FIMT Barcode Database

Developed by FABI

Insect pests threaten the sustainability of Eucalyptus and Pinus plantation and natural forests worldwide. Globally the number of invasive insect pests has been shown to increase exponentially over time.

A common challenge is the accurate and rapid identification of insect pests as this has implications for management and quarantine decisions. In many instances feasible management options cannot be implemented due to the identification of the insect being unknown.

The FIMT website serves as a tool for rapid identification of insects associated with Eucalyptus and Pinus trees and is intended to assist researchers and field-based scientists focussing on forest health. The database contains sequences generated from insect pests of Eucalyptus and Pinus, generated using two mitochondrial DNA regions, namely Cytochrome Oxidase I (COI) and Cytochrome b. Relevant sequences from GenBank have also been included. The insects sequenced at the Forestry and Agricultural Biotechnology Institute have also been morphologically identified by a taxonomist. See the About page for more information.

Forest Insects Mitochondrial (FIMT) Barcode Database

What can this website be used for?

This website provides a tool for identification of insect associated with Eucalyptus and Pinus. This can be achieved by submitting a sequence of the insect of interest, which is then compared to curated sequences in the database, which contains sequences of a range of Eucalyptus and Pinus forestry pests. By comparing the unknown sequence to reference sequences in the database, the identification of the insect pest can be confirmed. If no sequences in the database match the query sequence, then the output phylogenetic tree will indicate the most closely related group. Identification may be at the species level or at the order level depending on the specimens in the database.

What can this website not be used for?

The trees generated from this database are for support of identification only. It is intended to help guide decision makers and researchers, not for publication. Sequences will not be provided. For this purpose, users are referred to GenBank for sequences of interest, or to contact relevant research groups who have produced the data.

Primers

There are many primers available for use in amplification of mitochondrial data. Primers amplifying the barcoding region are a popular choice. Primers used for generating sequences for this database include:

Cytochrome b primers:

• CP1 (5’-GAT GAT GAA ATT TTG GAT C-3’) (Harry et al., 1998)
• CB2 (5’-ATT ACA CCT CCT AAT TA TTA GGA AT-3’) (Jermiin & Crozier, 1994)

Cytochrome oxidase I primers (barcoding region):

• LCO1490 (C1-J- 1514) (5’-GGTCAACAAATCATAAAGATATTGG- 3’) (Folmer et al., 1994)
• HCO2198 (C1-N- 2173) (5’-TAAACTTCAGGGTGACCAAAAAATCA- 3’) (Folmer et al., 1994)
• LepF (5'-ATTCAACCAATCATAAAGATATTGG-3′) (Herbert et al., 2003
• LepR (5′-TAAACTTCTGGATGTCCAAAAAATCA-3') (Herbert et al., 2003
• Alias Jerry (C1-J-2183) (5’- CAA CAT TTA TTT TGA TTT TTT GG-3’) (Simon et al., 1994
• Alias Pat (TL2-N-3014) (5’- TCC AAT GCA CTA ATC TGC CAT ATT A-3’) (Simon et al., 1994

Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294-299.

Harry M, Solignac M, Lachaise D (1998) Molecular Evidence for Parallel Evolution of Adaptive Syndromes in Fig-Breeding Lissocephala (Drosophilidae). Molecular Phylogenetics and Evolution, 9, 542-551.

Jermiin LS, Crozier RH (1994) The Cytochrome b Region in the Mitochondrial DNA of the Ant Tetraponera rufoniger: Sequence Divergence in Hymenoptera May Be Associated with Nucleotide Content. Journal of Molecular Evolution, 38, 282-294.

Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. P Roy Soc B-Biol Sci 270, 313–321.

Simon C, Frati F, Beckenbach AT, Crespi B, Liu H, et al. (1994) Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Annls ent Soc Am 87, 651–701.

What will happen to my sequence data?

Query sequences uploaded will be verified for accuracy before being added to the database. Basic phylogenetic trees generated from this database, GenBank sequences as well as the query sequence, are used solely for identification purposes and not for publication. No sequences will be used by the hosts of the website or provided to any other individuals, without prior correspondence with and approval from the owner of the sequence data.

Please support this effort

This website is intended to support the world of the community of practitioners and researchers working on health of Eucalyptus and Pinus plantations globally. The stronger this database is, the better it can help plan research programmes and make decisions regarding management and quarantine for sustainable and healthy plantation forests.

 

(c) 2016 All rights reserved. Forestry and Agricultural Biotechnology Institute.