‘rsi2021 Bicinformatc tools support decision-making in plant disease management | Elsevier Enhanced Reader Trends in Plant Science OC arin Ez Review Bioinformatic tools support decision-making in plant disease management ‘An-Yu Dong ®,' Zheng Wang ®, ' Jun-Jie Huang ®,' Bao-An Song ®, ' and Ge-Fei Hao ® ** Food loss due to pathogens is a major concem in agriculture, requiring the need Highlights for advanced disease detection and prevention measures to minimize pathogen syyrovta bokronatials sup damage to plants. Novel bioinformatic tools have opened doors for the low-cost cies on macro putogon rapid identification of pathogens and prevention of disease. The numberof these fea and ptt inerny as tools is growing fast and a comprehensive and comparative summary of these stleailigentbe cuore resources is currently lacking. Here, we review all current bioinformatic tools used to identity the mechanisms of pathogen pathogenicity, plant resistance Aris toe fx prt pxtogon protein identification, and the detection and treatment of plant disease. We com- _Ssmones cc pcr ant pt pare functionality, data volume, data sources, performance, and applicability of Esse murean paluosiay all tools to provide a comprehensive toolbox for researchers in plant disease managenreant: Homology end festre based pred ‘on oc acct defn of ‘row pert eaetaren pare, Plant disease research for sustainable food production ia Hunger and malnutrition are the biggest risks to health worldwide (hiips:/www.un.org/on). In Magento een 2019, nearly 690 million people suffered from hunger, an increase of 10 milion compared fdbeasdktaconardcas snr ‘with the statistics for 2018. Feeding the ever-increasing population is a major challenge," ‘especially in light of the current coronavirus disease 2019 (COVID-19) pandemic, which —Agocharica Yoga conta, and ‘could increase the number of chronically hungry people by more than 130 milion by the end of — Bevestivo dsascs oR esa 2020 thtiosi/fvww.wio int). Decreasing resources, climate change, and a growing popuation ache Frodens fo a deemie contribute to the need of maximizing crop production to ensure food security, Disease from infection with pathogens (e.g, bacteria, fungi, and acmycetes) causes approximately 30% of crop yield loss globally, and the direct economic impact as high as US$40 bition per year [1]. Certain types of pathogens seem to become more prominent, For example, the elatve propor. tion of fungal alerts increased from 1 to 7% ofthe total numiberin the ProMED database during the period between 1995 and 2010 [2,3]. Therefore, an in-depth understanding and management of plant diseases caused by pathogens is essential to select and cutive cisease-resistant crops: accordingy. In recent yeas, research on plant diseases caused by pathogens has generated a weat of infor mation, enabing the development of aplethoraofnovelbicinfomatic tools. For example, PRYtOPEN ey a [4 Effector? [5], PathoPtant [6], and interSPPI [7] can be used to analyze the mechanisms of Gren Pastis and hgfesRel pathogen pathogenicity; PRGdb [8] and RAGPredictor [9] a applicable in resistance Soeraneeng Key Laborato of Gran {F) protein (see Glossary) identification; image-based disease recognition, such as Prati [10] Pete are Aareutua Broengreeng, Minty of Eaten, ‘and Leaf Doctor [1], are used to detect plant ceases; and FungiPAD [12], PlantPepDB [13]. Gants erfsmarehsrd bevaoment of ‘and APDS [14 can provide agents to control plant diseases. These bioinformatic tools have ie Chania Qushou Useesy, achieved sufficient scientiic maturity, making decisions on plant disease management more eco SH¥eng 55028, RC orrical and rapid. However, a detaled overview and comparison ofthese resourves is lacking. Here, we summarize the functions, advantages, limitations, and applications of the existing bioin- .¢omeepondence formatic tools on plant disease management (Figure 1). Ths review covers four main topics: () a ghaoogateducn (Hao) ® penta perv ms psa 5 ee hitpsreader elsevier comireaderisdiplS 136019852110011997t0ken=486501DAASD7C41915EDADSS8A297DB1AS5083F4529DS7602804A7... 1/15‘rsi2021 Bicinformatc tools support decision-making in plant disease management | Elsevier Enhanced Reader Trends in Plant Science tt ee fonction as () teu — Mag ati ter rin ttn hat anontasie Fiabfisactsd LOCARZER Pate in Pues ps ptcon Tesi ParSsowe Figure 1. The most poputar analytical and decksion support bicinformatc tools for plant fsease sty. Ths ‘gure anows varoue ante end aeceion support to, ncudng pathogen genomes, pnt gene tact, plan pathogen taactons, pathogen ett patan pedcton, pr eastance prctan fresco, lant daaass erage, Image hand pint eocase detoctn, srochema coro bsogeal corr ana bopestdes We eeu, anal, ‘Sompared, an testes these tot ound pathogen pathogen, lant esistance poten, and plant danas detection 1nd restmant. Thay are recorenendod sod on tor uta fer spacte experants along wih prormanca Fil (etal and arajsofeach tocar shown Tabs 1-4 tho man toe. Ciscussion on tools for pathogen genomes, effector protein predictions, and host-pathogen in- teractions to explore mechanisms of pathogen pathogenicity (a comparison ofthe prediction too's for plant Ai proteins to study immune responses: (i) a summary of plant cisease image atabases and thet application in image-based disease detection; and (v) a summary ofthe ‘agrochemical, biological control, and biopesticide databases for plant disease treatment, Exploring mechanisms of pathogen pathogenicity Pants have evolved sophisticated defense systoms agaist pathogon infection. In response, pathogens suppress plantimmunity by secreting effector proteins and interacting with target pro- tens [15,16], To devalop new strategies of plant disease control, researchers have to elucidate the complex molecular mechanisms underying pathogen infection. Whole-genome sequencing technology has enabled the sequencing of an increasing number of pathogens, and a large ‘amount of genetic data have been accumulated. Thus, bioinforratic tools for analyzing pathogen genomes, effectors, and interspecies interactions have been developed to understand disease infection mechanisms and pathogenic targets. Genome databases of plant pathogons Specific bioinformatic too's have been developed to link the genomes of the pathogen and the host and to study the relationships between genetic diversity and disease. For example, 954 Tend inPet cence, Sep 2021, Vl 25,08 Glossary ‘virdence (i proteins: ts product by lt pathogens They ase naked patsy recogned by pnt sare ces ansaid ea70" oped ier Deep learning DL css of lapprechos Recs ates fern expe st allayrsorastokofmutipe pocosing kyo, whee tro output of rela eunedsattoipa kr fhoret layer, meer pssbie to iety Igpreel dcs to cerrlax ‘ster, toctr protons: rotors hat rmangulsshost ca rut ard ‘uncon, ry fctg reecbon (oxne or veleros face aor Ingasing dete espoees ctr 1 arts at -Mactine fearing MAL 0 ssc of nica retgeee. is. corporal ‘mode apron tat aes pats ‘rom aig aa to rake automat cons wit roaming eka Fesstance (proteins: puns cexpesoes nrespersotoptnogen toc They can xt ior, protons pathos, ras den (me cirenson ced eeatn cease hitpsreader elsevier comireaderisdipilS 136013852110011997t0ken=48650 1DAASD7C41915EDAD558A797DB1 AS6083F4529D6760280407. ans,‘rsi2021 Bicinformatc tools support decision-making in plant disease management | Elsevier Enhanced Reader Trends in Plant Science © CelPress Ez PhytoPath provides genome-scale data from pathogens with information about plant infec tion phenotypes [4]. It provides access to the complete assembly of genome and gene models of phytopathogens by using the Ensembi Genomes browser {17}. Many pathogenic ‘molecules interact directly with one or several extracellular or intracellular host target mole- cules. NIASGBdb consists of a genetic resources and plant diseases database, which is constantly undated. It links the genetic resources of plants and pathogens to plant disease information {18}; however, it lacks a classification of plant gene functions. By contrast, Plant Reactome is very detalled and can analyze the metabolic and regulatory pathways in plants, [19]. Nevertheless, it does not cover a wide range of biological processes. Fortunately, MapMan can compensate for these limitations because it can display large genomic Gatasats as diagrams of metabolic pathways or other biological processes [20,21]. Currently, data can be supplemented from microorganism genome databases, such as FungiDB [22], PATRIC [23], and MBGD [24] (Table 1), but there is stil a need for more com- prehensive plant pathogen genome databases. ‘Machine leaming based prediction of fungal effectors ‘The prediction of fungal effectors is challenging compared with bacteria and oomycetes because of lack af uniform sequence characteristics, such as the conserved N. terminal sequence moti [25-27]. Machine learning (ML) classifiers may leam the rules of effectors trom negative and positive traning examples without applying user-selected thresholds [28]. EtfectorP'.0 was the fist ML (naive Bayes) classifier developed to predict fungal effector proteins from socretomes, {29} eliminates the reiance on manually set thresholds, such as small size and cysteine rich- ness, EffectorP2.0 uses an ensemble classifier, which shows a lower false-positive rate than EffectorP'.0 [5 but, it has a data imbalance problem in model traning. Because 21 840 proteins have been used as negative samples, only 94 experimental verified fungal effectors serve as positive samples. Interestingly, FunEtfector-Pred has been developed by using a genetic algo- rthm and a granular support voctor-basod undersamnpling strategy, training with an imbalanced ‘eeu o1eue)_Seb4 Dey GT 0 UOIENNLE padsoosien rear dopaysirdn a 1 ote exch o2done3 easton rears dopayey ay ose Bury 0 wp ee) Sipiod aya ROU Ho Lod ‘SURIOIS eOUEISHO! UB PE SUELO O12aYo ROUT 04 SOO, BAIPALS Z CEL. 958 Tenn Pet Sommen, Sep be 221, Vl 25, hitpsreader elsevier comireaderisdipllS 13601385210011997t0ken=48650 1DAASD7C41915EDADSS8A297DB1ASG083F4529DS76O2804A7... 5/15Bicinformatc tools support decision-making in plant disease management | Elsevier Enhanced Reader Trends in Plant Science ‘rsi2021 aasaneret oL/6or0n/aa cz wsv ‘BUSNSAUOLOTN 908 soroomcTous oyna esnmayuosenalysca om ok wisys oopeub.8s crpeouver ved weepmerss019 sowssorz eet rice Coe - OHeL ns upton jo uopapaig de vaed oyna {5098 waREDIE-019 ayes m0 soo a sw visvH Mpa Boece Pons mis ‘upton 0 voropais {POSSE 75 Trance n Prt cence, Sepanber 2021, VL 26,86. 9 959 hitpsreader elsevier comireaderisdipilS 136013852110011997t0ken=48650 1DAASD7C41915EDAD558A797DB1 AS6083F4529D6760280407.‘rsi2021 Ez © CelPress Bicinformatc tools support decision-making in plant disease management | Elsevier Enhanced Reader Trends in Plant Science Table 3, Performance of toks for fungal effector pron and plant resistance proten prediction rtd foc tom Etec? 1.0 7as8% 9005% aroma Ftec202.0 RK O1I5% Evkaryotc protons 2000 fem efocirP2 forthe pupcenct — FunEtictorPred OTAD% 03.45% model compan fag) Preicton of prt eons ‘Annotated Rpts 81 Ho TAR (pst) raco aoe narnotate rotors (47968 rm TAR uate reat) NiGemmesueepe OR Ranguy ue | ARGpedcir 800 *viscketcouttr spactoty of ptt regs saps (17 969, bocaus erat ernest canon Ror prt Ino TAR aes, \We compared the data volume, functions, and sources ofthe tools mentioned eater (Table 1). HPIDB possesses 531 PPIs, which i the largest experimentally validated dataset. For function ality, HPIDB, PCPP', and’ VirusMentha have PPI network visualzations that make intricate intere- lationships seem inutive. There are three main tynes of data sources: database integration, text ‘mining, and computation fied format through thei «a predetion. HPIDB and VirusMentha use database integrationin .uni- IMEx consortium [42], enabing users to download, combine, vsualze, ‘and analyze the data from muttiple sources ina single forrnat. PHI-base uses text mining, making italifcut to quarantoe te further manvall checking, 3. rolabilty ofthis automaticaly extracted knowledge, which thus needs PCPPI database stores the caloulated PPI data, whereas InterSPPI oro- Vides a platform for predicting PPIs. In general, only a few databases are related tothe experimen- tally vaidated plant-pathe 109en PPls, and the data acquisition methods, especialy fr text ining, should be further improved to ensure the reliability of data [43 Prediction of plant R proteins PaantR proteins specifically recognize avirulence (Avr) proteins produced by pathogens to ac: tivate the downstream si involved in pathogenicity ignaiing responses that inilate plant dofense [4-46]. Avis ar effectors ‘and induce effector-iggered invmunity (ET) [47,48]. Compared with a wide range of Avr proteins, the currently discovered R proteins are rare [49]. Experimental methods for obtaining R proteins, such as transposon tagging, map-based cloning, and poly- merase chain reaction technology, always exhibit alow efficiency and have a high cost [60,51]. ‘Therefore, developing bi joinformatic tools for potential R protein prediction could help highlight gene diversification and discover new resistance capabiities, ‘Some prediction tools have been developed based on the sivilerty alignment of domains/motifs. Usual, R proteins possess modular domain structures, which require several dynamic intorac- tions between spectic domains to perform thei function [52]. Most FR proteins contain the folow- ing domains: leucine-ich repeat sequences (LAR), nucleotide binding sites (NBS), and serine/ threonine kinases (STKs) [53]. Aignment is mainty based on the hidden Markov model HMM) based method [54]. Oni ine, PRG is the most popular resource for providing compretiensive annotations and predictions of plant R protein. It includes 153 validated R proteins and 17 072 candidate R proteins [55]. ADRAGO module was used to automaticaly annotate and predict R proteins from any transcriptome or proteome. It uses HMMERVS, COILS2.2, and TMHMM2.0c software to detect LARS, NBSs, and other domains [5]. In adcition, some loca tools, such as 960 Tenn Pet cence, Sep be 2021, Vl 28,08 hitpsreader elsevier comireaderisdipilS 136013852110011997t0ken=48650 1DAASD7C41915EDAD558A797DB1 AS6083F4529D6760280407. ans,‘rsi2021 Bicinformatc tools support decision-making in plant disease management | Elsevier Enhanced Reader Trends in Plant Science © CelPress Ez GAugury [5], NLRparser [57], and NLGenomeSweener [58], were designed to predict siitar domains (domain differences shown in Table 1 in he supplementalinformation ontine). The cur- rent methods of identiying R proteins using the homology-based method are effective, but they ‘may miss existing unidentified or low simiity protein sequences. Fortunately, some methods based on R protein-ke feature extraction can be used asa supplement (able 2) Some ML-based too have been developed that can learn ‘R protein rues’ fom training Samples [59,60], RRGPredictor has emerged based on set theory and text mining for predicting F proteins. Th input is a TSV fle goneratod by nterProScan, which is capable of identifying and Classifying R proteins at the ganomic loval 61]. It strongly penalizes gaps and accounts for the ‘absence and presence ofthe primary domains of the R proteins, thus conferng a better plasticity ofthe analyss [9]. Because R proteins are commonly expressed primary during infection, annota- tions that ere based on transciptomic datain the absence ofinfecton wl generally ries the majority Of these proteins. NLR-Annotator is a tool wth universal applicability across diverse plant taxa to ‘oN this problem [52]. The power and novaty ofthis tools that itis completely independent of tran- ‘srpt support, thus enabing rapid de novo interrogation ofthe R protein complement of a genome: without rekance on gene expression of other pipelines [6%]. These tools may address the cravbacks. Cf relying on prior definitions of 2 gene model for plant R protein annotation. To guide readers in choosing an appropriate tod, we instaled these tools on our server and com= pared the performance with an independent test set (391 annotated disease R proteins from the TTAIR database [64], We compared the sensitivity, instalation process, speed, output, and user Interface of these tools (Table and Table S1 in the supplemental information online). We found that () the sensitivty of RG/Augury was the highest (98.40%), whereas the sensitivity of DRAGO was the lowest (88.20%%} (i the installation process of DRAGO was the easiest, ait does not need to compile; but, for PAugury, more than 20 modules need to be instaled, thus it Is considered to be dtficul; (i) we fished the test of the NLA-Annotator in minutes, while NuGenomeSweeper needed 2 h; and (v) DRAGO and RRGpredictor can identify most of the classes and domains of R proteins. We also vaidated the retabilty of our tests. The sensitivities of DRAGO and RRGpredictor were 88.20% and 96.60% respectively, which is consistent with the order of sensitivity test for DRAGO (87.00%) and RAGpredictor (90.00%) in the previous publication [61]. In adation, the test samples are both from TAI. This demonstrates that our testi ralable. It should be noted that DRAGO is easier and more intuitive for bench scientists to operate, while other too's require knowledge of command-tne operation. Plant disease diagnosis To prevent plant diseases, image-based digital technologies have been used to diagnose cisease. A large amount of image data are being gathered in real ime, and, atthe same time, different artical iteligence (Al) algorithms are used to provide optimized decisions. This has resulted in minimized cost and is being applied by the majority of farmers, These methods seek to improve plant disease rating data quality by reducing human errors [65]. We analyzed and ‘compared digital technologies in this area. Pant disease image databases Pant cisease image datasets support the ML algorithms for mage segmentation and classifica tion [6]. These databases were divided into two categories. Images were validated by experts in some databases. As shown in Table 4, PlantVilage, the most popular mage crowdsourcing platform, contains over 50 000 images of heathy and infected leaves of 150 crops and over 11800 iseases [86]. Because these images are taken using laboratory equipment, they may have poor efficany in the real world. Conversely, images of PiantDisease [67], RoCoLe [68], and Thence n Prt Scarce, Septanbar 2021 Ve 2686.8 961 hitpsreader elsevier comireaderisdipllS 13601985210011997t0ken=48650 1DAASD7C41915EDADSS8A297DB1ASG083F4529DS7EO2804A7... 9/5‘rsi2021 Bicinformatc tools support decision-making in plant disease management | Elsevier Enhanced Reader Ez © CelPress Table 4 Rescuroes for the dlagnosis and treeiment of plant iseases Trends in Plant Science Plt dessse dagross: plat doseso mage databases Platioge Valdatad oy onsen, hiipe/ipanevlage ps ot ‘homost commer sedans datasets, rote ten in [oso sxtupsand shomaqanstagray bacon Recote att by experts ips/ddiog/0 s7eRDIeysoaeG 2 and nage datas rspared fer cofse captured in a range of ‘eal condone Pntasee| Vals onperts nips comnataresano) and capt na ang DeerLcaring PariDiccsos tre codecs 008 Valdaod by omer tpn goats rep enpiacmbcapat/ Prntoe Casares ancora a ipso compratcya ‘mo gutinos lave Objet Detector Dat ‘mertonedin APN, ‘BRUNSWICK Proses ipe/cectranpaewen gro caf. 002/ gresouten ara Detox ?Oaturo=en-CA low ozaiten rages Plant cecases gna: mage-tased oo fr dee lant dlaasos Pane ‘cory lt looses hipped Seoogtetet ‘oer lant ceases ips comatsnegouny orelope deaploaring pap nays oat Deter unt he sverty of iii /tines sole comvulappect ocr! ‘Seasons estirate ‘unity he sverty oF Fiip/tures appl con/WebObecsMEStoeea/ —_ anases PCN Paste acon pw street retest PAN ste acton ipsa potdoeso.cea? 962 Tenn Pet cence, Sep 2021, Vl 28, No.8 Deas and nest reschemeal contol rene srt Inorstonc ‘deca, st ad Iraresc isoaso, host and torus he ste grup ard paso bangs vacates, wo ps use escipton anduse tet on ver 250 wee Date URL Poste 50.000 mages, 150 pats, 1800 deeance 1500 rage, ‘plat, soa 18334 mapas, 12epmtes 46513 mages, 21 pints, 2508 rags, ‘3 pnt spose, 27 dee 02 rages, pln, 180 orase opens, "00 dosose ‘epi, 25 dscase Sploms, Sooses ‘pint, 1 ecoase ft agers: 822 urges, Srcdos, St rematies hitpsreader elsevier comireaderisdipllS 13601385210011997t0ken=486501DAASD7C41915EDADSS8A297DB1ASG083F4529D57602804A... 10/15‘rsi2021 Bicinformatc tools support decision-making in plant disease management | Elsevier Enhanced Reader Trends in Plant Science “Tablo 4. 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To allow use ot the deep learning (DL) technique, Images in PODB were subdivided according to certain ceria, and the number of images was in- creased 10 48.513 [69]. Moreover, mages were classified according tothe guideines mentioned in APSNat (ttps://wwww apsnet.org/edcenter/resources/commonnames/Pages/defaul. asp»). “nde n Part Scere Soptarbr 202, Ve 2,Na.® 963 hitpsreader elsevier comireaderisdipilS 136013852110011997t0ken=48650 1DAASD7C41915EDAD558A797DB1 AS6083F4529D6760280407. wis‘rsi2021 Ez © CelPress Bicinformatc tools support decision-making in plant disease management | Elsevier Enhanced Reader Trends in Plant Science PaantDoc is a multleat image dataset that contains 2598 data points in otal across 13 plant spe- ies and up to 17 classes of diseases. Itinvoves approximately 300 human hours of effort to an- rotate intemet-scraped images [70]; but, some images are still misclassified due to a lack of professional experience. Itis worth mentoning that PlantVilage is widely used due to its excellent performance, but other image databases are rarely used for model traning. Image-based tools for detecting plant diseases DDigtal vision technology may be used for detecting plant seases in areas whore farmers do not have _aoceRs to expats, Several tools ave boon developed to identify dsaase or quantify dssase sovarly (Table 4), Plantx,a mobile apo, could assist in detecting darnage to plants based onimages end mo- be internet connectty. The time- and geotagged image can be uploaded to a cloud server, and RF based algorithms are used to analyze optical pattems and detect ciseases. The suggested infor- ‘mation on disease management, inducing chemical and biological control methods, is fed back to the user withn afew seconds [10]. Addtionaly, GoogLeNet, based on DL, isa command-ine pipeline that has been verified to have good acouracy [77]; but, these tools carnot quanti the seventy of is ‘ease. To overcome this problem, Leaf Doctor [1] and the Estimate app [72,76] were developed to ‘quantity disease severiy by using standard area diagrams (SADs). SADs may visualy relate sarnping Unis to reference images of known sovertes. These too's were doveloped to improv the accuracy and precision of disease severity estimation by reducing humen ear to some extent. However, cO- infection, ctferent ight conditions, disease stage identiication, nonaboratory dataset scarcity, and ‘Mtoe other issues are sil ostaces to image-based technologies [74,75]. Sensors, such as mea: sung relectance, temperature, o uoxescence, provide potential strategies to mitigate these chal lenges, especialy nearly detection of plant diseases [76]. We compared () the compatiilty (main items, and i) detection classes ofthese tools in Table 4 Regarding compatibity(), Plantx supports Android only, whereas Leaf Doctor and Estimate sup- port iOS only. Muitiple compatible tools are stil needed. Regarding main items (i), Pantixis the ‘most comprehensive tool, which includes triggers, symptoms, preventive measures, and biological ‘and chemical control methods, Regarding detection classes i, Piantx detects 400 classes of dis ‘8ase in 30 plants, whichis a much more comprehensive coverage than other tools. Therefore, itis ro surprise that Plantix, which is useful for farmers, has been downloaded more than 620 000 times. What is curently missing for Plantcis feature quantifying the severly ofthe disease, Plant disease treatment ‘The increasing prevalence of pathogen induced diseases and pesticide resistance highights the Urgent need for an effecve agent to treat plant diseases [77]. Currently, agrochemicals, biological Control, and biopesticide information have been systematically recorded in many public data. bases. The systematic analysis and comperison of these databases enables users to directly ac~ ‘0855 pesticide data of interest and speed up the discovery of dissase prevention strategies. ‘Agrochemical control ‘Agrochemicals provide a quick means of plant protection. Over the past decades, several data- bases have emerged to store agrocherrical information, wich promoted their application (Table 4). One of the most comprehensive agrocherical databases isthe PPDB. Itwas developed ‘over 20 years ago andl provides data from 404 agents on treated diseases and cxaps, eficacy and activity, use status (by region or county), type of crop, mode of action, etc. [78]- Compared with PDB, the Pesticide Action Network (PAN; hitp:/wwwossticideinfo.ora) has 1047 agents with Corresponding activity data and usage descriptions. In adation, the Compendium of Pesticide ‘Common Names (CPCN; http://www alanwood.neUpesticides/) and FungiPAD [12] is supple- ‘mented in this etd. Generaly, a single database contains onlya few annotations for agrochemicals 964 Ten inPet Semen, Sep 2021, Vl 28, No.8 hitpsreader elsevier comireaderisdpllS 13501385210011997token=4865D 1DAASD7C4195EDAD558A797D8 1 AS6093F4529D676028040, rans.‘rsi2021 Bicinformatc tools support decision-making in plant disease management | Elsevier Enhanced Reader Trends in Plant Science © CelPress Ez “There isa strong desie for estabshing a one stop database to obtain fuly comprehensive treat- Qutstanding questions: ‘ment information for agrochemicals. sta irésanceproblons st ost ‘model traning ot pamogen efector Biological control and biopesticides ana ple eastnce pot precocn Recent, the application of biological control and biopestcide strategies has provided opportu [Jo san we consist a ries to maa ecolegeal balance cause suppers song selecvy and darpens the de- Swart velopment of resistance. Accordingly databases related to biological contro! and biopesticides (naturally occurring chemicals and antimicrobial peptides) have been developed (Table 4). The _ ™/dlleut to carpare he pertrmance: SerPestes Daubnee BPD Mon/eton hotsacuiveensbecbindexhimytircompre. im Pane hensive cla relating to pestcices dered rom natural substances. The detabase provides 173. ancy rao tra agents, inking pheromones, insect predators, fung, bactra, and aturaly occuring cane mat oa ns ‘chemicals. PlantPepDB is a web-based repository dedicated to plant peptides that possess nu- “™#eomeersons? rmeous acts, such as antungaanibacteral ava ardimane acts, ha CAN oka Man yon be utilized as biopesticides [13]. In addition, other databases, such as APD [14], CAMPra [79], waning detasets and user driven test and DRAMP2.0 [80], are also useful in this context. These resources can provide a solid founda- “ids he fekd of plart-palhogan ne. scr Hic coe eng ten for developing treatment stteges based on bejcal contol or bopestides aes ‘eng cr a ec? Concluding remarks and future perspectives Here, we reed iinfomalitols thet promatereserch on lat cscases cause by patho awn nba dome gens Ft, we colectedthe pathogen genome databases, compared the scairacy oFpresc- isn wane tomes {on tos based on MI fc fingel efector pres, anc cussed he data volume, fncion and) ow tt on data source of plant-pathogen interaction tools. Second, we compared the performance of plant stage identification, nor la daasot Rprotehn prediction tool, including ther sensitivity, instalation process, speed, output classification, Sov: a mutple oar ses? are user rtetce, wih an pendent test se. This, we surerard pant cease mage dat oy dove asi ein son basso suppor the detecten model raring tase en ML. We ako compare he compatly, fom tsar bod man output tam, and detecion types of mage-based disease dagnoss too. Finaly, we Sn ard ba, cs revewod the agoctemcal,iogkal conto, ar! opel dlabates ot atop for "ane Srahok ere seating plant seas. ae We look forward to the development of those bioinformatic tols for many reasons. () Using ML to ‘explore the mechanisms of pathogen pathogenicity is an aspiration. Abundant genomic data and advances in ML might improve gene annotation, in particular for genes that are cificult to comecty predict with current methods. () To satisty different user groups, too's should provide both ‘command-line and graphical user interfaces. Comrand-Ine-based versions may be suitable for bioinformatic scientists when dealing with large-scale data. Conversely, wet laboratory re- searchers, who lack coding experience, often rely on graphical interfaces. i) To reach a good) User expetience, the workflow oftoois should be easy to understand. instalation of the tools should ‘also be as easy as passibe.(v] We propose updating tools fr detecting diseases in various plant ‘organs and different fsease phases, Tools also should be integrated into @ mobile application, hich may provide.a cheap solution and enable application in the iad. () Due to alackof prescrip tion inforraton, itis stl cliffcut to guide farmers in choosing appropriate treatment strategies from the databases for agrochemicals, biological contros, and biopesticides.(v) Tool designers should Pay more attention to updating ther platforms to ensure timeliness and integrty ofthe database. We also propose several key issues for future research (eee Ouistanding questions) ‘Acknowledgments, “Tsworkwas supped bythe Nar Natal Scan Foundation of Chin 31960548, 21772089, and 1853127, the Program ot roducing Teens of Dep tanneries of Crna [111 Progr, C2022), ante Fronts Science Cntr fr Asymmetc Syrihoss and Medical Mlcus, Doparrat of Education, Guizhou Province [anfacho KY rumibor 2020008, Trance nPrt cerca, Sepanber 2021, VL 26,869 965, hitpsreader elsevier comireaderisdiplS 13601985210011997t0ken=486501DAASD7C41915EDADSS8A297DB1AS5083F4529D57602804A... 19/15‘rsi2021 © CelPress Declaration of interests Noimtsrets are dacaed ‘Supplemental information Bioinformatic tools support decision-making in plant disease management | Elsevier Enhanced Reader ‘Trends in Plant Science ‘Seeiamertalnlematen associated whi ace can ba found anne at pss. og 0-1016 rt 2004.05.00. References 1 Sao Seta 0 Copmecintdeaner stern ‘ten gon bed ramen cen ra sa 2. 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