A Genomic Sequence Resource of GZU-Y2 Causing Leaf Spot Blight in

Overview

Journal J Fungi (Basel)

Date 2024 Sep 27

PMID 39330390

Authors

Xulong Shi

Yu Zhang

Jing Yang

Yunze Chen

Affiliations

Soon will be listed here.

Abstract

GZU-Y2, a new pathogen responsible for leaf spot blight disease, leads to significant damage and economic losses in some plantations. The current study annotated the genome of the isolate GZU-Y2 to advance our knowledge of the pathogen and facilitate improved disease management of leaf spot blight. The initial Pacbio-Illumina hybrid draft genome for GZU-Y2 resulted in a high-quality assembly with 62 contigs, characterized by an N50 length of 7.07 Mb. The complete genome of isolate GZU-Y2 was 58.97 Mbp, with a GC content of 50.65%. Importantly, the assembly exhibits remarkable integrity, with 97.93% of complete BUSCO validating genome completeness. The prediction results showed that a total of 15,918 protein-coding genes were annotated using multiple bioinformatics databases. The genome assembly and annotation resource reported here will be useful for the further study of fungal infection mechanisms and pathogen-host interaction.

References

Chen N . Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics. 2008; Chapter 4:Unit 4.10. DOI: 10.1002/0471250953.bi0410s05. View

Shi X, Zhang Y, Wang X, Pan Y, Yu C, Yang J . First Report of Leaf Spot Blight of Camellia oleifera Caused by Diaporthe mahothocarpus in China. Plant Dis. 2023; . DOI: 10.1094/PDIS-03-23-0569-PDN. View

Urban M, Cuzick A, Seager J, Wood V, Rutherford K, Venkatesh S . PHI-base: the pathogen-host interactions database. Nucleic Acids Res. 2019; 48(D1):D613-D620. PMC: 7145647. DOI: 10.1093/nar/gkz904. View

Liu X, Chaisiri C, Lin Y, Yin W, Luo C . Whole-Genome Sequence of Isolate NFHF-8-4, the Causal Agent of Citrus Melanose. Mol Plant Microbe Interact. 2021; 34(7):845-847. DOI: 10.1094/MPMI-01-21-0004-A. View

Dissanayake A, Liu M, Zhang W, Chen Z, Udayanga D, Chukeatirote E . Morphological and molecular characterisation of Diaporthe species associated with grapevine trunk disease in China. Fungal Biol. 2015; 119(5):283-94. DOI: 10.1016/j.funbio.2014.11.003. View

Campbell M, Haas B, Hamilton J, Mount S, Buell C . Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics. 2006; 7:327. PMC: 1769492. DOI: 10.1186/1471-2164-7-327. View

Cheng H, Concepcion G, Feng X, Zhang H, Li H . Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021; 18(2):170-175. PMC: 7961889. DOI: 10.1038/s41592-020-01056-5. View

Eddy S . Profile hidden Markov models. Bioinformatics. 1999; 14(9):755-63. DOI: 10.1093/bioinformatics/14.9.755. View

Sperschneider J, Gardiner D, Dodds P, Tini F, Covarelli L, Singh K . EffectorP: predicting fungal effector proteins from secretomes using machine learning. New Phytol. 2015; 210(2):743-61. DOI: 10.1111/nph.13794. View

10.

Wicker T, Sabot F, Hua-Van A, Bennetzen J, Capy P, Chalhoub B . A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 2007; 8(12):973-82. DOI: 10.1038/nrg2165. View

11.

Majoros W, Pertea M, Salzberg S . TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics. 2004; 20(16):2878-9. DOI: 10.1093/bioinformatics/bth315. View

12.

Bradley E, Okmen B, Doehlemann G, Henrissat B, Bradshaw R, Mesarich C . Secreted Glycoside Hydrolase Proteins as Effectors and Invasion Patterns of Plant-Associated Fungi and Oomycetes. Front Plant Sci. 2022; 13:853106. PMC: 8960721. DOI: 10.3389/fpls.2022.853106. View

13.

Li S, Song Q, Martins A, Cregan P . Draft genome sequence of Diaporthe aspalathi isolate MS-SSC91, a fungus causing stem canker in soybean. Genom Data. 2016; 7:262-3. PMC: 4778679. DOI: 10.1016/j.gdata.2016.02.002. View

14.

Pertea M, Kim D, Pertea G, Leek J, Salzberg S . Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016; 11(9):1650-67. PMC: 5032908. DOI: 10.1038/nprot.2016.095. View

15.

Gai Y, Xiong T, Xiao X, Li P, Zeng Y, Li L . The Genome Sequence of the Citrus Melanose Pathogen and Two Citrus-Related Species. Phytopathology. 2020; 111(5):779-783. DOI: 10.1094/PHYTO-08-20-0376-SC. View

16.

Mair W, Deng W, Mullins J, West S, Wang P, Besharat N . Demethylase Inhibitor Fungicide Resistance in Pyrenophora teres f. sp. teres Associated with Target Site Modification and Inducible Overexpression of Cyp51. Front Microbiol. 2016; 7:1279. PMC: 4990540. DOI: 10.3389/fmicb.2016.01279. View

17.

Udayanga D, Castlebury L, Rossman A, Chukeatirote E, Hyde K . The Diaporthe sojae species complex: Phylogenetic re-assessment of pathogens associated with soybean, cucurbits and other field crops. Fungal Biol. 2015; 119(5):383-407. DOI: 10.1016/j.funbio.2014.10.009. View

18.

Winnenburg R, Baldwin T, Urban M, Rawlings C, Kohler J, Hammond-Kosack K . PHI-base: a new database for pathogen host interactions. Nucleic Acids Res. 2005; 34(Database issue):D459-64. PMC: 1347410. DOI: 10.1093/nar/gkj047. View

19.

Garcia J, Lawrence D, Morales-Cruz A, Travadon R, Minio A, Hernandez-Martinez R . Phylogenomics of Plant-Associated Species. Front Microbiol. 2021; 12:652802. PMC: 8012773. DOI: 10.3389/fmicb.2021.652802. View

20.

Liu J, Wei Y, Yin Y, Zhu K, Liu Y, Ding H . Effects of Mixed Decomposition of var. and Litter on Microbial Diversity. Microorganisms. 2022; 10(6). PMC: 9229243. DOI: 10.3390/microorganisms10061117. View