High-Quality Genome Sequence Resource of Elsinoë arachidis Strain LY-HS-1, Causing Scab Disease of Peanut

HomePlant DiseaseVol. 106, No. 5High-Quality Genome Sequence Resource of Elsinoë arachidis Strain LY-HS-1, Causing Scab Disease of Peanut PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseHigh-Quality Genome Sequence Resource of Elsinoë arachidis Strain LY-HS-1, Causing Scab Disease of PeanutJiyu Su, Juan Liu, Yanping Hu, Yiping Wang, Yue Jia, Xinyu Liang, Shaobin Fan, Hongli Hu, and Jiandong BaoJiyu SuCollege of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, ChinaSearch for more papers by this author, Juan LiuCollege of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, ChinaSearch for more papers by this author, Yanping HuCollege of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, ChinaSearch for more papers by this author, Yiping WangCollege of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, ChinaSearch for more papers by this author, Yue JiaCollege of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, ChinaSearch for more papers by this author, Xinyu LiangCollege of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, ChinaSearch for more papers by this author, Shaobin FanCollege of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, ChinaSearch for more papers by this author, Hongli Hu†Corresponding authors: J. Bao; E-mail Address: baojd@zaas.ac.cn, and H. Hu; E-mail Address: huhongli7905@gmail.comhttps://orcid.org/0000-0003-3994-0596College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, ChinaSearch for more papers by this author, and Jiandong Bao†Corresponding authors: J. Bao; E-mail Address: baojd@zaas.ac.cn, and H. Hu; E-mail Address: huhongli7905@gmail.comhttps://orcid.org/0000-0003-3423-5118College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, ChinaThe Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaSearch for more papers by this author AffiliationsAuthors and Affiliations Jiyu Su1 Juan Liu2 Yanping Hu1 Yiping Wang2 Yue Jia1 Xinyu Liang1 Shaobin Fan1 Hongli Hu1 † Jiandong Bao2 3 † 1College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China 2College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China 3The Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China Published Online:31 Mar 2022https://doi.org/10.1094/PDIS-11-21-2549-AAboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Genome AnnouncementPeanut scab is one of the most serious diseases of peanut (Arachis hypogaea L.). The scab pathogen can infect leaves, stem, root, and fruit pods of peanut, and cause damage to the production and quality of peanut. The causal pathogen of this disease was first reported as Sphaceloma arachidis by Bitancourt and Jenkins (1940). Now it is considered to be the anamorphic stage of Elsinoë arachidis (Rossman et al. 2016). However, we know little about the genome of this fungus.Currently, all reported species of Elsinoë or Sphaceloma have been shown to cause disease in different plant species (Fan et al. 2017). Genomes of four Elsinoë spp. have been reported, including E. ampelina (the pathogen of grape scab) (Li et al. 2020), E. australis (the pathogen of sweet orange scab) (Shanmugam et al. 2020), E. batatas (the pathogen of sweet potato scab) (X. Zhang et al. 2021), and E. fawcettii (the pathogen of sour orange scab) (Shanmugam et al. 2020). However, the genomic information of E. arachidis is not yet clear. We obtained fungal strain LY-HS-1 from infected leaves of peanut with scab symptoms at Zhongdu Town, Longyan City, Fujian Province of China. This strain was identified as E. arachidis by combining morphological characteristics and multiloci phylogenetic analyses based on internal transcribed spacer, β-tubulin, and transcript elongation factor genes, as in a previous study (Z. Zhang et al. 2021). Colony characteristics of LY-HS-1 cultured on potato dextrose agar plates included light vinaceous fawn with darker areas, and sometimes black and humid margins. These observations conform to morphological attributes described for E. arachidis (Bitancourt and Jenkins 1940). There are two kinds of conidia of this strain; one is subglobose, hyaline, one-celled, 3.8 to 6.3 by 3.2 to 6.0 μm, and the other is short, oblong, hyaline, one-celled, 5.9 to 7.3 by 2.8 to 4.4 μm.High-quality genomic DNA was extracted from the 21-day-old mycelia cultivated on potato dextrose broth, and sent to the Center for Genomics and Biotechnology at Fujian Agriculture and Forestry University for whole-genome sequencing. We obtained 4,225,118,962 bp (approximately 125×; N50 = 12.28 kb) long reads using the PacBio RS II sequencing platform, and 5,010,874,200 bp (approximately 154×) 150-bp paired-end (PE150) short reads (fragment size approximately 350 bp) using the Illumina HiSeq 3000 sequencing platform (Table 1).Table 1. Genome characteristics of Elsinoë arachidis strain LY-HS-1FeaturesLY-HS-1PacBio long reads4.23 Gb (N50: 12.28 kb)Illumina short reads5.01 Gb (approximately 154×)Mapping rate (%)a97.43 (94.72)Assembly size (bp)32,441,132Contig number20Contig N50 (bp)3,832,059Contig L504Maximum contig length (bp)4,640,811GC content48.09%Repeat sequences21.49%Protein-coding genes9,435Genes annotated by Pfamb6,729Genes annotated by GOb4,238Genes annotated by KEGGb3,845Genes annotated by KOGb7,068Genes annotated by CAZysc405Pathogen–host interaction genes2,082Cytochrome P450 enzymes92Putative secreted proteins456SMBGCsd21aPercentage of mapped Illumina short reads by BWA.bPfam and Gene Ontology (GO) were annotated by InterProScan, while Kyoto Encyclopedia of Genes and Genomes (KEGG) and EuKaryotic Orthologous Groups (KOG) were annotated by eggNOG-mapper v2.cCAZys = carbohydrate-active enzymes.dSecondary metabolite biosynthesis gene clusters (SMBGCs) analyzed by antiSMASH v5.2.0.Table 1. Genome characteristics of Elsinoë arachidis strain LY-HS-1View as image HTML Because genome size is a key parameter for genome assembling, it was estimated by GenomeScope v2.0 (Ranallo-Benavidez et al. 2020) according to k-mer distribution of Illunima short reads (k = 21). The results showed that the average k-mer depth was 127 (Fig. 1A, main peak). The estimated genome size was 31,713,099 bp with 20.1% repeats (Fig. 1A).Fig. 1. Genome features of Elsinoë arachidis strain LY-HS-1. A, Genome size estimation using GenomeScope v2.0 with Illumina short reads. B, Completeness of genome assembly assessed by BUSCO v5.2.2 at fungi and ascomycota level. C, Orthologous gene clusters analysis among different species conducted by OrthoVenn2.Download as PowerPointA de novo draft genome assembly was first generated by HGAP4 (Chin et al. 2013), included in the SMRTlink software v6.0.0 (expected genome size = 32 Mb), using PacBio long reads. Then, the draft genome assembly was base corrected by NextPolish v1.3.1 (Hu et al. 2020) using both PacBio long reads and Illumina short reads. The final polished genome assembly of LY-HS-1 was 32.44 Mb in size (GC content = 48.09%), which is very close to the estimated genome size (31.71 Mb). The genome assembly consisted of 20 contigs with N50 of 3.83 Mb (L50 = 4), and a maximum length of 4.64 Mb (Table 1).Genome completeness was evaluated by benchmarking universal single-copy ortholog (BUSCO) v5.2.2 (Manni et al. 2021) and mapping rate of short genomic sequencing reads using BWA v0.7.17 (Li and Durbin 2009). The BUSCO completeness analysis showed that the genome assembly of LY-HS-1 contained 747 (98.55%) and 1,673 (98.07%) complete single-copy orthologs at the fungi (n = 758) and ascomycota (n = 1,706) level, respectively (Fig. 1B). In total, 97.43% of Illumina short reads were mapped to the final genome assembly, of which 94.72% reads were properly paired (Table 1). Also, telomere repeats (5′-TTAGGG-3′/5′-CCCTAA-3′) at the both end of contigs were detected to value the genome assembly completeness. Of 20 contigs, 8 contigs had both ends with telomere repeats; in other words, these contigs were reached at a telomere-to-telomere (T2T) chromosomal level. These results supported that our assembly has both high continuity and high completeness.Repeats were masked by RepeatMasker v4.1.2 (http://www.repeatmasker.org/) with a de novo repeat library generated by RepeatModeler v2.02 (http://www.repeatmasker.org/RepeatModeler/). In total, 6,970,582 bp (21.49%) repeat sequences were identified in the genome assembly of LY-HS-1 (Table 1). The repeats mainly consisted of long terminal repeat elements (5,359,827 bp, 76.89%) and unclassified interspersed repeats (1,102,080 bp, 15.81%). Using the soft-repeat-masked genome assembly, 9,435 protein-coding genes were identified by BRAKER v2.1.6 (Brůna et al. 2021), which integrated gene structure evidence from Augustus v3.4.0 (Stanke et al. 2008) and GeneMark-ET (Brůna et al. 2020) with the fungal homologous proteins fungi_odb10 (https://busco-data.ezlab.org/v5/data/lineages/) (Table 1).Gene functional annotation was conducted by eggNOG-mapper v2 (Huerta-Cepas et al. 2019) and InterProScan v5.52-86.0 (Jones et al. 2014) with a set of popular bioinformatic databases, including Pfam (6,729 genes, 71.32%), Gene Ontology (4,238 genes, 44.92%), Kyoto Encyclopedia of Genes and Genomes (3,845 genes, 40.75%), and EuKaryotic Orthologous Groups (7,068 genes, 74.91%) (Table 1). The top Pfam annotations included major facilitator superfamily (PF07690, 183 genes), protein kinase domain (PF00069, 116 genes), short chain dehydrogenase (PF00106, 93 genes), cytochrome P450 (PF00067, 92 genes), and fungal specific transcription factor domain (PF04082, 88 genes).We also identified 2,082 pathogen–host interaction genes (PHI-base v4.12, http://www.phi-base.org/), 405 carbohydrate-active enzymes distinguished by dbCAN2 (Lombard et al. 2014), and 456 putative secreted proteins following our previous pipeline (Bao et al. 2017) (Table 1). Furthermore, antiSMASH v5.2.0 (Blin et al. 2019) was applied to distinguish a total of 21 secondary metabolite biosynthesis gene clusters, which included 5 nonribosomal peptide synthetases (NRPSs), 6 NPRS-likes, 5 terpenes, and 5 type I polyketide synthases.To identify the potential host specificity determinants, whole-genome orthologous gene clustering were performed by OrthoVenn2 (Xu et al. 2019), comparing the genome assembly of E. arachidis strain LY-HS-1 with representative genome assemblies of the four previously reported Elsinoë spp. from other hosts (including Elsamp1 for E. ampelina, ASM538240v1 for E. australis, ASM1730932v2 for E. batatas, and ASM1297783v1 for E. fawcettii). The E. arachidis strain LY-HS-1 formed 8,559 orthologous gene clusters, of which, 6,918 (80.83%) were core gene clusters present in all five strains, and most of the core gene clusters (97.57%, 6,750 of 6,918) were single copy (Fig. 1C). The E. arachidis strain LY-HS-1 contained 26 unique gene clusters absent in other strains, and lost 374 gene clusters present in the other three strains (Fig. 1C). These present or absent gene variation may determine pathogenicity and host specificity of Elsinoë spp. The almost complete T2T genome assembly and well-annotated gene resources will help for better understanding of the pathogenicity of E. arachidis.The whole-genome assembly and genes reported in this article have been deposited in the Genome Warehouse (GWH) (https://ngdc.cncb.ac.cn/gwh/) (accession number GWHBFXO00000000) in the China National Center for Bioinformation National Genomics Data Center (CNCB-NGDC Members and Partners 2021). The raw sequence reads also are publicly accessible at Genome Sequence Archive (https://ngdc.cncb.ac.cn/gsa/) in CNCB-NGDC under accession number CRA005396 (BioProject: PRJCA007219).The author(s) declare no conflict of interest.Literature CitedBao, J., Chen, M., Zhong, Z., Tang, W., Lin, L., Zhang, X., Jiang, H., Zhang, D., Miao, C., Tang, H., Zhang, J., Lu, G., Ming, R., Norvienyeku, J., Wang, B., and Wang, Z. 2017. PacBio sequencing reveals transposable elements as a key contributor to genomic plasticity and virulence variation in Magnaporthe oryzae. Mol. Plant 10:1465-1468. https://doi.org/10.1016/j.molp.2017.08.008 Crossref, ISI, Google ScholarBitancourt, A. A., and Jenkins, A. E. 1940. Novas especies de Elsinoë e Sphaceloma sobre hospedes de importancia economica. Arq. Inst. Biol. (Sao Paulo) 11:45-58. Google ScholarBlin, K., Shaw, S., Steinke, K., Villebro, R., Ziemert, N., Lee, S. Y., Medema, M. H., and Weber, T. 2019. AntiSMASH 5.0: Updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 47:W81-W87. https://doi.org/10.1093/nar/gkz310 Crossref, ISI, Google ScholarBrůna, T., Hoff, K. J., Lomsadze, A., Stanke, M., and Borodovsky, M. 2021. BRAKER2: Automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genomics Bioinf. 3:lqaa108. https://doi.org/10.1093/nargab/lqaa108 Crossref, Google ScholarBrůna, T., Lomsadze, A., and Borodovsky, M. 2020. GeneMark-EP+: Eukaryotic gene prediction with self-training in the space of genes and proteins. NAR Genomics Bioinf. 2:lqaa026. https://doi.org/10.1093/nargab/lqaa026 Crossref, Google ScholarChin, C. S., Alexander, D. H., Marks, P., Klammer, A. A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E. E., Turner, S. W., and Korlach, J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10:563-569. https://doi.org/10.1038/nmeth.2474 Crossref, ISI, Google ScholarCNCB-NGDC Members and Partners. 2021. Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Res. 49:D18-D28. https://doi.org/10.1093/nar/gkaa1022 Crossref, ISI, Google ScholarFan, X. L., Barreto, R. W., Groenewald, J. Z., Bezerra, J. D. P., Pereira, O. L., Cheewangkoon, R., Mostert, L., Tian, C. M., and Crous, P. W. 2017. Phylogeny and taxonomy of the scab and spot anthracnose fungus Elsinoë (Myriangiales, Dothideomycetes). Stud. Mycol. 87:1-41. https://doi.org/10.1016/j.simyco.2017.02.001 Crossref, ISI, Google ScholarHu, J., Fan, J., Sun, Z., and Liu, S. 2020. NextPolish: A fast and efficient genome polishing tool for long-read assembly. Bioinformatics 36:2253-2255. https://doi.org/10.1093/bioinformatics/btz891 Crossref, ISI, Google ScholarHuerta-Cepas, J., Szklarczyk, D., Heller, D., Hernández-Plaza, A., Forslund, S. K., Cook, H., Mende, D. R., Letunic, I., Rattei, T., Jensen, L. J., von Mering, C., and Bork, P. 2019. eggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47:D309-D314. https://doi.org/10.1093/nar/gky1085 Crossref, ISI, Google ScholarJones, P., Binns, D., Chang, H. Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., Pesseat, S., Quinn, A. F., Sangrador-Vegas, A., Scheremetjew, M., Yong, S. Y., Lopez, R., and Hunter, S. 2014. InterProScan 5: Genome-scale protein function classification. Bioinformatics 30:1236-1240. https://doi.org/10.1093/bioinformatics/btu031 Crossref, ISI, Google ScholarLi, H., and Durbin, R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760. https://doi.org/10.1093/bioinformatics/btp324 Crossref, ISI, Google ScholarLi, Z., Fan, Y., Chang, P., Gao, L., and Wang, X. 2020. Genome sequence resource for Elsinoë ampelina, the causal organism of grapevine anthracnose. Mol. Plant-Microbe Interact. 33:576-579. https://doi.org/10.1094/MPMI-12-19-0337-A Link, ISI, Google ScholarLombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P. M., and Henrissat, B. 2014. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42:D490-D495. https://doi.org/10.1093/nar/gkt1178 Crossref, ISI, Google ScholarManni, M., Berkeley, M. R., Seppey, M., Simão, F. A., and Zdobnov, E. M. 2021. BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Methods Mol. Biol. 38:4647-4654. https://doi.org/10.1093/molbev/msab199 Google ScholarRanallo-Benavidez, T. R., Jaron, K. S., and Schatz, M. C. 2020. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat. Commun. 11:1432. https://doi.org/10.1038/s41467-020-14998-3 Crossref, ISI, Google ScholarRossman, A. Y., Allen, W. C., and Castlebury, L. A. 2016. New combinations of plant-associated fungi resulting from the change to one name for fungi. IMA Fungus 7:1-7. https://doi.org/10.5598/imafungus.2016.07.01.01 Crossref, ISI, Google ScholarShanmugam, G., Jeon, J., and Hyun, J. K. 2020. Draft genome sequences of Elsinoë fawcettii and Elsinoë australis causing scab diseases on Citrus. Mol. Plant-Microbe Interact. 33:135-137. https://doi.org/10.1094/MPMI-06-19-0169-A Link, ISI, Google ScholarStanke, M., Diekhans, M., Baertsch, R., and Haussler, D. 2008. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24:637-644. https://doi.org/10.1093/bioinformatics/btn013 Crossref, ISI, Google ScholarXu, L., Dong, Z., Fang, L., Luo, Y., Wei, Z., Guo, H., Zhang, G., Gu, Y. Q., Coleman-Derr, D., Xia, Q., and Wang, Y. 2019. OrthoVenn2: A web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res. 47:W52-W58. https://doi.org/10.1093/nar/gkz333 Crossref, ISI, Google ScholarZhang, X., Zou, H., Yang, Y., Fang, B., and Huang, L. 2021. Genome resource for Elsinoë batatas, the causal agent of stem and foliage scab disease of sweet potato. Phytopathology. https://doi.org/10.1094/PHYTO-08-21-0344-A Link, ISI, Google ScholarZhang, Z., Xu, S., Kong, M., Dai, H., Liu, Y., and Miao, M. 2021. Isolation, identification and artificial inoculation of Ustilago esculenta on Zizania latifolia. Hortic. Plant J. 7:347-358. https://doi.org/10.1016/j.hpj.2020.08.004 Crossref, ISI, Google ScholarFunding: This work was supported by grants from the National Natural Science Foundation of China (31800008), FAFU Technology and Innovation Project (CXZX2016137), Natural Science Foundation of Fujian Province, China (2019J01385), and Starting Research Foundation for Young Scholars from Zhejiang Academy of Agricultural Sciences (10403010120CF0401G/002).The author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Vol. 106, No. 5 May 2022SubscribeISSN:0191-2917e-ISSN:1943-7692 Download Metrics Downloaded 481 times Article History Issue Date: 28 Apr 2022Published: 31 Mar 2022Accepted: 28 Jan 2022 Pages: 1506-1509 Information© 2022 The American Phytopathological SocietyFundingNational Natural Science Foundation of ChinaGrant/Award Number: 31800008FAFU Technology and Innovation ProjectGrant/Award Number: CXZX2016137Natural Science Foundation of Fujian Province, ChinaGrant/Award Number: 2019J01385Starting Research Foundation for Young Scholars from Zhejiang Academy of Agricultural SciencesGrant/Award Number: 10403010120CF0401G/002KeywordsElsinoë arachidisgenome assemblyLY-HS-1peanut scabThe author(s) declare no conflict of interest.PDF download