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High-Quality Genome Sequence Resource of Lasiodiplodia theobromae JMB122, a Fungal Pathogen Causing Peach Gummosis

2022; American Phytopathological Society; Volume: 35; Issue: 10 Linguagem: Inglês

10.1094/mpmi-01-22-0013-a

1943-7706

Jian Meng, Dongmei Zhang, Jiajia Pan, Xueke Wang, Chunfa Zeng, Kaijie Zhu, Fan Wang, Junwei Liu, Guohuai Li,

Plant Pathogens and Resistance

HomeMolecular Plant-Microbe Interactions®Vol. 35, No. 10High-Quality Genome Sequence Resource of Lasiodiplodia theobromae JMB122, a Fungal Pathogen Causing Peach Gummosis PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseHigh-Quality Genome Sequence Resource of Lasiodiplodia theobromae JMB122, a Fungal Pathogen Causing Peach GummosisJian Meng, Dongmei Zhang, Jiajia Pan, Xueke Wang, Chunfa Zeng, Kaijie Zhu, Fan Wang, Junwei Liu, and Guohuai LiJian MengKey Laboratory of Horticultural Plant Biology-Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China, Dongmei ZhangKey Laboratory of Horticultural Plant Biology-Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China, Jiajia PanKey Laboratory of Horticultural Plant Biology-Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China, Xueke WangKey Laboratory of Horticultural Plant Biology-Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China, Chunfa ZengKey Laboratory of Horticultural Plant Biology-Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China, Kaijie ZhuKey Laboratory of Horticultural Plant Biology-Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China, Fan WangJiangxi Oil-tea Camellia, Jiujiang University, Jiujiang 332005, Jiangxi Province, China, Junwei Liu†Corresponding authors: J. Liu; E-mail Address: junwei.liu@mail.hzau.edu.cn, and G. Li; E-mail Address: liguohuai@mail.hzau.edu.cnhttp://orcid.org/0000-0002-8842-2253Key Laboratory of Horticultural Plant Biology-Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China, and Guohuai Li†Corresponding authors: J. Liu; E-mail Address: junwei.liu@mail.hzau.edu.cn, and G. Li; E-mail Address: liguohuai@mail.hzau.edu.cnKey Laboratory of Horticultural Plant Biology-Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei Province, ChinaAffiliationsAuthors and Affiliations Jian Meng1 Dongmei Zhang1 Jiajia Pan1 Xueke Wang1 Chunfa Zeng1 Kaijie Zhu1 Fan Wang2 Junwei Liu1 † Guohuai Li1 † 1Key Laboratory of Horticultural Plant Biology-Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China 2Jiangxi Oil-tea Camellia, Jiujiang University, Jiujiang 332005, Jiangxi Province, China Published Online:29 Sep 2022https://doi.org/10.1094/MPMI-01-22-0013-AAboutSectionsView articlePDFSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat View articleGenome AnnouncementPeach (Prunus persica) fungal gummosis is one of the most common and destructive diseases and severely restricts the growth and production of peach orchards throughout southern China, the United States, and Japan. Among the causal agents, Lasiodiplodia theobromae is a most-virulent pathogen that induces copious necrosis and gummosis, eventually resulting in reduced tree vigor and lifespan (Li et al. 2014; Wang et al. 2011; Zhang et al. 2020). This pathogen has a wide geographic distribution as the biotic agent in many economically important crops and woody trees, such as apple ring rot, grapevine bot canker, and mango dieback (Zhang et al. 2020). Although the genomic information of several L. theobromae strains has been reported, such as L. theobromae CSS-01S and LA-SOL3 isolated from grapevine (Felix et al. 2019; Yan et al. 2018), L. theobromae AM2As isolated from cacao (Ali et al. 2020), and L. theobromae CITRA15 isolated from citrus (Zheng et al. 2021), the genome sequence of strain JMB122, a major causal agent of peach gummosis, was not available.In this study, strain JMB122 was cultured on potato dextrose agar medium at 28°C for 2 days under a 12-h-light and 12-h-dark cycle (300 μmol s−1 m−2). Genomic DNA was extracted using the Omega fungal DNA kit D3390 according to manufacturer instructions. The genome of L. theobromae JMB122 was sequenced using a whole-genome shotgun strategy by Illumina HiSeq X-ten sequencing with the PacBio single molecule, real-time long-read sequencing platform. Illumina HiSeq results were used to correct errors in the assembled PacBio sequences with Canu (v1.7).The de novo genome draft assembly of L. theobromae JMB122 is shown in Table 1. The estimated genome size was 46.93 Mb with a GC content of 53.49% and was larger than other strains reported, such as L. theobromae CSS-01S (43.3 Mb) (Yan et al. 2018), L. theobromae LA-SOL3 (43.9 Mb) (Felix et al. 2019), L. theobromae AM2As (43.7 Mb) (Ali et al. 2020), and L. theobromae CITRA15 (43.3 Mb) (Zheng et al. 2021). The largest scaffold size was 6.13 Mb and the N50 value of scaffolds was 4.65 Mb. The assembly showed a high completeness of 100%, using BUSCO version 3.0.2 (Simao et al. 2015). Gene predictions generated a total of 12,289 protein-coding genes, using the MAKER2 software (Holt and Yandell 2011). Transposon sequence analysis of L. theobromae JMB122 was carried out for the assembled gene sequences against the transposon Repbase database (Bao et al. 2015), using RepeatMasker software (version 4.0.7). The total length of repeat sequences was 25,495 bp, covering 0.05% of the genomic size. Among them, 58 DNA transposons, five long terminal repeats (LTRs), and 262 non-LTR transposons were identified. For RNA analysis, 161 transfer RNAs were obtained by RNA-scan-SE, and 17 ribosomal RNAs were predicted using Barrnap. These basic genomic features are shown in Figure 1. Gene synteny was analyzed using TBtools and MCscanX (Chen et al. 2020; Wang et al. 2012). The results revealed an overall gene collinearity between L. theobromae JMB122 and three other genome assemblies and a better completeness in JMB122 assemblies, with more continuous and detailed genomic sequences. Interestingly, JMB122 showed higher homology with strain CSS-01S than the other strains, LA-SOL3 and AM2As (Supplementary Fig. S1).Table 1. Genomic features of Lasiodiplodia theobromae JMB122AnnotationGene annotatedGenome size (Mb)46.93GC Content (%)53.49Sequence coverage310×Predicted protein-coding genes12,289Number of contigs15Contig N50 size (bp)4,654,331Secreted proteins1,113EffectorP 3.0273DNA transposons58Long terminal repeat (LTR) retrotransposons5Non-LTR retrotransposons262Table 1. Genomic features of Lasiodiplodia theobromae JMB122View as image HTML Fig. 1. The genomic features of Lasiodiplodia theobromae JMB122. The genome size of strain JMB122 is 46.93 Mb. A, Scaffolds (15), B, coding sequences (12,289), C, pathogen-host interaction genes (1,839), D, carbohydrate enzymes (525), E, secreted proteins (1,113), F, transfer RNA (161), and G, ribosomal RNA (17).Download as PowerPointIt is well-known that the secreted proteins of pathogens, especially effector proteins, play a crucial role in the pathogenicity and virulence of fungi (Koeck et al. 2011). In total, 1,113 proteins were predicted as putative secreted proteins, which contained N-terminal signal peptide (SignalP 5.0) and no transmembrane domain behind the region signal peptide (TMHMM 2.0) (Almagro Armenteros et al. 2019; Krogh et al. 2001). Of the secreted proteins, 273 candidate effector proteins were further identified by EffectorP 3.0 (Sperschneider and Dodds 2022). Functional annotation of these genes was conducted using the following databases: National Center for Biotechnology Information non-redundant protein (11,595 genes, 94.35%), Swiss-Prot proteins (7,683 genes, 62.52%), Kyoto Encyclopedia of Genes and Genomes (3,666 genes, 29.83%), Pfam (8,251 genes, 67.14%), Gene Ontology (7,450 genes, 60.62%), Cluster of Orthologous Groups of proteins (9,696 genes, 78.90%), Pathogen Host Interactions (1,839 genes, 14.96%), and Carbohydrate-Active EnZyme (525 genes, 4.27%).In this study, we present a draft genome sequence of L. theobromae JMB122, a primary pathogen causing peach gummosis in China. This high-quality genome data represents a new valuable source for future studies on molecular diagnostics and disease management of peach gummosis.Data AvailabilityThis whole-genome shotgun project has been deposited in the DDBJ/ENA/GenBank database under accession number JAJSDP000000000 (PRJNA789396 for BioProject and SAMN24108378 for BioSample). 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The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.DetailsFiguresLiterature CitedRelated Vol. 35, No. 10 October 2022ISSN:0894-0282e-ISSN:1943-7706 Download Metrics Article History Issue Date: 8 Oct 2022Published: 29 Sep 2022Accepted: 16 Jun 2022 Pages: 938-940 InformationThe author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.Funding National Key Research and Development Program of ChinaGrant/Award Number: 2018YFD1000300 Natural Science Foundation of ChinaGrant/Award Number: 3217180554 China Agriculture Research System of MOF and MARAGrant/Award Number: CARS-30 Keywordsfungal diseasegenome assemblyLasiodiplodia theobromaepeach gummosisThe author(s) declare no conflict of interest.PDF download