柳树痂囊腔菌的基因组测序和比较基因组分析

doi:10.12302/j.issn.1000-2006.202108023

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南京林业大学学报（自然科学版） ›› 2022, Vol. 46 ›› Issue (3): 143-150.doi: 10.12302/j.issn.1000-2006.202108023

柳树痂囊腔菌的基因组测序和比较基因组分析

程强(), 赵丽娟

南京林业大学,林木遗传与生物技术省部共建教育部重点实验室,南方现代林业协同创新中心,江苏南京 210037

收稿日期:2021-08-12 接受日期:2021-10-22 出版日期:2022-05-30 发布日期:2022-06-10
基金资助:
国家自然科学基金面上项目(31870658)

Draft genomes sequence of Elsinoë murrayae and comparative genomic analysis

CHENG Qiang(), ZHAO Lijuan

Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037,China

Received:2021-08-12 Accepted:2021-10-22 Online:2022-05-30 Published:2022-06-10

摘要/Abstract

摘要：

【目的】报道柳树痂囊腔菌(Elsinoë murrayae)的全基因组序列,与甜橙痂囊腔菌杨树致病型的基因组进行比较分析,为阐述柳树痂囊腔菌的致病和适应性机制提供参考。【方法】采用Illumina HiSeq 2500 测序仪对柳树痂囊腔菌的全基因组序列进行测序,预测蛋白编码基因,筛选与致病相关的碳水化合物活性酶基因、小分泌蛋白基因和次生代谢产物基因簇。根据痂囊腔属真菌基因的直系同源关系,筛选柳树痂囊腔菌和甜橙痂囊腔菌杨树致病型之间共有特异性的基因和二者之间差异基因,并进行GO富集分析。鉴定柳树痂囊腔菌的交配类型位点,使用特异性引物进行PCR,检测分离株的交配类型。【结果】组装获得了1个20.7 Mb基因组,完整度99%;预测出8 256个蛋白编码基因,其中包括486个碳水化合物活性酶基因,193个小分泌蛋白基因和16个次生代谢产物基因簇 (GenBank登录号:NKHZ00000000)。系统进化和共线性分析显示柳树痂囊腔菌和甜橙痂囊腔菌杨树致病型亲缘关系最近,两者之间具有12个在其他痂囊腔菌中没有的共有特异性基因。两个真菌的比较基因组分析,筛选出752和1 746个差异基因,主要参与碳水化合物代谢和毒素代谢的生物学过程。已有分离株的交配类型均为MAT1-2。【结论】获得柳树病原真菌-柳树痂囊腔菌的基因组,筛选出痂囊腔菌中负责寄主适应性的候选基因,分析了柳树痂囊腔菌交配系统,这可为柳树病害防治和柳树-病原真菌相互作用研究提供关键信息。

关键词: 柳树痂囊腔菌, 柳树疮痂叶斑病, 基因组, 甜橙痂囊腔菌, 交配类型

Abstract:

【Objective】 This study reported the complete genome sequence of Elsinoë murrayae and comparisons with the Elsinoë australis poplar spot anthracnose (PSA) pathotype, aiming to provide a reference for explaining the pathogenic and specialized mechanism of E. murrayae. 【Method】 A draft genome sequence of E. murrayae was sequenced to annotate protein-coding genes and carbohydrate-active enzyme genes. Small secreted protein genes and secondary metabolite biosynthetic gene clusters were screened. According to the orthologous relationship of the genes of Elsinoë spp., the common specific genes of E. murrayae and E. australis (PSA) were identified, and the differential genes between E. murrayae and E. australis (PSA) were screened out and analyzed using GO enrichment. The mating type locus was identified, and the mating type of isolates was detected using PCR with specific primers. 【Result】 A 20.7 Mb genome with 99% completeness was obtained. A total of 8 256 protein-coding genes were predicted, including 486 carbohydrate-active enzyme genes, 193 small secreted protein genes, and 16 secondary metabolite biosynthetic gene clusters (GenBank accession No.: NKHZ00000000). The phylogenetic analysis and whole genome synteny comparisons showed that E. murrayae and E. australis (PSA) had the closest relationship, and the two fungi had 12 common specific genes which were not found in other Elsinoë spp. Compared with the two fungi, 752 and 1 746 different genes were screened, of which encoding proteins were mainly involved in carbohydrate metabolic processes and toxin metabolic processes. The mating type of all the isolates was MAT1-2. 【Conclusion】 The genome of E. murrayae, a fungal pathogen of willow, was reported for the first time. The candidate genes responsible for the host specialization were screened, and the mating system of E. murrayae was analyzed. These studies provided key information for willow disease control and willow-pathogen interaction.

Key words: Elsinoë murrayae, willow leaf scab disease, genome, Elsinoë australis, mating type

中图分类号:

S763

程强,赵丽娟. 柳树痂囊腔菌的基因组测序和比较基因组分析[J]. 南京林业大学学报（自然科学版）, 2022, 46(3): 143-150.

CHENG Qiang, ZHAO Lijuan. Draft genomes sequence of Elsinoë murrayae and comparative genomic analysis[J].Journal of Nanjing Forestry University (Natural Science Edition), 2022, 46(3): 143-150.DOI: 10.12302/j.issn.1000-2006.202108023.

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参考文献 30

[1]	DICKMANN D I. Silviculture and biology of short-rotation woody crops in temperate regions: then and now[J]. Biomass Bioenergy, 2006, 30(8/9):696-705.DOI: 10.1016/j.biombioe.2005.02.008. doi: 10.1016/j.biombioe.2005.02.008
[2]	ZHAO P, KAKISHIMA M, WANG Q, et al. Resolving the Melampsora epitea complex[J]. Mycologia, 2017, 109(3):391-407.DOI: 10.1080/00275514.2017.1326791. doi: 10.1080/00275514.2017.1326791
[3]	WANG Y L, LU Q, JIA X Z, et al. First report of branch canker caused by Cytospora atrocirrhata on Populus sp.and Salix sp.in China[J]. Plant Dis, 2013, 97(3):426.DOI: 10.1094/PDIS-09-12-0854-PDN. doi: 10.1094/PDIS-09-12-0854-PDN
[4]	AYLWARD J, STEENKAMP E T, DREYER L L, et al. A plant pathology perspective of fungal genome sequencing[J]. IMA Fungus, 2017, 8(1):1-15.DOI: 10.5598/imafungus.2017.08.01.01. doi: 10.5598/imafungus.2017.08.01.01
[5]	BUTIN H, KEHR R. Sphaceloma murrayae Jenk.& Grods.,a pathogen new to Europe on Salix spp.[J]. Forest Pathol, 2004, 34(1):27-31.DOI: 10.1046/j.1439-0329.2003.00344.x. doi: 10.1046/j.1439-0329.2003.00344.x.
[6]	SPIERS A G, HOPCROFT D H. Some electron microscope observations of conidium ontogeny of Sphaceloma murrayae on Salix[J]. N Z J Bot, 1992, 30(3):353-358.DOI: 10.1080/0028825X.1992.10412912. doi: 10.1080/0028825X.1992.10412912
[7]	ZHAO L J, ZHANG W T, XIAO H J, et al. Molecular identification and characterization of Elsinoë murrayae (Synonym:Sphaceloma murrayae) from weeping willow[J]. J Phytopathol, 2018, 166(2):143-149.DOI: 10.1111/jph.12670. doi: 10.1111/jph.12670
[8]	ZHAO L J, XIAO H J, MA X J, et al. Elsinoë australis causing spot anthracnose on poplar in China[J]. Plant Dis, 2020, 104(8):2202-2209.DOI: 10.1094/pdis-11-19-2349-re. doi: 10.1094/pdis-11-19-2349-re
[9]	LUO R B, LIU B H, XIE Y L, et al. SOAPdenovo2:an empirically improved memory-efficient short-read de novo assembler[J]. GigaScience, 2012, 1(1):18.DOI: 10.1186/2047-217X-1-18. doi: 10.1186/2047-217X-1-18
[10]	WATERHOUSE R M, SEPPEY M, SIMÃO F A, et al. BUSCO applications from quality assessments to gene prediction and phylogenomics[J]. Mol Biol Evol, 2018, 35(3):543-548.DOI: 10.1093/molbev/msx319. doi: 10.1093/molbev/msx319
[11]	TER-HOVHANNISYAN V, LOMSADZE A, CHERNOFF Y O, et al. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training[J]. Genome Res, 2008, 18(12):1979-1990.DOI: 10.1101/gr.081612.108. doi: 10.1101/gr.081612.108
[12]	LAGESEN K, HALLIN P, RØDLAND E A, et al. RNAmmer:consistent and rapid annotation of ribosomal RNA genes[J]. Nucleic Acids Res, 2007, 35(9):3100-3108.DOI: 10.1093/nar/gkm160. doi: 10.1093/nar/gkm160
[13]	LOWE T M, CHAN P P. tRNAscan-SE on-line:integrating search and context for analysis of transfer RNA genes[J]. Nucleic Acids Res, 2016, 44(1):54-57.DOI: 10.1093/nar/gkw413. doi: 10.1093/nar/gkw413
[14]	ZHANG H, YOHE T, HUANG L, et al. dbCAN2:a meta server for automated carbohydrate-active enzyme annotation[J]. Nucleic Acids Res, 2018, 46(1):95-101.DOI: 10.1093/nar/gky418. doi: 10.1093/nar/gky418
[15]	ALMAGRO ARMENTEROS J J, TSIRIGOS K D, SØNDERBY C K, et al. Signal P 5.0 improves signal peptide predictions using deep neural networks[J]. Nat Biotechnol, 2019, 37(4):420-423.DOI: 10.1038/s41587-019-0036-z. doi: 10.1038/s41587-019-0036-z
[16]	KROGH A, LARSSON B, VON HEIJNE G, et al. Predicting transmembrane protein topology with a hidden Markov model:application to complete genomes[J]. J Mol Biol, 2001, 305(3):567-580.DOI: 10.1006/jmbi.2000.4315. doi: 10.1006/jmbi.2000.4315
[17]	BLIN K, SHAW S, STEINKE K, et al. antiSMASH 5.0:updates to the secondary metabolite genome mining pipeline[J]. Nucleic Acids Res, 2019, 47(1):81-87.DOI: 10.1093/nar/gkz310. doi: 10.1093/nar/gkz310
[18]	KUMAR S, STECHER G, TAMURA K. MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Mol Biol Evol, 2016, 33(7):1870-1874.DOI: 10.1093/molbev/msw054. doi: 10.1093/molbev/msw054
[19]	CASTILLO A I, NELSON A D L, HAUG-BALTZELL A K, et al. A tutorial of diverse genome analysis tools found in the CoGe web-platform using Plasmodium spp.as a model[J]. Database (Oxford), 2018,2018(10.1093):database.DOI: 10.1093/database/bay030. doi: 10.1093/database/bay030
[20]	LI L, STOECKERT C J, ROOS D S. OrthoMCL: identification of ortholog groups for eukaryotic genomes[J]. Genome Res, 2003, 13(9):2178-2189. DOI: 10.1101/gr.1224503. doi: 10.1101/gr.1224503
[21]	CHEN C J, CHEN H, ZHANG Y, et al. TBtools:an integrative toolkit developed for interactive analyses of big biological data[J]. Mol Plant, 2020, 13(8):1194-1202.DOI: 10.1016/j.molp.2020.06.009. doi: 10.1016/j.molp.2020.06.009
[22]	STERGIOPOULOS I, DE WIT P J. Fungal effector proteins[J]. Annu Rev Phytopathol, 2009, 47:233-263.DOI: 10.1146/annurev.phyto.112408.132637. doi: 10.1146/annurev.phyto.112408.132637
[23]	EBERT M K, SPANNER R E, DE JONGE R, et al. Gene cluster conservation identifies melanin and perylenequinone biosynthesis pathways in multiple plant pathogenic fungi[J]. Environ Microbiol, 2019, 21(3):913-927.DOI: 10.1111/1462-2920.14475. doi: 10.1111/1462-2920.14475
[24]	LI Z, FAN Y C, CHANG P P, et al. Genome sequence resource for Elsinoë ampelina,the causal organism of grapevine anthracnose[J]. Mol Plant Microbe Interact, 2020, 33(4):576-579.DOI: 10.1094/MPMI-12-19-0337-A. doi: 10.1094/MPMI-12-19-0337-A
[25]	JEFFRESS S, ARUN-CHINNAPPA K, STODART B, et al. Genome mining of the Citrus pathogen Elsinoë fawcettii;prediction and prioritisation of candidate effectors,cell wall degrading enzymes and secondary metabolite gene clusters[J]. PLoS One, 2020, 15(5):e0227396.DOI: 10.1371/journal.pone.0227396. doi: 10.1371/journal.pone.0227396
[26]	SHANMUGAM G, JEON J, HYUN J W. Draft genome sequences of Elsinoë fawcettii and Elsinoë australis causing scab diseases on Citrus[J]. Mol Plant Microbe Interactions, 2020, 33(2):135-137.DOI: 10.1094/mpmi-06-19-0169-a. doi: 10.1094/mpmi-06-19-0169-a
[27]	FAN X L, BARRETO R W, GROENEWALD J Z, et al. Phylogeny and taxonomy of the scab and spot anthracnose fungus Elsinoë (Myriangiales,Dothideomycetes)[J]. Stud Mycol, 2017, 87:1-41.DOI: 10.1016/j.simyco.2017.02.001. doi: 10.1016/j.simyco.2017.02.001
[28]	NI M, FERETZAKI M, SUN S, et al. Sex in fungi[J]. Annu Rev Genet, 2011, 45:405-430.DOI: 10.1146/annurev-genet-110410-132536. doi: 10.1146/annurev-genet-110410-132536
[29]	WILKEN P M, STEENKAMP E T, WINGFIELD M J, et al. Which MAT gene? Pezizomycotina (Ascomycota) mating-type gene nomenclature reconsidered[J]. Fungal Biol Rev, 2017, 31(4):199-211.DOI: 10.1016/j.fbr.2017.05.003. doi: 10.1016/j.fbr.2017.05.003
[30]	CHUNG K R. Elsinoë fawcettii and Elsinoë australis:the fungal pathogens causing Citrus scab[J]. Mol Plant Pathol, 2011, 12(2):123-135.DOI: 10.1111/j.1364-3703.2010.00663.x. doi: 10.1111/j.1364-3703.2010.00663.x.

参数features	值 value
测序总长/Gb total sequencing length	6.3
总读序/Mb total reads	42
覆盖度/倍 coverage	241
基因组大小/bp genome size	20 718 688
scaffold数量 No. of scaffolds	98
GC含量/% GC content	54.49
N50/bp	598 889
最大scaffold/bp the largest scaffold	1 241 890
完整度/% completeness	99
基因总数量 total genes	8 317
蛋白编码基因数量 protein-coding genes	8 256
RNA编码基因数量 RNA genes	66
GenBank登录号 GenBank accession No.	NKHZ00000000

真菌 fungi	共线性长度/Mb the aligned sequence size	平均一致性/% the average identity	共线性基因数量 the aligned gene No.
EauPSA NL1	19.86	74.5	6 561
EauSOS Ea-1	19.55	74.4	6 278
E. ampelina YL-1	19.50	73.21	6 239
E. fawcettii SM16-1	19.83	73.21	6 234
E. fawcettii DAR-70024	19.84	73.19	6 298
E. fawcettii53147a	19.44	73.13	6 448
Myriangium duriaei	17.01	70.14	3 854

类型 type	蛋白编码基因位点编号 protein coding gene ID	备注 note
Emu特有候选效应因子 specific candidate effectors	CAC42_3192, CAC42_8023, CAC42_2167, CAC42_1169, CAC42_2412, CAC42_1591, CAC42_5276, CAC42_5678, CAC42_4451, CAC42_1857, CAC42_1930, CAC42_1933, CAC42_7685, CAC42_1560, CAC42_3502, CAC42_4601, CAC42_1000	在公共数据中无同源蛋白
Emu NL1与 Eau NL1(PSA) 共有特异性蛋白 the common specific proteins	CAC42_1526/B9Z65_5383,CAC42_1565/B9Z65_5438,CAC42_4946/B9Z65_8048,CAC42_5245/B9Z65_1324,CAC42_5855/B9Z65_7325,CAC42_6081/B9Z65_2782,CAC42_6597/B9Z65_8691,CAC42_7074/B9Z65_8229,CAC42_7195/B9Z65_4792,CAC42_7243/B9Z65_1695,CAC42_812/B9Z65_6144,CAC42_817/B9Z65_6139	只在E. murrayae 和E. australis中存在,而在Elsinoë属其他真菌中不存在的蛋白
Emu NL1编码的差异蛋白中的小分泌蛋白 the small secreted proteins	CAC42_1169, CAC42_3924, CAC42_6199, CAC42_1000, CAC42_1442, CAC42_1560, CAC42_1591, CAC42_167, CAC42_1716, CAC42_1857, CAC42_1930, CAC42_1933, CAC42_1940, CAC42_1950, CAC42_2080, CAC42_2167, CAC42_2188, CAC42_2412, CAC42_2777, CAC42_3191, CAC42_3192, CAC42_3469, CAC42_3502, CAC42_4233, CAC42_4451, CAC42_4601, CAC42_4934, CAC42_5276, CAC42_5346, CAC42_5678, CAC42_5688, CAC42_569, CAC42_5736, CAC42_5768, CAC42_6556, CAC42_6573, CAC42_673, CAC42_6843, CAC42_7315, CAC42_7685, CAC42_8023, CAC42_8203	E. murrayae NL1与E. australis NL1比对,所发现的差异蛋白,其中42个为小分泌蛋白

柳树痂囊腔菌的基因组测序和比较基因组分析

Draft genomes sequence of Elsinoë murrayae and comparative genomic analysis

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