
assembly acquired with the key parameter K=59. The assembly generated 502 contigs
73
with a N50 of 307,958 bp, and resulting in 306 scaffolds with a N50 of 580,701 bp.
74
Finally, a 38.9 Mb draft genome sequence with a 58.81% G+C content of Trametes sp.
75
AH28-2 was obtained (Table 1).
76
By combining several different gene predictors including Homology (genewise
77
software, version 2.2.0) (Birney et al., 2004), SNAP (version 2010-07-08) (Johnson et
78
al., 2008), Augustus (version 2.6.1) (Keller et al., 2011), and Genemarkes (version
79
2.3e) (Ter-Hovhannisyan et al., 2008), a number of 12,397 protein-coding gene
80
models were predicted, with an average sequence length of 1,963 bp. The genome
81
contains 326 tRNA, 1 rRNA and 34 snRNA, with a total length of 32,781 bp,
82
accounting for 0.08% of the genome. The length of all genes was up to 24,345,232 bp,
83
which contained 18,608,442 bp of exons and 5,736,790 bp of introns. The repetitive
84
sequences represented approximately 3.06% of the genome, and a total number of
85
1,191,235 bp repeat sequences were identified, the majority of which were LTR
86
(2.13% of the genome). No more large scale dispersed segmental duplication was
87
observed. Approximately 70% of the genes were annotated by similarity searches
88
against homologous sequences and protein domains.
89
A total of 30 Trametes sp. AH28-2 genes could be assigned to lignin-degrading 5
90
enzyme system, including 13 lignin peroxidases, 6 manganese peroxidases, 7 laccases,
91
and 4 versatile peroxidases. Additionally, genome annotation identified 173 P450
92
genes, 36 glutathione S-transferase genes, and 52 different ABC transporter genes,
93
indicating that Trametes sp. AH28-2 possesses a complicated system in lignin and
94
xenobiotics metabolism.
95 96
Nucleotide sequence accession number
97
This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank
98
under the accession LJJJ00000000. The version described in this paper is version
99
LJJJ01000000.
100 101
Acknowledgement
102
This work was supported by grants from the National Natural Sciences Foundation of
103
China (31170056, 30770058, 30470056), National Natural Science Foundation of
104
Anhui Province (1308085QC46), the Introduction Project of Academic and
105
Technology Leaders in Anhui University (32030066).
106 107
References
108
Birney, E., Clamp, M., Durbin, R., (2004) GeneWise and Genomewise. Genome Res.
109
14, 988-995.
110
Janusz, G., Kucharzyk, K.H., Pawlik, A., Staszczak, M., Paszczynski, A.J., (2013)
111
Fungal laccase, manganese peroxidase and lignin peroxidase: gene expression 6
112
and regulation. Enzyme Microb. Technol. 52, 1-12.
113
Johnson, A.D., Handsaker, R.E., Pulit, S.L., Nizzari, M.M., O'Donnell, C.J., de
114
Bakker, P.I.W., (2008) SNAP: a web-based tool for identification and annotation
115
of proxy SNPs using HapMap. Bioinformatics 24, 2938-2939.
116
Keller, O., Kollmar, M., Stanke, M., Waack, S., (2011) A novel hybrid gene prediction
117
method employing protein multiple sequence alignments. Bioinformatics 27,
118
757-763.
119
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G.,
120
Kristiansen, K., Li, S., Yang, H., Wang, J., Wang, J., (2010) De novo assembly of
121
human genomes with massively parallel short read sequencing. Genome Res. 20,
122
265-272.
123 124
Pollegioni, L., Tonin, F., Rosini, E., (2015) Lignin-degrading enzymes. FEBS J. 282, 1190-1213.
125
Syed, K., Yadav, J.S., (2012) P450 monooxygenases (P450ome) of the model white
126
rot fungus Phanerochaete chrysosporium. Crit. Rev. Microbiol. 38, 339-363.
127
Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y.O., Borodovsky, M., (2008) Gene
128
prediction in novel fungal genomes using an ab initio algorithm with
129
unsupervised training. Genome Res. 18, 1979-1990.
130
Xiao, Y., Zhang, M., Wu, J., Wang, Y., Hang, J., Zeng, W., Shi, Y., (2001) Factors of
131
laccase producing and fermentation conditions by a new white-rot fungus
132
AH28-2. Chinese Journal of Biotechnology 17, 579-583.
133
Xiao, Y.Z., Chen, Q., Hang, J., Shi, Y.Y., Xiao, Y.Z., Wu, J., Hong, Y.Z., Wang, Y.P., 7
134
(2004) Selective induction, purification and characterization of a laccase isozyme
135
from the basidiomycete Trametes sp. AH28-2. Mycologia 96, 26-35.
136
Zhang, H., Hong, Y.Z., Xiao, Y.Z., Yuan, J., Tu, X.M., Zhang, X.Q., (2006) Efficient
137
production of laccases by Trametes sp. AH28-2 in cocultivation with a
138
Trichoderma strain. Appl. Microbiol. Biotechnol. 73, 89-94.
139
8
140
Table 1 The characteristics of assembly scaffold and genome of Trametes sp. AH28-2 Scaffold
Contig
Total Number
306
502
Total Length (bp)
38,904,488
38,560,147
N50 (bp)
580,701
307,958
Max Length (bp)
1,776,945
1,776,945
GC Content (%)
58.81%
58.81%
Number of Gene
12,397
Number of Exons
79,191
Number of Intron
66,794
Length of Gene (bp)
24,345,232
Length of Exons (bp)
18,608,442
Average Length of Gene (bp)
1,963.80
Total Length of Repeat Size 1,191,235 (bp) tRNA Number
326
rRNA Number
1
ncRNA Number (#)
34
141
9