Draft genomes sequence of Elsinoë murrayae and comparative genomic analysis

doi:10.12302/j.issn.1000-2006.202108023

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2022, Vol. 46 ›› Issue (3): 143-150.doi: 10.12302/j.issn.1000-2006.202108023

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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

Abstract

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

CLC Number:

S763

CHENG Qiang, ZHAO Lijuan. Draft genomes sequence of Elsinoë murrayae and comparative genomic analysis[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2022, 46(3): 143-150.

Figures/Tables 7

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References 30

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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

Draft genomes sequence of Elsinoë murrayae and comparative genomic analysis

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