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 good gene to explore true bugs diversity - for about 10% of genus problems appears (cryptic species and non discrimination of some species)
Some Genus with more taxa than expected Alpagut (cryptic taxa): Notonecta Graphosoma Nezara 11 genus (5,7% of genus studies) Eurydema Nysius Macrolophus Adelphocoris Cardiastethus Elatophilus Orius
.020 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 More species as expected
Macrolophus pygmaeus
Genus Macrolophus
Macrolophus pygmaeus like
Macrolophus pygmaeus like
Probably two new undescribed species
.021 [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 good gene to explore true bugs diversity - for about 10% of genus problems appears (cryptic species and non discrimination of species)
Genus for witch COI is non resolutive: Aelia Arocatus Ischnodemus 6 genus (3,1 % of genus studied) Physatocheila Nabis Lygus
.022 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 COI non resolutive
N. rugosus
Genus Nabis N. ferus N. brevis N. pseudoferus
N. provencalis N. ferus
N. punctatus N. pseudoferus
Some misidentifations to be corrected after morphological review of vouchers Morever COI is not fully resolutive to separate all European species
.023 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 10 years Barcoding CBGP : Results
Arthropoda Heteroptera 21 169 2 123
http://arthemisdb.supagro.inra.fr/DefaultInfo.aspx?Page=Home
For the moment we have produced many sequences. Most of them are not accessible because they have not yet been validated and published.
Sq validated We now expect to validate and publish as many (avalaible for blast) sequences as possible to make them accessible. 570 Heteroptera 2 123 Sq published (fully avalaible) 264
.024 [email protected] : INRA-CBGP Montpellier IHS VI meeting La Plata 3-7 dec 2018 MERCI
.025 [email protected] : INRA-CBGP Montpellier