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<article xmlns:ns1="http://www.w3.org/1999/xlink" xmlns:ns3="http://www.w3.org/1998/Math/MathML">
    <front>
        <journal-meta>
            <journal-title-group>
                <journal-title>OENO One</journal-title>
            </journal-title-group>
        </journal-meta>
        <article-meta>
            <title-group>
                <article-title>Metagenomic ecosystem monitoring of soft scale insects and mealybug communities</article-title>
            </title-group>
            <aff id="aff1">
                <sup>
                    <italic>1</italic>
                </sup> Australian Wine Research Institute, Urrbrae, SA 5064, Australia</aff>
            <aff id="aff2">
                <sup>
                    <italic>2</italic>
                </sup> School of Agriculture, Food and Wine, The University of Adelaide, SA, 5064. Australia</aff>
            <contrib-group>
                <contrib contrib-type="author">
                    <name>
                        <surname>Ward</surname>
                        <given-names>ChrisM.</given-names>
                    </name>
                    <xref ref-type="aff" rid="aff1">
                        <sup>
                            <italic>1</italic>
                        </sup>
                    </xref>
                </contrib>
                <contrib contrib-type="author">
                    <name>
                        <surname>Onetto</surname>
                        <given-names>CristobalA.</given-names>
                    </name>
                    <xref ref-type="aff" rid="aff1">
                        <sup>
                            <italic>1</italic>
                        </sup>
                    </xref>
                </contrib>
                <contrib contrib-type="author">
                    <name>
                        <surname>Heuvel</surname>
                        <given-names>StevenVanDen</given-names>
                    </name>
                    <xref ref-type="aff" rid="aff1">
                        <sup>
                            <italic>1</italic>
                        </sup>
                    </xref>
                </contrib>
                <contrib contrib-type="author">
                    <name>
                        <surname>Borneman</surname>
                        <given-names>RobynDixon1andAnthonyR.</given-names>
                    </name>
                    <xref ref-type="aff" rid="aff1">
                        <sup>
                            <italic>1</italic>
                        </sup>
                    </xref>
                </contrib>
                <contrib contrib-type="author">
                    <name>
                        <surname></surname>
                        <given-names>2</given-names>
                    </name>
                    <xref ref-type="corresp" rid="cor1">
                        <sup>
                            <italic>*</italic>
                        </sup>
                    </xref>
                </contrib>
            </contrib-group>
            <author-notes>
                <corresp id="cor1">
                    <sup>
                        <italic>*</italic>
                    </sup> corresponding author: anthony.borneman@awri.com.au</corresp>
            </author-notes>
            <abstract>
                <sec id="Abstract">
                    <title>Abstract</title>
                    <p>Soft scale insects and mealybugs are phloem-feeding Hemipterans that are considered major pests in agriculture and horticulture throughout the world. However, correct taxonomic identification in the field can be difficult, making it hard for growers to implement control strategies. In viticulture, soft scale insects are a major issue due to their ability to secrete honeydew, which facilitates the development of sooty mould, and their propensity for being transmission vectors of several viral diseases of grapevine. To facilitate the rapid identification and quantification of vineyard-associated insects a metagenomic-based bioinformatic pipeline (MitoMonitor) was developed for generalised ecosystem monitoring, which automated the assembly and classification of insect mitochondrial genomes from shotgun sequencing data using the Barcode of Life Database API. The proof-of-concept application of MitoMonitor on metagenomic data obtained from eight samples from South Australian vineyards led to the identification of <italic>Parthenolecanium corni</italic> (European fruit scale)—which was thought to be absent in Australian vineyards—as the dominant coccoid species across the samples, with less frequent, and also lower abundance of <italic>Pseudococcus viburni </italic>(obscure mealybug) and <italic>Pseudo. longispinus </italic>(long-tailed mealybug). In addition, parisitoidism by <italic>Coccophagus scutellaris</italic> (Aphelinidae) wasps was also detected. The discovery of <italic>Parth. corni</italic> as a member of scale communities in these samples has significant implications for the development of effective control strategies for this important group of pests in affected areas.</p>
                    <p/>
                    <p>Keywords: grapevine, scale, mealybug, metagenomics, DNA barcoding</p>
                </sec>
            </abstract>
        </article-meta>
    </front>
    <body>
        <sec id="Introduction">
            <title>Introduction</title>
            <p>Worldwide, the family Coccidae (Coccomorpha) contains more than 1100 species classified as 163 genera, although only 80 species have been described as occurring in Australia (<xref ref-type="bibr" rid="ref17">García Morales <italic>et al.</italic>, 2016</xref>). Likewise, of the 2143 described Pseudococcidae (Coccomorpha), only 210 have been detected as contemporary Australian populations (<xref ref-type="bibr" rid="ref17">García Morales <italic>et al.</italic>, 2016</xref>; <xref ref-type="bibr" rid="ref28">Moir, 2021</xref>).</p>
            <p>Several coccids have been shown to affect the grapevine <italic>Vitisvinifera</italic> , including various species within the genera <italic>Ceroplastes</italic>, <italic>Coccus</italic>, <italic>Cryptinglisia</italic>, <italic>Eulecanium</italic>, <italic>Mesolecanium</italic>, <italic>Neopulvinaria</italic>, <italic>Neolecanium</italic>, <italic>Parasaissetia</italic>, <italic>Parthenolecanium</italic>, <italic>Pseudokermes</italic>, <italic>Pulvinaria</italic>, <italic>Saissetia</italic> and <italic>Trijuba</italic> (<xref ref-type="bibr" rid="ref5">Ben-Dov, 1977</xref>; <xref ref-type="bibr" rid="ref6">Ben-Dov and Hodgson, 1997</xref>; <xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic>, 2013</xref>; <xref ref-type="bibr" rid="ref34">Rakimov <italic>et al.</italic>, 2015</xref>). Among these, <italic>Parth. persicae</italic> (European peach scale), <italic>Parth. pruinosum</italic> (frosted scale), and <italic>Coccus hesperidum</italic> (brown soft scale) are frequently encountered in Australian vineyards, while <italic>Co. longulus</italic> (long brown scale), <italic>Parasaissetia nigra</italic> (black scale), and <italic>Saissetia</italic> species have also been observed at a lower frequency (<xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic>, 2013</xref>).</p>
            <p>Recent surveys conducted in Australia to assess disease pressure and the distribution of Coccids indicate that soft scale insects are rapidly becoming a significant pest of grapevines (<xref ref-type="bibr" rid="ref15">Essling, 2018</xref>; <xref ref-type="bibr" rid="ref40">Venus, 2017</xref>). The distribution of soft scale insects and mealybugs appears to be uneven across different grape-growing regions, with Western Australia and Queensland showing less frequent infestations than other states (<xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic>, 2013</xref>).</p>
            <p>While severe infestations of soft scale insects and mealybugs can have direct detrimental effects on vine growth through the depletion of nutrients (<xref ref-type="bibr" rid="ref36">Schulze-Sylvester <italic>et al.</italic>, 2021</xref>), the main negative impacts of infestation manifest themselves through secondary effects. Firstly, the secretion of sugar-rich honeydew as a by-product of soft scale insect and mealybug feeding facilitates the growth of sooty mould throughout the vine, which can lead to quality reductions and/or total loss of the grape crop (<xref ref-type="bibr" rid="ref6">Ben-Dov and Hodgson, 1997</xref>).</p>
            <p>In addition to promoting sooty mould, soft scale insects and mealybugs also represent known or suspected vectors of grapevine ampelo- and viti-viruses, including grapevine virus A (GVA) (<xref ref-type="bibr" rid="ref21">Hommay <italic>et al.</italic>, 2008</xref>) and grapevine leafroll-associated viruses (GLRaV) 1 and 3 (<xref ref-type="bibr" rid="ref1">Bahder <italic>et al.</italic>, 2013</xref>; <xref ref-type="bibr" rid="ref14">Engelbrecht and Kasdorf, 1990</xref>; <xref ref-type="bibr" rid="ref37">Sforza <italic>et al.</italic>, 2003</xref>). Infection by these viruses can have negative effects on yield and fruit quality, including reduced accumulation of sugars, increased acidity and irregular flavour profiles (<xref ref-type="bibr" rid="ref19">Goheen and Cook, 1959</xref>; <xref ref-type="bibr" rid="ref30">Naidu <italic>et al.</italic>, 2014</xref>). The mobile nymph stages of both types of insects are thought to transmit these viruses between adjacent vines, although recent studies indicate that passive aerial dispersal of the nymphs can promote long-distance dispersal throughout a vineyard (<xref ref-type="bibr" rid="ref3">Barrass <italic>et al.</italic>, 1994</xref>; <xref ref-type="bibr" rid="ref22">Hommay <italic>et al.</italic>, 2019</xref>).</p>
            <p>Studies have demonstrated the existence of several natural enemies of coccids in Australia, including parasitoid wasps, beetles, moth larvae, and lacewings (<xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic>, 2013</xref>; <xref ref-type="bibr" rid="ref34">Rakimov <italic>et al.</italic>, 2015</xref>). Therefore, chemical control strategies for coccids are only recommended in severe infestation cases to avoid harming the beneficial parasitoids that inhabit the vineyards (<xref ref-type="bibr" rid="ref16">Frank, 2012</xref>; <xref ref-type="bibr" rid="ref34">Rakimov <italic>et al.</italic>, 2015</xref>b).</p>
            <p>Ecosystem monitoring utilising molecular and/or next generation sequencing methodologies have been used to successfully characterise beetle species richness (<xref ref-type="bibr" rid="ref11">Crampton-Platt <italic>et al.</italic>, 2015</xref>) and airborne fungal diversity (<xref ref-type="bibr" rid="ref2">Banchi <italic>et al.</italic>, 2018</xref>), and to track pollinator populations (<xref ref-type="bibr" rid="ref20">Harper <italic>et al.</italic>, 2023</xref>). However, successful species classification generally requires reliable and well populated genetic databases to first be developed to carry out high-throughput monitoring (<xref ref-type="bibr" rid="ref11">Crampton-Platt <italic>et al.</italic>, 2015</xref>). Targeted ecosystem monitoring was previously carried out by <xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic> (2013)</xref>, utilising a COX1 amplicon to identify individual soft scale insects that infested grapevines across several Australian vineyards. The results of this work led to the conclusion that <italic>Parth. persicae</italic> was the dominant soft scale insect present, with secondary infestations commonly observed by <italic>Parth. pruinosum</italic>.</p>
            <p>In order to facilitate the rapid identification and quantification of vineyard-associated insects, an untargeted ecosystem monitoring protocol was developed and its utility was demonstrated by determining the composition of insect populations associated with soft scale insect infestation. Shotgun metagenomic sequencing was employed on population scrapings from vines in four wine regions of South Australia subject to soft scale insect infestation. To enable the high-throughput analysis of the large datasets produced by this approach, a rapid pipeline for assembling and classifying the insect mitochondrial genomes present was established, taking advantage of the Barcode of Life Database (BOLD) API (<xref ref-type="bibr" rid="ref35">Ratnasingham and Hebert, 2007</xref>).</p>
        </sec>
        <sec id="Materials-and-methods">
            <title>Materials and methods</title>
            <sec id="1.-Collection-and-DNA-extraction-and-sequencing">
                <title>1. Collection and DNA extraction and sequencing</title>
                <p>In 2022, samples were collected from eight different vineyards in South Australia (Table 1) by taking scrapings containing multiple individuals of soft scale insects from infested vines. The choice of vines for sampling was based on visible soft scale insect infestation; a row within each vineyard was randomly selected and scrapings were taken every 2–3 bays alternating between the left and right sides of the row. The scrapings were sampled from several parts of the vine (trunk, shoots, backs of leaves and bunches) to ensure different life stages could be captured. All the scales from one vine were put in the same tube in ethanol to preserve tissue. DNA isolation was carried out by grinding scrapings taken from one plant per vineyard using a Geno/Grinder 2010 (SPEX), followed by extraction using the DNEasy Plant Kit (Qiagen).</p>
                <p>Sequencing libraries were prepared using the Illumina DNA library kit and sequenced on an Illumina NovaSeq 6000 using 2 x 150bp chemistry (Ramaciotti Centre for Genomics, University of New South Wales, Sydney, Australia). Quality control was carried out on short read data using fastqc (</p>
                <p>
                    <ext-link ext-link-type="url" ns1:href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/">https://www.bioinformatics.babraham.ac.uk/projects/fastqc/</ext-link>
                </p>
                <p>) and ngsReports (<xref ref-type="bibr" rid="ref42">Ward <italic>et al.</italic>, 2020b</xref>).</p>
                <p>All sequencing data can be obtained from NCBI under the BioProject accession PRJNA986325.</p>
                <p>
                    <table-wrap position="float" orientation="portait">
                        <label>Table</label>
                        <caption>
                            <title>Table 1. Assembly statistics for each metagenomic sample.</title>
                        </caption>
                        <alternatives>
                            <table style="table table-bordered table-striped affichage-tableau">
<col width="12%"/>
<col width="12%"/>
<col width="12%"/>
<col width="12%"/>
<col width="12%"/>
<col width="12%"/>
<col width="12%"/>
<col width="12%"/>
<col width="12%"/>
<col width="12%"/>
<col width="12%"/>
<col width="12%"/>
<thead>
    <tr>
        <td xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">titre du tableau </td>
    </tr>
</thead>
<tr>
    <th>Sample</th>
    <th>Location</th>
    <th>Contigs</th>
    <th>Total length (kb)</th>
    <th>Longest contig</th>
    <th>N<sub>50</sub>
    </th>
    <th>Full mitochondrial <break/>genomes</th>
    <th>Unique <break/>insect taxa</th>
</tr>
<tr>
    <th>7361</th>
    <th>Langhorne Creek</th>
    <th>452</th>
    <th>425.6</th>
    <th>44283</th>
    <th>955</th>
    <th>4</th>
    <th>6</th>
</tr>
<tr>
    <th>7372</th>
    <th>McLaren Vale</th>
    <th>305</th>
    <th>212.5</th>
    <th>10753</th>
    <th>747</th>
    <th>0</th>
    <th>3</th>
</tr>
<tr>
    <th>7373</th>
    <th>McLaren Vale</th>
    <th>963</th>
    <th>787.4</th>
    <th>12427</th>
    <th>1023</th>
    <th>1</th>
    <th>2</th>
</tr>
<tr>
    <th>7374</th>
    <th>Langhorne Creek</th>
    <th>910</th>
    <th>735.4</th>
    <th>15563</th>
    <th>1078</th>
    <th>1</th>
    <th>1</th>
</tr>
<tr>
    <th>7375</th>
    <th>Adelaide Hills</th>
    <th>873</th>
    <th>717.9</th>
    <th>15198</th>
    <th>1124</th>
    <th>1</th>
    <th>2</th>
</tr>
<tr>
    <th>7376</th>
    <th>Adelaide Hills</th>
    <th>1015</th>
    <th>786.6</th>
    <th>15297</th>
    <th>900</th>
    <th>1</th>
    <th>1</th>
</tr>
<tr>
    <th>7377</th>
    <th>Barossa Valley</th>
    <th>940</th>
    <th>689.8</th>
    <th>6523</th>
    <th>861</th>
    <th>1</th>
    <th>2</th>
</tr>
<tr>
    <th>7378</th>
    <th>Barossa Valley</th>
    <th>981</th>
    <th>763.3</th>
    <th>15429</th>
    <th>911</th>
    <th>1</th>
    <th>2</th>
</tr>
                            </table>
                        </alternatives>
                        <table-wrap-foot>
                            <fn>
<p/>
                            </fn>
                        </table-wrap-foot>
                    </table-wrap>
                </p>
            </sec>
            <sec id="2.-Genome-assembly-and-analysis">
                <title>2. Genome assembly and analysis</title>
                <p>Mitochondrial genome assembly was first carried out by mapping raw sequence reads to all available and complete insect mitochondrial genomes (n = 12880) in the NCBI GenBank using BWA-mem (<xref ref-type="bibr" rid="ref25">Li, 2013</xref>) and sorted using SAMtools (<xref ref-type="bibr" rid="ref27">Li <italic>et al.</italic>, 2009</xref>); all unmapped reads were removed. Read IDs of mitochondrial mapped reads were used to extract putative mitochondrial reads from the original <italic>fastq</italic> files using seqtk subseq (<xref ref-type="bibr" rid="ref24">Li, 2012</xref>). Putative mitochondrial reads were then assembled using megahit under default settings. Contigs were remapped back to the RefSeq insect mitochondrial genome database using minimap2 (<xref ref-type="bibr" rid="ref26">Li, 2018</xref>) with the ‘splice' alignment preset. Contigs that were successfully mapped to the insect mitochondrial database were extracted using seqkit subseq (<xref ref-type="bibr" rid="ref38">Shen <italic>et al.</italic>, 2016</xref>). Each mitochondrial contig was then annotated independently using MITOS (<xref ref-type="bibr" rid="ref8">Bernt <italic>et al.</italic>, 2013</xref>) with the insect mitochondrial genetic code and the MITOS reference database.</p>
                <p>COX1 sequences were extracted from each of the contig annotations and provided as a seed sequence to NOVOplasty (<xref ref-type="bibr" rid="ref13">Dierckxsens <italic>et al.</italic>, 2017</xref>) to carry out circularised assembly of the mitochondrial genome using the raw short reads. Mitochondrial genes, rRNAs, and tRNAs were then annotated within each circularised genome using MITOS (<xref ref-type="bibr" rid="ref8">Bernt <italic>et al.</italic>, 2013</xref>) with the insect mitochondrial genetic code and MITOS reference database.</p>
            </sec>
            <sec id="3.-Species-assignment-and-phylogenetics">
                <title>3. Species assignment and phylogenetics</title>
                <p>Taxa identification was carried out using two methods. First, COX1 sequences were extracted from all putative mitochondrial contigs and queried against the ‘COX1' BOLD database in a highly parallelised manner using the BOLD.R (<xref ref-type="bibr" rid="ref29">Mudalige, 2021</xref>) and futures parallelisation (<xref ref-type="bibr" rid="ref7">Bengtsson, 2020</xref>) R packages to pass sequences to the BOLD API (<xref ref-type="bibr" rid="ref35">Ratnasingham and Hebert, 2007</xref>). Second, mitochondrial contigs were queried against the RefSeq Insect mitochondrial genome database from above using BLASTn (<xref ref-type="bibr" rid="ref9">Camacho <italic>et al.</italic>, 2009</xref>).</p>
                <p>COX1 sequences identified as <italic>Parthenolecaniumcorni</italic>  using the BOLD database were extracted using geaR (<xref ref-type="bibr" rid="ref41">Ward <italic>et al.</italic>, 2020a</xref>) and aligned to the two COX1 amplicon loci available for this genus using MAFFT (<xref ref-type="bibr" rid="ref23">Katoh and Standley, 2013</xref>) and maximum likelihood phylogenies were constructed using the best fit model argument in IQ-TREE (<xref ref-type="bibr" rid="ref32">Nguyen <italic>et al.</italic>, 2015</xref>).</p>
                <p>To provide further evidence that <italic>Parthenolecanium sp.</italic> from the Langhorne Creek scraping were <italic>Parth. corni, </italic>the<italic/>individuals were visually assessed for taxonomic characteristics, including dorsal tubular duct density and tubular duct presence on the dorsum of the anal cleft, which according to <xref ref-type="bibr" rid="ref18">Gill (1988)</xref>, differentiates <italic>Parth. pruinosum </italic>from <italic>Parth. corni</italic>.</p>
            </sec>
            <sec id="4.-MitoMonitor-pipeline">
                <title>4. MitoMonitor pipeline</title>
                <p>The MitoMonitor pipeline was written utilising the snakemake workflow framework and can be accessed at github.com/AWRI/MitoMonitor.</p>
            </sec>
        </sec>
        <sec id="Results-and-Discussion">
            <title>Results and Discussion</title>
            <sec id="1.-Highly-parallelised,-automated-assembly-of-insect-mitochondrial-genomes-from-metagenomic-samples-using-MitoMonitor">
                <title>1. Highly parallelised, automated assembly of insect mitochondrial genomes from metagenomic samples using MitoMonitor</title>
                <p>Ecosystem monitoring using high throughput genomic methods is a powerful tool to deconvolute the composition of mixed population samples (<xref ref-type="bibr" rid="ref2">Banchi <italic>et al.</italic>, 2018</xref>; <xref ref-type="bibr" rid="ref11">Crampton-Platt <italic>et al.</italic>, 2015</xref>; <xref ref-type="bibr" rid="ref20">Harper <italic>et al.</italic>, 2023</xref>). The transformation of shotgun sequencing data into estimated species and abundance requires a multi-stage procedure of genome assembly, annotation and species assignment. To facilitate the automated and reproducible implementation of these bioinformatic workflows, the MitoMonitor pipeline was developed. MitoMonitor is a snakemake implementation that extracts putative mitochondrial reads from short read data and assembles them utilising a metagenomic assembly method in megahit. Putative mitochondrial contigs are then compared to a database of all the insect mitochondrial genomes available on NCBI to remove nuclear and non-insect mitochondrial fragments. Insect mitochondrial contigs are automatically annotated using the invertebrate genetic code, circularised and classified to taxonomic origin utilising information present in databases from both NCBI and BOLD (Figure 1). </p>
                <p/>
                <p>
                    <fig>
                        <label>Table</label>
                        <caption>
                            <title>Figure 1. Workflow schematic of the MitoMonitor pipeline implemented in snakemake. </title>
                            <p/>
                        </caption>
                        <graphic mimetype="image" ns1:type="simple" ns1:href="image1.jpeg"/>
                    </fig>
                </p>
                <fig>
                    <label>Table</label>
                    <caption>
                        <title>Figure 1. Workflow schematic of the MitoMonitor pipeline implemented in snakemake. </title>
                        <p/>
                    </caption>
                    <graphic mimetype="image" ns1:type="simple" ns1:href="image1.jpeg"/>
                </fig>
                <p/>
            </sec>
            <sec id="2.-Application-of-MitoMonitor-to-investigate-insect-communities-associated-with-soft-scale-infestation-of-grapevine">
                <title>2. Application of MitoMonitor to investigate insect communities associated with soft scale infestation of grapevine</title>
                <p>To investigate the composition of insect populations associated with soft scale insect infestation, shotgun metagenomic sequencing was employed on population scrapings from areas of soft scale insect infestation from vines across four wine regions within South Australia, which was then passed through the MitoMonitor pipeline. Individual grapevines were surveyed for soft scale insect infestation across eight vineyards in Langhorne Creek, Adelaide Hills, Barossa Valley and McLaren Vale (Table 1), with an average of 28.9 ± 14 Gb of sequencing data produced across the samples.</p>
                <p>MitoMonitor confidently classified an average of 2.5 ± 0.78 M reads as having a mitochondrial origin, which were retained for subsequent assembly and analysis. Assembled putative mitochondrial contigs ranged in size from 0.22 to 44.2 kb, and an average of 804 ± 270 mitochondrial contigs were recovered per metagenomic assembly (Table 1). Mitochondrial annotation identified a COX1 coding sequence present in 4.9 % of all mitochondrial contigs, suggesting many contigs are likely fragments derived from the same species (Table 1).</p>
                <p>Classification of COX1 against BOLD identified seven Insect taxa across all samples, confidently (≥ 0.95 probability) assigning six to species level. COX1 sequences classified to any insect lineages were then utilised as seed sequences for circularised mitochondrial genome assembly, resulting in circularised complete assemblies for four unique taxa (Table 1). Across the eight vineyard samples, complete mitochondrial genomes, containing 12 protein-coding genes and 2 rRNA arrays, were recovered for <italic>Parth. corni </italic>(15.5 kb), <italic>Pseudo. viburni</italic> (15.2 kb), <italic>Anatrachyntis badia </italic>(Lepidoptera)<italic/>(15.4 kb) and <italic>Corticarina gibbosa </italic>(Coleoptera)<italic/>(16.1 kb). Whereas partial mitochondrial genomes were recovered for <italic>Coccophagus scutellaris </italic>(Hymenoptera) (6.5 kb), and <italic>Pseudo. longispinus </italic>(0.88 kb).</p>
                <p>When considering individual samples, multiple Hemipteran pest species were identified within the same scraping, suggesting that soft scale insect and mealybugs can co-occur in close proximity to each other (Figure 2). Only DNA from a single insect species, predicted to be <italic>Parth. corni</italic>, was identified across all 8 locations (Figure 2), with all 8 samples sharing 100 % DNA identity across the mitochondrial COX1 locus. Three of the sampled sites were also predicted to contain DNA from <italic>Pseudococcus </italic>species, with two samples being predicted to contain <italic>Pseudo. viburni</italic> (7361, Langhorne Creek; 7372, McLaren Vale),<italic/>while the third was predicted to contain mitochondrial DNA from <italic>Pseudo. longispinus </italic>(7373, McLaren Vale) (Figure 2).</p>
                <p>Previous studies have highlighted the presence of several natural enemies of coccids in Australia, including parasitoid wasps, beetles, moth larvae, and lacewings (<xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic>, 2013</xref>; <xref ref-type="bibr" rid="ref34">Rakimov <italic>et al.</italic>, 2015</xref>). Mitochondrial genome fragments were recovered for two distinct Hymenopteran taxa from three different locations. The parasitoid wasp <italic>Coccophagus scutellaris</italic> was identified in the samples from the Barossa Valley, both of which contained <italic>Parth. corni</italic> as the only other predicted insect taxon. A single mitochondrial fragment with best BLAST hits against multiple Chalcidoid wasp mitochondrial genomes was also identified in the 7361 Langhorne Creek sample, although the exact species associated with this sequence remains unknown due to gaps in the available databases that link taxonomic assignments to appropriate genetic information.</p>
                <p>The MitoMonitor ecosystem monitoring process is therefore capable of determining the abundance of specific soft scale insect and mealybug species, while detecting insect species that can act as potential biocontrol agents for these pests. As such, this pipeline could be used as an important biodiversity monitoring tool for assessing the impact of various biocontrol strategies, although a complete description of all potential species is limited by the completeness of reference databases. Therefore, collaboration between taxonomists and molecular biologists is required to increase the power of databases and broaden the analytical power of the methodology.</p>
                <p>In addition to mitochondrial genomes from mealybugs, soft scale insects and their potential parasitoids, complete mitochondrial genomes were recovered for the insect species <italic>Anatrachyntis badia </italic>(Florida Pink Scavenger)<italic/>and <italic>Corticarina gibbosa</italic> (a species of Minute Brown Scavenger Beetle) in sample 7361 from Langhorne Creek, as well as a partial mitochondrial genome from an unknown species of <italic>Liposcelis </italic>(bark louse)<italic/>in scrapings taken from the Adelaide Hills (7375), Langhorne Creek (7361) and McLaren Vale (7372). This would suggest that these species may also be living within or be associated with colonies of soft scale insect and mealybug; however, due to the limited number of samples, the full scope of ecological diversity across the vineyards is likely to have been underestimated.</p>
                <p/>
                <p>
                    <fig>
                        <label>Table</label>
                        <caption>
                            <title>Figure 2. Abundance estimates of insect species present in Australian vineyard samples.</title>
                            <p>Insect abundance estimates based on shotgun sequencing reads mapped against assembled mitochondrial fragments that were classified as insect species, either using the BOLD API or by BLASTn against insect NCBI GenBank mitochondrial genomes. Species abundance is presented as the log2 of total read depth per million reads in each sample. A full table of these values can be found in Table S1.</p>
                        </caption>
                        <graphic mimetype="image" ns1:type="simple" ns1:href="image2.png"/>
                    </fig>
                </p>
                <fig>
                    <label>Table</label>
                    <caption>
                        <title>Figure 2. Abundance estimates of insect species present in Australian vineyard samples.</title>
                        <p>Insect abundance estimates based on shotgun sequencing reads mapped against assembled mitochondrial fragments that were classified as insect species, either using the BOLD API or by BLASTn against insect NCBI GenBank mitochondrial genomes. Species abundance is presented as the log2 of total read depth per million reads in each sample. A full table of these values can be found in Table S1.</p>
                    </caption>
                    <graphic mimetype="image" ns1:type="simple" ns1:href="image2.png"/>
                </fig>
                <p/>
            </sec>
            <sec id="3.-Evidence-for-Parthenolecanium-corni-in-South-Australian-vineyards">
                <title>3. Evidence for Parthenolecanium corni in South Australian vineyards</title>
                <p>While <italic>Parth. corni</italic> was described in the Australian taxonomic record from a single set of samples in 1976 (<xref ref-type="bibr" rid="ref4">Belbin <italic>et al.</italic>, 2021</xref>), since then its presence has not been recorded and it was not previously considered to be an active pest species in Australia. Instead, all subsequent taxonomic studies on the distribution of soft scale insects in Australian vineyards have identified <italic>Parth. persicae</italic> and <italic>Parth. pruinosum</italic> as the only species of <italic>Parthenolecanium</italic>
                    <bold>
                        <italic/>
                    </bold>observed (<xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic>, 2013</xref>). Given the ubiquitous detection of <italic>Parth. corni</italic> in the metagenomic samples, additional phylogenetic analysis was carried out on the COX1 sequence against datasets derived from BOLD and NCBI to confirm the MitoMonitor classification.</p>
                <p>Phylogenetic reconstruction utilising all available sequences for the <italic>Parthenolecanium </italic>genus across the COX1-5P region revealed that the <italic>Parth. corni</italic> COX1 7361 haplotype was monophyletic, with all other publicly available COX1 sequences for <italic>Parth. corni </italic>and a maximum genetic distance of 0.9 % across the accessions (Figure 3). Furthermore, the <italic>Parth. corni </italic>7361 haplotype generated by MitoMonitor was identical to sequences obtained from Australian (GBMNA27795-19), Chinese (GBMNC41505-2), and Chilean (GBMIN67815-17, GBMIN67813-17, GBMHH24788-19, and GBMHH24786-19) populations of <italic>Parth. corni </italic>(haplotype H2, Table 2). The two <italic>Parth. persicae </italic>haplotypes present in BOLD were separated by a single base difference. However, both haplotypes shared a genetic distance of 9.1 % from the <italic>Parth. corni</italic> 7361 COX1 haplotype (Table 2). In comparison, the single publicly available <italic>Parth. pruinosum </italic>COX1-5P, which was also identical to several sequences from isolates of <italic>Parth. corni</italic>, differed by 0.18 % from the 7361 COX1 haplotype.</p>
                <p>
                    <table-wrap position="float" orientation="portait">
                        <label>Table</label>
                        <caption>
                            <title>Table 2. Genetic distance (%) between the Parthenolecanium COX1 haplotypes. </title>
                        </caption>
                        <alternatives>
                            <table style="table table-bordered table-striped affichage-tableau">
<col width="11%"/>
<col width="11%"/>
<col width="11%"/>
<col width="11%"/>
<col width="11%"/>
<col width="11%"/>
<col width="11%"/>
<col width="11%"/>
<col width="11%"/>
<col width="11%"/>
<col width="11%"/>
<col width="11%"/>
<col width="11%"/>
<thead>
    <tr>
        <td xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">titre du tableau </td>
    </tr>
</thead>
<tr>
    <th>
        <italic>Parth. corni</italic>
        <break/> 7361</th>
    <th>
        <italic>Parth. corni</italic>
        <break/> H1</th>
    <th>
        <italic>Parth. corni</italic>
        <break/> H2</th>
    <th>
        <italic>Parth. corni/ pruinosum</italic>
    </th>
    <th>
        <italic>Parth. persicae</italic> H1</th>
    <th>
        <italic>Parth. persicae</italic>
        <break/> H2</th>
    <th>
        <italic>Parth. persicae</italic>
    </th>
    <th>
        <italic>Parth. pruinosum</italic>
    </th>
    <th>
        <italic>Parth. corni/ pruinosum</italic>*</th>
</tr>
<tr>
    <th>COX1-5P</th>
    <th>0.94</th>
    <th>0</th>
    <th>0.18</th>
    <th>9.1</th>
    <th>9.1</th>
    <th/>
    <th/>
    <th/>
</tr>
<tr>
    <th>COX1-central</th>
    <th/>
    <th/>
    <th/>
    <th/>
    <th/>
    <th>9.1</th>
    <th>1.8</th>
    <th>0</th>
</tr>
                            </table>
                        </alternatives>
                        <table-wrap-foot>
                            <fn>
<p>*Haplotype from “unusual” Parth. pruinosum isolated from Gumeracha South Australia.</p>
                            </fn>
                        </table-wrap-foot>
                    </table-wrap>
                </p>
                <p>While the COX1-5P fragment is the <italic>defacto</italic>  standard for molecular-based phylogenetic reconstruction in insects, technical issues necessitated<italic/>the use of an alternate marker from within the central region of the COX1 mitochondrial gene (COX1-central) in an earlier study by (<xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic>, 2013</xref>). It was therefore not possible to compare the COX1-central data with the curated sequences within BOLD (<xref ref-type="bibr" rid="ref35">Ratnasingham and Hebert, 2007</xref>).</p>
                <p>As MitoMonitor provided complete mitochondrial genomes for the predicted <italic>Parth. corni</italic> samples in this study, it was possible to construct a second phylogeny that encompassed sequences form the COX1-central locus produced in <xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic> (2013)</xref>, in addition to a single, independent COX1-central<italic/>sequence from <italic>Parth. corni</italic> (NCBI:AB439534.1) (Figure 4). As seen for COX1-5P, the <italic>Parth. corni</italic> 7361 COX1 haplotype was highly divergent (9.1 %) from the sequences associated with <italic>Parth. persicae</italic> (<xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic>, 2013</xref>), clearly distinguishing the two species at the molecular level.</p>
                <p/>
                <p>
                    <fig>
                        <label>Table</label>
                        <caption>
                            <title>Figure 3. Phylogenetic reconstruction of the COX1-5P locus.</title>
                            <p>Phylogenetic reconstruction of the <italic>Parth. corni</italic> 7361 haplotype against publicly available <italic>Parthenolecanium</italic> datasets across the COX1-5P universal locus sourced from Barcode of Life Database (BOLD). Publicly available data are denoted by their BOLD accessions.</p>
                        </caption>
                        <graphic mimetype="image" ns1:type="simple" ns1:href="image3.png"/>
                    </fig>
                </p>
                <fig>
                    <label>Table</label>
                    <caption>
                        <title>Figure 3. Phylogenetic reconstruction of the COX1-5P locus.</title>
                        <p>Phylogenetic reconstruction of the <italic>Parth. corni</italic> 7361 haplotype against publicly available <italic>Parthenolecanium</italic> datasets across the COX1-5P universal locus sourced from Barcode of Life Database (BOLD). Publicly available data are denoted by their BOLD accessions.</p>
                    </caption>
                    <graphic mimetype="image" ns1:type="simple" ns1:href="image3.png"/>
                </fig>
                <p/>
                <p>However, unlike the COX1-5P region, which could not differentiate <italic>Parth. corni</italic> and <italic>Parth. pruinosum</italic>, the 7361 haplotype was shown to be identical to the <italic>Parth. corni</italic> AB439534.1 accession, but distinct (1.8 % difference) from the majority of <italic>Parth. pruinosum</italic> samples (Table 2). The exception to this clear species delineation was the presence of sequences from two isolates from Gumeracha, South Australia (KC784922.1 and KC789423.1), which has previously been flagged as representing taxonomically-divergent <italic>Parth. pruinosum</italic> (<xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic>, 2013</xref>).</p>
                <p/>
                <p/>
                <p>
                    <fig>
                        <label>Table</label>
                        <caption>
                            <title>Figure 4. Phylogenetic reconstruction of the COX1-central locus.</title>
                            <p>Phylogenetic reconstruction of the <italic>Parth. corni</italic> 7361 haplotype against publicly available <italic>Parthenolecanium</italic> datasets utilising the COX1-central locus (<xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic>, 2013</xref>). Samples of <italic>Parth. pruinosum</italic> that displayed unusual taxonomic and lifecycle traits from <xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic> (2013)</xref> are highlighted in pink. Publicly available data are denoted by their NCBI GenBank accessions.</p>
                        </caption>
                        <graphic mimetype="image" ns1:type="simple" ns1:href="image4.png"/>
                    </fig>
                </p>
                <fig>
                    <label>Table</label>
                    <caption>
                        <title>Figure 4. Phylogenetic reconstruction of the COX1-central locus.</title>
                        <p>Phylogenetic reconstruction of the <italic>Parth. corni</italic> 7361 haplotype against publicly available <italic>Parthenolecanium</italic> datasets utilising the COX1-central locus (<xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic>, 2013</xref>). Samples of <italic>Parth. pruinosum</italic> that displayed unusual taxonomic and lifecycle traits from <xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic> (2013)</xref> are highlighted in pink. Publicly available data are denoted by their NCBI GenBank accessions.</p>
                    </caption>
                    <graphic mimetype="image" ns1:type="simple" ns1:href="image4.png"/>
                </fig>
                <p/>
                <p>In addition to providing information from both COX1 loci (5P and central), the availability of a complete mitochondrial genome for the <italic>Parth. sp.</italic> identified in this study<italic/>allowed the two phylogenies to be directly compared. By combining the associated metadata information from both topologies it is likely that the <italic>Parth. corni</italic> species designation given to the 7361 haplotype by the BOLD classification (which includes vouchered museum specimens and sequences from the Centre for Biodiversity Genomics) is likely to be correct. Furthermore, it also indicates that both Gumeracha sequences are likely to represent <italic>Parth. corni</italic>,<italic/>rather than “an unusual” representation of <italic>Parth. pruinosum</italic> (<xref ref-type="bibr" rid="ref33">Rakimov <italic>et al.</italic>, 2013</xref>).</p>
                <p>While the failure to observe <italic>Parth. corni</italic> as a historical pest within Australian vineyards may be due to a recent biological incursion, it may also be a case of misidentification due to complications within the <italic>Parthenolecanium </italic>taxonomic record, as several studies question the validity of current species limits (<xref ref-type="bibr" rid="ref12">Danzig, 1997</xref>; <xref ref-type="bibr" rid="ref18">Gill, 1988</xref>; <xref ref-type="bibr" rid="ref31">Nakahara, 1981</xref>). Specifically, <xref ref-type="bibr" rid="ref18">Gill (1988)</xref> stated that <italic>Parth. pruinosum </italic>was indistinguishable in the field from <italic>Parth. corni </italic>if the powdery wax was absent, which is generally the case when dealing with dead and/or dried individuals. However, a lack of tubular ducts on the dorsum, including on the anal cleft, can be used as a taxonomic character to delineate <italic>Parth. corni </italic>and <italic>Parth. pruinosum</italic>. Accordingly, the distinct lack of tubular ducts along the dorsum of individual soft scale insects isolated from the South Australian vineyard scrapings (Figure S1), further supports the notion that the sequence data obtained from the metagenomic datasets were derived from <italic>Parth. corni</italic>.</p>
                <p>The discovery of <italic>Parth. corni</italic> as a common component of soft scale communities within these South Australian vineyards is consistent with recent observations of multivoltine reproduction within soft scale populations in many Australian viticultural regions (<xref ref-type="bibr" rid="ref40">Venus, 2017</xref>). First described in California (Coquillett) <italic>Parth. pruinosum</italic> is generally described as univoltine (<xref ref-type="bibr" rid="ref17">García Morales <italic>et al.</italic>, 2016</xref>; <xref ref-type="bibr" rid="ref18">Gill, 1988</xref>; <xref ref-type="bibr" rid="ref39">Ueda <italic>et al.</italic>, 2008</xref>), as is <italic>Parth. persicae</italic>,<italic/>the other major soft scale insect species previously reported in Australian vineyards (<xref ref-type="bibr" rid="ref17">García Morales <italic>et al.</italic>, 2016</xref>; <xref ref-type="bibr" rid="ref18">Gill, 1988</xref>). In contrast, <italic>Parth. corni</italic> is frequently described as multivoltine (<xref ref-type="bibr" rid="ref17">García Morales <italic>et al.</italic>, 2016</xref>), especially in warmer climates (<xref ref-type="bibr" rid="ref10">Canard, 1960</xref>; <xref ref-type="bibr" rid="ref18">Gill, 1988</xref>).</p>
                <p>Whether the presence of <italic>Parth. corni </italic>is due to misidentification, incursion, or a combination of both, it has significant implications for the control of soft scale insects within Australian viticulture: current agrochemical applications, which target soft scale insect nymphs, are based on the control of strictly univoltine species (<italic>Parth. persicae</italic> and <italic>Parth. pruinosum</italic>), in which nymphs are present at a single defined time each year. The multivoltine nature of <italic>Parth. corni</italic> dictates that a spread of life stages exists throughout the year, likely rendering univoltine-based control strategies far less effective, and which could potentially explain the increasing prevalence of serious soft scale insect infestations in Australian vineyards.</p>
            </sec>
        </sec>
        <sec id="Conclusion">
            <title>Conclusion</title>
            <p>Soft scale insects are a major pest in global viticulture due to their ability to facilitate the development of sooty mould and their propensity for being transmission vectors of grapevine viral diseases. The development of the metagenomic-based ecosystem monitoring approach described in this study has resulted in a proof-of-concept to detect and quantify major pest species, together with key parasitoids and other associated insect species. The discovery of <italic>Parth. corni</italic> as a significant member of infesting soft scale insects in South Australia corroborates empirical observations of soft scale insects with multivoltine lifestyles; it thus has significant implications for the development of effective control strategies for this important group of pests in these areas.</p>
        </sec>
        <sec id="Acknowledgements">
            <title>Acknowledgements</title>
            <p>This work was supported by the AWRI and by Australian grapegrowers and winemakers through their investment body Wine Australia, with matching funds from the Australian Government. The AWRI is a member of the Wine Innovation Cluster (WIC) in Adelaide. Special thanks to Marcel Essling for valuable discussions regarding control measures for soft scale insects in the Australian Viticultural industry, as well as to the grapegrowers that provided access to their vineyards and/or assisted with sample collection.</p>
            <p/>
        </sec>
    </body>
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