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Ten Years of Heteroptera Barcoding at CBGP: Outputs and Prospects

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Ten Years of Heteroptera Barcoding at CBGP: Outputs and Prospects Ten years of Heteroptera barcoding at CBGP: outputs and prospects. Jean-Claude Streito, Guénaëlle Genson, Eric Pierre, Astrid Cruaud, Jean Yves Rasplus To cite this version: Jean-Claude Streito, Guénaëlle Genson, Eric Pierre, Astrid Cruaud, Jean Yves Rasplus. Ten years of Heteroptera barcoding at CBGP: outputs and prospects.. 6. Quadrennial IHS Meeting, Dec 2018, La Plata, Argentina. hal-02788356 HAL Id: hal-02788356 https://hal.inrae.fr/hal-02788356 Submitted on 5 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Ten years of Heteroptera barcoding at CBGP : outputs and prospects Streito Jean-Claude; Genson Guénaëlle; Pierre Éric; Cruaud Astrid & Rasplus Jean-Yves [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 Barcoding at CBGP : 10 years My lab : INRA-CBGP (Centre for Biology and Management of Populations) Where : Montpellier, France My job : Produce tools for identification of Arthropods Morphology and molecular (barcoding) .02 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 Barcoding at CBGP : 10 years We are interested in Arthropods of agronomic interest Pests: Beneficial : Invasive : .03 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 Barcoding at CBGP : 10 years We have increased true bugs barcoding in recent years Many true bug species have become major pests in Europe in recent years, Pests: especially on fruit and vegetable crops Lygus spp., Nezara viridula, Gonocerus acuteangulatus ... Several predatory true bugs are used as biocontrol agents, especially Mirid and Beneficial: Anthocorid species Invasive : Several alien species have become invasive, including Halyomorpha halys, Corythucha arcuata… .04 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 _01 Material and Methods .05 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 Barcoding at CBGP : methods Standard Barcode: COI 656 pb (Herbert et al., 2003) First: Classical PCR and Sanger sequencing For 3 years: two-step PCR and Miseq sequencing .06 IHS VI meeting La Plata 3-7 dec 2018 Barcoding at CBGP : methods We switched to the production of barcodes by NGS for many reasons: - lower cost for massive sample runs - a better understanding of artifacts (pseudogenes, heteroplasmy...) - the ability to detect parasitism Sanger: only one sequence obtained for each bug (the barcode of the bug or that of its potential parasitoid). NGS: several thousand sequences produced for each bug (the barcode of the bug but also that of its potential parasitoids, its endosymbionts etc.) .07 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 Barcoding at CBGP : methods International databases provide barcodes: BOLD Systems. Editor BOLD Canada. DDBJ - DNA Data Bank of Japan. Editor : DDBJ Center. GenBank - NCBI. Editor : NCBI, National Center for Biotechnology Information. But none of them fully meet our needs: - many of the insects we are interested in have not yet been sequenced - international DB (especially GenBank) contain too many misidentifications to allow reliable assignation To design our identification tools: - we fill the gaps and contribute to barcoding of life - our constant concern is to avoid sequences incorrectly identified (contaminations, misidentifications, pseudogenes…) .08 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 Species to be Sampling Identification Databases included conditioning Web portal Orius albidipennis storage Orius horwathi Orius laevigatus Orius laticollis Orius lindbergi Orius majusculus Orius minutus Orius niger Orius pallidicornis Orius vicinus Orius insidiosus Orius navaishae Orius tantillus DNA extraction and Collections storage ADN PCR amplification COI + nuDNA Sequencing 2nd quality control Phylogenetic Sequence correction analysis 1st quality control Protocol used at CBGP for the production and validation of sequences .09 Barcoding at CBGP : methods One important step: a non-destructive DNA extraction that allows vouchering and morphological re-examination by a taxonomist Extraction Dissection Vouchers Observation .010 Barcoding at CBGP : methods Last quality control : validation of sequences by phylogenetic inference .011 [email protected] : INRA-CBGP Montpellier _02 Results .012 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 10 years Barcoding CBGP : Results Number of sequences produced : All database: 21 169 COI sequences Heteroptera: 2 123 COI sequences http://arthemisdb.supagro.inra.fr/DefaultInfo.aspx?Page=Home Famillies: 35 Genus: 202 Species: 363 A database (Arthemis DB@se) focusing on pests and their natural enemies is continually implemented. .013 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 10 years Barcoding CBGP : Results Representation of biogeographical regions: 5% 75% 5% 11% 3% 1% .014 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 10 years Barcoding CBGP : Results % Number of sequences produced: sequences Heteroptera: 2 123 COI sequences Pests 38% Beneficials 28% Invasive 12% Other bugs 22% .015 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 10 years Barcoding CBGP : Results Number of sequences by families Species COI COI Sub-order Infra-orders Super-famillies Famillies world Bold CBGP ENICOCEPHALOMORPHA AENICTOPECHEIDAE 20 1 0 (425 espèces) ENICOCEPHALIDAE 405 2 0 CERATOCOMBIDAE 52 2 2 DIPSOCORIDAE 51 2 2 DIPSOCOROMORPHA HYPSIPTERYGIDAE 4 - 0 (395 espèces) SCHIZOPTERIDAE 287 2 0 STEMMOCRYPTIDAE 1 - 0 GERRIDAE 751 65 3 GERROIDEA HERMATOBATIDAE 9 - 0 VELIIDAE 962 29 1 GERROMORPHA HEBRIDAE 221 5 0 (2 120 espèces) HEBROIDEA MACROVELIIDAE 3 0 0 PARAPHRYNOVELIIDAE 2 1 0 MESOVELIOIDEA MESOVELIIDAE 46 14 0 HETEROPTERA HYDROMETROIDEA HYDROMETRIDAE 126 6 1 (45 318 espèces) AEPOPHILIDAE 1 - 0 SALDOIDEA LEPTOPODOMORPHA SALDIDAE 335 42 3 (381 espèces) LEPTOPODIDAE 39 1 0 LEPTOPOIDEA OMANIIDAE 6 - 0 APHELOCHEIRIDAE 78 2 0 NAUCOROIDEA NAUCORIDAE 391 7 1 POTAMOCORIDAE 8 4 0 BELOSTOMATIDAE 160 28 0 NEPOIDEA NEPIDAE 268 19 0 NEPOMORPHA CORIXOIDEA CORIXIDAE 607 89 1 (2 309 espèces) HELOTREPHIDAE 180 2 0 NOTONECTOIDEA NOTONECTIDAE 400 30 2 PLEIDAE 38 5 0 GELASTOCORIDAE 111 5 0 OCHTEROIDEA OCHTERIDAE 68 2 0 .016 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 10 years Barcoding CBGP : Results Number of sequences by families: Species COI COI Sous-ordres Infra-ordres Superfamilles Familles World Bold CBGP ANTHOCORIDAE 507 93 41 CIMICIDAE 110 18 1 CIMICOIDEA LYCTOCORIDAE 27 6 0 PLOKIOPHILIDAE 13 0 0 POLYCTENIDAE 32 1 0 CURALIIDAE 1 0 0 VELOCIPEDOIDEA VELOCIPEDIDAE 31 1 0 HETEROPTERA CIMICOMORPHA JOPPEICOIDEA JOPPEICIDAE 1 1 0 (45 318 espèces) (21 277 espèces) MEDOCOSTIDAE 1 - 0 NABOIDEA NABIDAE 386 42 12 MICROPHYSOIDEA MICROPHYSIDAE 25 8 0 MIRIDAE 11 101 879 107 MIROIDEA THAUMASTOCORIDAE 19 1 1 TINGIDAE 2 124 89 33 PACHYNOMIDAE 21 0 0 REDUVIOIDEA REDUVIIDAE 6 878 236 2 .017 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 10 years Barcoding CBGP : Results Number of validated sequences by families: Species COI COI Sous-ordres Infra-ordres Superfamilles Familles World Bold CBGP ARADIDAE 1 931 87 0 ARADOIDEA TERMITAPHIDIDAE 9 1 0 ALYDIDAE 359 26 0 COREIDAE 3 178 125 9 COREOIDEA HYOCEPHALIDAE 3 1 0 RHOPALIDAE 295 46 12 STENOCEPHALIDAE 16 9 1 IDIOSTOLOIDEA IDIOSTOLIDAE 4 0 0 ARTHENEIDAE 20 2 0 BERYTIDAE 174 20 2 BLISSIDAE 436 10 3 COLOBATHRISTIDAE 84 1 0 HETEROPTERA PENTATOMOMORPHA CRYPTORHAMPHIDAE 4 - 0 (45 318 espèces) (18 411 espèces) CYMIDAE 54 9 1 GEOCORIDAE 280 16 5 HENICOCORIDAE 1 - 0 LYGAEOIDEA HETEROGASTRIDAE 100 3 0 LYGAEIDAE 968 90 26 MALCIDAE 29 - 0 MESCHIIDAE 5 - 0 NINIDAE 13 1 0 OXYCARENIDAE 150 17 4 PACHYGRONTHIDAE 78 5 0 PIESMATIDAE 44 5 2 RHYPAROCHROMIDAE 1 850 127 15 .018 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 10 years Barcoding CBGP : Results Number of validated sequences by families: Nombre COI COI Sous-ordres Infra-ordres Superfamilles Familles d’espèces Bold CBGP ACANTHOSOMATIDAE 317 47 1 APHYLIDAE 3 - 0 CANOPIDAE 16 1 0 CYDNIDAE 765 25 2 CYRTOCORIDAE 11 1 0 DINIDORIDAE 110 9 0 LESTONIIDAE 2 1 0 MEGARIDIDAE 18 - 0 PENTATOMOIDEA PARASTRACHIIDAE 4 0 0 HETEROPTERA PENTATOMOMORPHA PENTATOMIDAE 4 841 438 56 (45 318 espèces) (18 411 espèces) PHLOEIDAE 4 1 0 PLATASPIDIDAE 604 8 1 SCUTELLERIDAE 531 34 5 TESSARATOMIDAE 250 6 1 THAUMASTELLIDAE 3 2 0 THYREOCORIDAE 220 9 0 UROSTYLIDAE 181 6 0 LARGIDAE 106 14 0 PYRRHOCOROIDEA PYRRHOCORIDAE 340 34 2 Total 45 318 2977 363 .019 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 10 years Barcoding CBGP : Results Several similar studies has been conducted (Jung et al, 2011; Park et al., 2011; Raupach et al., 2014 etc.) we found quite similar results: - standard COI bacode is a
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