Transcriptome sequencing and analysis of potential pathogenicity-related genes in Isaria fumosorosea

doi:10.3969/j.issn.1004-1524.20221707

Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (9): 2169-2180.DOI: 10.3969/j.issn.1004-1524.20221707

• Plant Protection • Previous Articles Next Articles

Transcriptome sequencing and analysis of potential pathogenicity-related genes in Isaria fumosorosea

XIE Meiqiong¹(), WANG Longjiang², HE Yurong³, LYU Lihua⁴

1. College of Life Sciences and Resources and Environment, Yichun University, Yichun 336000, Jiangxi, China
2. College of Chemistry and Bioengineering, Yichun University, Yichun 336000, Jiangxi, China
3. College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
4. Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China

Received:2022-11-29 Online:2023-09-25 Published:2023-10-09

Abstract

Abstract:

In order to explore the expression patterns of transcriptome genes of Isaria fumosorosea and to provide data for the functional study of I. fumosorosea, the transcriptom of I. fumosorosea IFCF01 was sequenced and analyzed using high-throughput non-parametric sequencing technology. A total of 540 896 444 clean reads were obtained by transcriptome sequencing. A total of 36 466 unigenes with the total length of 34 551 468 bp and an average length of 947 bp were obtained after assembly. The functional annotation showed that a total of 22 741 unigenes were annotated in 6 major databases,such as Nr, GO, COG and KEGG, accounting for 62.36% of the total unigenes. A total of 21 737 unigenes were annotated in the Nr database, with the highest number of anotation to Beauveria bassiana. 10 888 unigenes were annotated to 25 functional categories in COG database, and the number of genes involved in general function predicted only was the largest, matching on 4 060 unigenes. The GO annotation shoewed that a total of 9 617 unigenes were annotated, distributed in 49 subcategories of three functional modules: biological process function, molecular function and cell composition. A total of 14 364 unigenes were annotated in the KEGG database, involving 108 KEGG metabolic pathways. With the help of pathogen-host interaction gene database, a total of 86 unigenes associated with the potential pathogenicity of I. fumosorosea were identified. A total of 8 572 simple sequence repeats (SSR) loci were detected in transcriptome data of I. fumosorosea, with a frequency of 18.18%. The results of this study could lay the foundation for gene resources mining, functional gene research and SSR molecular markers for I. fumosorosea.

Key words: Isaria fumosorosea, transcriptome sequencing, gene, SSR molecular marker

CLC Number:

S476.12

XIE Meiqiong, WANG Longjiang, HE Yurong, LYU Lihua. Transcriptome sequencing and analysis of potential pathogenicity-related genes in Isaria fumosorosea[J]. Acta Agriculturae Zhejiangensis, 2023, 35(9): 2169-2180.

Figures/Tables 10

References 34

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数据库Database	数量Number	比例Proportion/%
Nr	21 737	59.61
Nt	12 419	34.06
Swiss-Prot	14 243	39.06
KEGG	14 364	39.39
COG	10 888	29.86
GO	9 617	26.37
合计Total	22 741	62.36

数据库Database	数量Number	比例Proportion/%
Nr	21 737	59.61
Nt	12 419	34.06
Swiss-Prot	14 243	39.06
KEGG	14 364	39.39
COG	10 888	29.86
GO	9 617	26.37
合计Total	22 741	62.36

KEGG通路 KEGG pathway	数量 Number	比例 Proportion/%	通路ID Pathway ID
代谢途径Metabolic pathways	4 584	32	ko01100
次生代谢物的生物合成Biosynthesis of secondary metabolites	1 897	13	ko01110
淀粉和蔗糖代谢Starch and sucrose metabolism	1 727	12	ko00500
氨基糖和核苷酸糖代谢Amino sugar and nucleotide sugar metabolism	833	6	ko00520
RNA转运RNA transport	829	6	ko03013
内质网中的蛋白质加工Protein processing in endoplasmic reticulum	570	4	ko04141
MAPK信号通路-酵母MAPK signaling pathway-yeast	530	4	ko04011
mRNA监测通路mRNA surveillance pathway	474	3	ko03015
嘌呤代谢Purine metabolism	458	3	ko00230
细胞周期-酵母Cell cycle-yeast	435	3	ko04111
剪接体Spliceosome	354	2	ko03040
赖氨酸降解Lysine degradation	337	2	ko00310
减数分裂-酵母Meiosis-yeast	321	2	ko04113
嘧啶的代谢Pyrimidine metabolism	312	2	ko00240
RNA降解RNA degradation	293	2	ko03018
ABC运输工具ABC transporters	273	2	ko02010
核糖体Ribosome	246	2	ko03010
过氧物酶体Peroxisome	230	2	ko04146
精氨酸和脯氨酸代谢Arginine and proline metabolism	229	2	ko00330
内吞作用Endocytosis	224	2	ko04144

KEGG通路 KEGG pathway	数量 Number	比例 Proportion/%	通路ID Pathway ID
代谢途径Metabolic pathways	4 584	32	ko01100
次生代谢物的生物合成Biosynthesis of secondary metabolites	1 897	13	ko01110
淀粉和蔗糖代谢Starch and sucrose metabolism	1 727	12	ko00500
氨基糖和核苷酸糖代谢Amino sugar and nucleotide sugar metabolism	833	6	ko00520
RNA转运RNA transport	829	6	ko03013
内质网中的蛋白质加工Protein processing in endoplasmic reticulum	570	4	ko04141
MAPK信号通路-酵母MAPK signaling pathway-yeast	530	4	ko04011
mRNA监测通路mRNA surveillance pathway	474	3	ko03015
嘌呤代谢Purine metabolism	458	3	ko00230
细胞周期-酵母Cell cycle-yeast	435	3	ko04111
剪接体Spliceosome	354	2	ko03040
赖氨酸降解Lysine degradation	337	2	ko00310
减数分裂-酵母Meiosis-yeast	321	2	ko04113
嘧啶的代谢Pyrimidine metabolism	312	2	ko00240
RNA降解RNA degradation	293	2	ko03018
ABC运输工具ABC transporters	273	2	ko02010
核糖体Ribosome	246	2	ko03010
过氧物酶体Peroxisome	230	2	ko04146
精氨酸和脯氨酸代谢Arginine and proline metabolism	229	2	ko00330
内吞作用Endocytosis	224	2	ko04144

COG功能描述COG function description	数量Number	比例Proportion/%
ABC型多药转运系统,ATP酶和渗透酶成分	21	24
推测的多铜氧化酶Putative multicopper oxidases	18	21
ABC-type multidrug transport system, ATPase and permease components
RNA结合蛋白(RRM域) RNA-binding proteins (RRM domain)	12	14
RTX毒素和相关的Ca²⁺结合蛋白RTX toxins and related Ca²⁺-binding proteins	11	13
NADPH:醌还原酶和相关的Zn依赖性氧化还原酶	8	9
NADPH:quinone reductase and related Zn-dependent oxidoreductases
酰胺酶A亚单位和相关的酰胺酶	4	5
Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases
超家族I DNA和RNA螺旋酶和螺旋酶亚基	2	2
Superfamily I DNA and RNA helicases and helicase subunits
参与染色质重塑的转录因子,含溴结构域	2	2
参与大肠杆菌素摄取的膜蛋白Membrane protein involved in colicin uptake	1	1
Transcription factor involved in chromatin remodeling, contains bromodomain
翻译起始因子2 (IF-2; GTPase) Translation initiation factor 2 (IF-2; GTPase)	1	1
未知Unknown	6	7

Transcriptome sequencing and analysis of potential pathogenicity-related genes in Isaria fumosorosea

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重复次数 Number of repeats	单核苷酸重复 Mono-nucleotide repeats	二核苷酸重复 Di-nucleotide repeats	三核苷酸重复 Tri-nucleotide repeats	四核苷酸重复 Quad-nucleotide repeat	五核苷酸重复 Penta-nucleotide repeats	六核苷酸重复 Hexa-nucleotide repeats	总数 Total	比例 Proportion/%
4	0	0	0	0	136	193	329	3.84
5	0	0	1 890	157	15	0	2 062	24.06
6	0	630	1 223	72	0	0	1 925	22.46
7	0	405	908	0	0	0	1 313	15.32
8	0	247	56	0	0	0	303	3.53
9	0	201	0	0	0	0	201	2.34
10	0	230	0	0	0	0	230	2.68
11	0	145	0	0	0	0	145	1.69
12	611	11	0	0	0	0	622	7.26
13	424	0	0	0	0	0	424	4.95
14	309	0	0	0	0	0	309	3.60
15	192	0	0	0	0	0	192	2.24
16	121	0	0	0	0	0	121	1.41
17	79	0	0	0	0	0	79	0.92
18	51	0	0	0	0	0	51	0.59
19	84	0	0	0	0	0	84	0.98
20	62	0	0	0	0	0	62	0.72
21	64	0	0	0	0	0	64	0.75
22	35	0	0	0	0	0	35	0.41
23	18	0	0	0	0	0	18	0.21
24	3	0	0	0	0	0	3	0.03
总数Total	2,053	1,869	4,077	229	151	193	8 572
百分比	23.95	21.80	47.56	2.67	1.76	2.25		100
Percentage/%

重复类型 Repeat type	重复基序 Repeat motif	数量 Number	发生频率 Frequency/%
单核苷酸Mono	A/T	1 810	88.16
	C/G	243	11.84
小计Subtotal		2 053
二核苷酸Di	AC/GT	667	35.69
	AG/CT	1043	55.81
	AT/AT	64	3.42
	CG/CG	95	5.08
小计Subtotal		1 869
三核苷酸Tri	CCG/CGG	1159	28.43
	AGC/CTG	794	19.48
	AAG/CTT	536	13.15
	ACG/CGT	473	11.60
	AGG/CCT	423	10.38
	ACC/GGT	390	9.57
其他Others		302	7.41
小计Subtotal		4 077
四核苷酸Tetra	AAAG/CTTT	34	14.85
	AGGC/CCTG	33	14.41
	ACAG/CTGT	30	13.10
	ATCC/ATGG	29	12.66
	ACCT/AGGT	21	9.17
	AGCC/CTGG	20	8.73
	ACTC/AGTG	19	8.30
其他Others		43	18.78
小计Subtotal		229
五核苷酸Penta	AAAAG/CTTTT	34	22.52
	AAAAT/ATTTT	20	13.25
	AGAGG/CCTCT	15	9.93
	AGGGC/CCCTG	12	7.95
	AGCCC/CTGGG	6	3.97
	AGGCG/CCTCG	5	3.31
其他Others		59	39.07
小计Subtotal		151
六核苷酸Hexa	ACGGCG/CCGTCG	16	8.04
	AGCGGC/CCGCTG	9	4.52
	ACTGCC/AGTGGC	7	3.52
	ACCGGC/CCGGTG	6	3.02
	ACGCCC/CGTGGG	6	3.02
	AGCCGG/CCGGCT	6	3.02
其他Others		149	74.87
小计Subtotal		199

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[3]	YUAN Xiaochun, WANG Yifan, WANG Yayan, SUN Haoran, MENG Ke, LI Xinhai. Identification and analysis of alternative splicing events related to sheep hair follicle development based on RNA sequencing technology [J]. Acta Agriculturae Zhejiangensis, 2023, 35(9): 2056-2067.
[4]	LI Biyuan, YUE Zhichen, ZHAO Yanting, LEI Juanli, HU Qizan, TAO Peng. Identification and functional analysis of the BrLCYB gene of lycopene β-cyclase from Chinese cabbage [J]. Acta Agriculturae Zhejiangensis, 2023, 35(9): 2090-2096.
[5]	SONG Chuansheng, KANG Xiaofei, FAN Qingzhong, WANG Jungang, SHI Xue, ZHANG Ziru, TAN Qingqing, ZENG Xiaojiao, LIU Fang, LI Yingsai, HOU Changyue. Cloning, sequence analysis, prokaryotic expression of thymidine kinase from jujube witches’-broom phytoplasma [J]. Acta Agriculturae Zhejiangensis, 2023, 35(8): 1763-1772.
[6]	YUAN Ye, LIU Rui, WANG Lingyun, SHEN Meng, YE Xuelian, QUAN Xinhua, WANG Ruisen, YAO Xiangtan. Genetic diversity analysis of Trapa L. cultivars in Jiangsu and Zhejiang Provinces using SLAF-seq [J]. Acta Agriculturae Zhejiangensis, 2023, 35(8): 1773-1781.
[7]	XUE Chengjin, ZHAO Lanxin, ZHAO Degang, HUANG Xiaozhen. Identification and expression analysis of NPR gene family members and cloning of cold-induced CsNPR3 gene in tea plants (Camellia sinensis) [J]. Acta Agriculturae Zhejiangensis, 2023, 35(7): 1511-1522.
[8]	ZHANG Li, WANG Yuanyuan, WANG Rui, LIU Lixia. Cloning sequencing and bioinformatics analysis of DRA gene of yak [J]. Acta Agriculturae Zhejiangensis, 2023, 35(7): 1564-1570.
[9]	SHOU Weisong, HE Yanjun, SHEN Jia, XU Xinyang. Genome-wide identification and bioinformatics analysis of SWEET gene family in melon [J]. Acta Agriculturae Zhejiangensis, 2023, 35(7): 1591-1603.
[10]	LI Bicong, LI Huiying, XIAO Yao, LUO Sha, ZHOU Qinghong, HUANG Yingjin, ZHU Qianglong. Genome-wide identification and expression analysis of expansin gene family in corm expansion of Colocasia esculenta [J]. Acta Agriculturae Zhejiangensis, 2023, 35(7): 1604-1616.
[11]	LIU Guangrui, ZONG Yuan, LI Yun, CAO Dong, LIU Baolong, BAO Xuemei, LI Jianmin. Cloning and functional research of MYB transcription factor AsMYB44 from Angelica sinensis [J]. Acta Agriculturae Zhejiangensis, 2023, 35(6): 1253-1264.
[12]	ZHANG Xinye, LI Wenjing, ZHU Shu, SUN Yanxiang, WANG Congyan, YAN Xunyou, ZHOU Zhiguo. Identification and analysis of PAT gene family in three kinds of Apiaceae vegetable crops [J]. Acta Agriculturae Zhejiangensis, 2023, 35(6): 1315-1327.
[13]	LUO Hailin, YUAN Lei, YAN Jiahui, GUO Qingyun. Cloning and identification of Pepper cryptic virus 2 in Qinghai Province, China [J]. Acta Agriculturae Zhejiangensis, 2023, 35(6): 1368-1374.
[14]	JIA Beiping, LYU Xuan, YANG Qing, WANG Yinan, LI Wanxiao, XIE Xindi, ZHU Yingqi, WANG Bei, YIN Dongdong, ZHANG Yunkai, WANG Qing, WANG Guijun. Isolation, identification and genetic evolution analysis of novel goose astrovirus in Anhui Province, China [J]. Acta Agriculturae Zhejiangensis, 2023, 35(5): 1048-1057.
[15]	ZHANG Shuhong, ZHANG Yunfeng, WU Qiuying, GAO Fengju, LI Yazi, JI Jingxin, XU Ke, FAN Yongshan. Identification and bioinformatics analysis of alcohol dehydrogenase gene family of Setosphaeria turcica [J]. Acta Agriculturae Zhejiangensis, 2023, 35(5): 1108-1115.