Genome data for 25 isolates of the prevalent forest and nursery pathogen, Phytophthora cinnamomi, from New Zealand

TL;DR

This paper provides genome data for 25 isolates of a plant pathogen in New Zealand, helping to understand its genetic diversity and improve detection methods.

Contribution

The study provides draft genome assemblies for 25 isolates of Phytophthora cinnamomi from New Zealand, enabling genetic diversity analysis.

Findings

The average genome size of the isolates was 129 MB.

The average N90 value of the assemblies was 297,992 bp.

The data will support development of detection and diagnostic tools.

Abstract

Phytophthora cinnamomi is a globally distributed plant pathogen with a remarkably broad host range. It is considered one of the greatest threats to natural and productive ecosystems, especially under changing climatic conditions. In New Zealand, this pathogen has been present for a long time, but the genetic diversity is not well understood. We describe here draft genome assemblies for 25 isolates of P. cinnamomi from New Zealand trees, forests and nurseries. The genome assembly data showed an average size of 129 MB with an average N90 value of 297,992 bp. This data will enable the analysis of genetic diversity of New Zealand P. cinnamomi isolates, and the development of accurate detection and diagnostic tools.

Full text

Specifications TableSubjectBiologySpecific subject areaOomycete plant pathogen genomicsType of dataGenomic data, presented in TablesData collectionGenomics data for twenty-five Phytophthora cinnamomi isolates from various plant hosts in New Zealand were generated from purified and sequenced DNA. The genomic DNA was sequenced on an Illumina NovaSeq 6000 sequencing platform.Data source locationScion (The New Zealand Forest Research Institute Ltd.), Titokorangi Drive, Private Bag 3020, Rotorua 3046, New ZealandData accessibilityRepository name: NCBIData identification number: BioProject number PRJNA1197507.Direct URL to data: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1197507/The data has been deposited in GenBank SRA archive found at NCBI, meeting their requirements for submission.Related research articleNot applicable.

Value of the Data

1

• •This report describes genomic data from a collection of 25 Phytophthora cinnamomi isolates from various native and exotic trees and woody shrubs in New Zealand, as well as avocado.
• •Phytophthora cinnamomi is a ubiquitous forest, horticulture and nursery pathogen in New Zealand with a long association with forestry.
• •Globally P. cinnamomi has a very wide distribution and host range and is responsible for devastating forest and horticultural diseases.
• •The genomic data provided in this study will facilitate future studies to address the genetic population diversity, evolutionary analyses and host-pathogen interactions*.*
• •Predicting the evolution of pathogens under changing climatic conditions is critical to mitigate future risk.

Background

2

Phytophthora cinnamomi Rands, first isolated in 1922 from cinnamon trees in Sumatra, now has a worldwide distribution, infecting more than 3000 plant hosts [1]. In New Zealand, P. cinnamomi has been long associated with plants and trees in many land use systems [2], including exotic and native trees, forests and plant nurseries [[3], [4], [5]]. Phytophthora cinnamomi has caused devastating plant and tree losses including local extinctions, flow-on biodiversity impacts and ecosystem collapse in some cases, with limited options for eradication [1,[6], [7], [8]]. It is considered one of the top 100 worst alien invasive species [9] and this ‘biological bulldozer’ [10] is ranked number seven of the top 10 oomycete pathogens in plant pathology [11].

Genomic resources for P. cinnamomi are available from a number of different hosts from across the globe [12,13]. A larger resource pool, including broad hosts from New Zealand, enables analysis of the genetic diversity, evolutionary potential and the risk this pathogen may pose under conditions of climate change [14,15]. The isolates used in this study were collected as part of past and present biosecurity surveillance and forest research programs in New Zealand and are housed and maintained in Scion’s National Forest Culture Collection (NZFS). Isolates were selected to capture differences in temporal, geographic or host association.

Data Description

3

This data article is comprised of genomics resources of a large collection of Phytophthora cinnamomi isolates (Table 1) [16], with draft genome assemblies (Table 2). The average size of the genomes was 129 MB with an average N90 value of 297,992 bp. The quality of the genome assemblies, using BUSCO (Benchmarking Universal Single-Copy Orthologs) and the Stramenopile database [17], demonstrated 98–100 % completeness (Table 2). The assembly data presented here provides a resource for future population and genomic analyses, as well as the development of diagnostic tools.Table 1Phytophthora cinnamomi isolates used in this study.Table 1:NZFSaHostSubstrateYear CollectedRegion of New ZealandBioSample Accession102Larix deciduasoil1968NelsonSAMN45808063102.16Pinus radiatasoil1999NorthlandSAMN45808062609Eucalyptus nitensbstem tissue2001TaupoSAMN45808064627Pinus lambertianabroots2001Bay of PlentySAMN45808057939Betula pendulasoil2003AucklandSAMN45808044979Quercus robursoil2003AucklandSAMN458080491012Quercus palustrisstem lesion2003AucklandSAMN458080482316Pinus radiatasoil2005AucklandSAMN458080462545Xeronema callistemonsoil and roots2005AucklandSAMN458080502657Pseudotsuga menziesiibplant tissues and soil2006TaupoSAMN458080662960Araucaria heterophyllasoil2007AucklandSAMN458080433030Agathis australissoil2008AucklandSAMN458080423876Agathis australissoil and roots2014Bay of PlentySAMN458080514342Persea americanasoil2016NorthlandSAMN458080604359Persea americanasoil2016NorthlandSAMN458080614411Persea americanasoil2017Bay of PlentySAMN458080544424Persea americanasoil2017Bay of PlentySAMN458080554458Persea americanasoil2017Bay of PlentySAMN458080564801Gevuina avellanabroot collar2019Bay of PlentySAMN458080524805Coprosma robustasoil and roots2019AucklandSAMN458080455108Quercus sp.stem canker2020Bay of PlentySAMN458080585347Pinus radiatasoil2021AucklandSAMN458080475425Knightia excelsabsoil2021Bay of PlentySAMN458080535434Pinus radiataroot collar2022TaupoSAMN458080655436Vitex lucenssoil2021Bay of PlentySAMN45808059aNational Forest Culture Collection, Scion, Rotorua, New Zealand (NZFS)bIsolated from a plant production nurseryTable 2Summarised genome information for 25 Phytophthora cinnamomi isolates.Table 2:Assembly StatisticsPhytophthora cinnamomi NZFS isolate number102102.166096279399791012231625452657296030303876Number of scaffolds > 50 Kb118119119117120121121123123121125121117Assembly length (Mb)142.41105.99146.28143.10140.67144.05124.24122.10121.39145.00152.01126.36123.12Largest Scaffold size (Kb)2934296230852927306830932994299430213094309431102888N50 length (bp)32470027999826244089681648382318642424852466484081572523041641359N90 length (bp)431292162592426594439703393586410383251731239442237589414543418820257952260417GC%54.2853.9354.3154.2154.4154.0454.0254.1153.7954.1953.9153.8353.78Complete & single copy BUSCOs (%)a1009910098100100100999999999998Complete & duplicated BUSCOs (%)0000000000011Fragmented BUSCOs (%)0002000111101Missing BUSCOs (%)0100000000000Assembly Statistics (cont’d)434243594411442444584801480551085425543454365437Number of scaffolds > 50 Kb119122122121122121122122121117121121Assembly length (Mb)122.92112.33125.32154.80121.75127.80126.09110.56126.26124.03112.56124.03Largest Scaffold size (Kb)290829793079307731263007312730143131293429933059N50 length (bp)5515229809023322638230025160722444922623129073823061034369296951238255N90 length (bp)259132189187254016495686237515275360257685184380257123263961183046248088GC%53.953.7253.7954.6553.7653.9153.8853.9553.8153.8153.7953.77Complete & single copy BUSCOs (%)1001009999999899100991009999Complete & duplicated BUSCOs (%)000001000000Fragmented BUSCOs (%)001111101011Missing BUSCOs (%)000000000000aBenchmarking universal single-copy orthologs (BUSCO) [17]

Experimental Design, Materials and Methods

4

Isolate preparation, growth and DNA extraction

4.1

Cultures for 25 P. cinnamomi isolates (Table 1) were revived from the NZFS collection and hyphal tipping was performed to ensure cultures were pure [18]. The identity of the cultures was confirmed using end-point PCR with P. cinnamomi species-specific primers Ycin3F and Ycin4R [19].

Cultures were grown on 80–100 ml clarified carrot medium for 14–21 days at 20 °C. Cultures were washed three times in sterile distilled water and frozen overnight at −80 °C prior to freeze-drying mycelium for 24–48 h. Tissue lysis was performed by grinding mycelium with liquid nitrogen in sterile mortar and pestles and DNA was extracted with a Qiagen DNeasy Plant Maxi Kit, eluting in 2 ml nuclease-free water. DNA was purified and concentrated using AMPure XP beads according to the manufacturer’s instructions (Beckman Coulter Life Sciences, Australia). DNA was quantified using a Qubit dsDNA BR Assay where concentrations ranged from 31.2 to 830 ng/ul and the DNA quality was assessed using a Nanodrop where 260/280 ratios ranged from 1.42 to 1.9.

DNA sequencing and genome assembly

4.2

DNA libraries were prepared using NEBNext® Ultra™ IIDNA Library Prep Kit (New England BioLabs, MA, USA). The genomic DNA from each isolate was sequenced using paired 150-nt Illumina reads on the Novaseq™ 6000 platform at Novogene Co., Ltd. (Beijing, China), via the Massey University Genome Service (Palmerston North, New Zealand). DNA sequence quality was assessed using FastQC (version 0.11.9) [20]. Genome data were assembled de novo using SPAdes v 3.5.0 [21] and RagTag [22]. Completeness of the genome assemblies was assessed using BUSCO (Benchmarking Universal Single-Copy Orthologs) using the Stramenopile database [17]. Raw sequence data are available via GenBank and the BioSample accession numbers listed in Table 1. The summarised genome assembly statistics are presented in Table 2.

Limitations

Not applicable.

Ethics Statement

This work does not involve human subjects, animal experiments, or any data collected from social media platforms.

Credit Author Statement

RLM: Conceptualization and design of the project, funding acquisition, methodology and data curation, project administration, supervision and writing – original draft**; KR:** methodology and formal analyses including bioinformatic analysis, GV: methodology and formal analysis**, JS, TF:** formal analysis, supervision, and resources, DH: data curation, supervision and delivery, RB: data curation, project administration including responsibility for overall program delivery. All authors contributed to the writing and reviewing of the manuscript.