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Digitization Through DNA Barcoding and Informatics

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Digitization Through DNA Barcoding and Informatics Connecting Biodiversity Collections in the Pacific: Digitization through DNA Barcoding and Informatics Thursday 11 July 2013 TIME Presenter TITLE, AUTHORS and ABSTRACT 11:00 – 11:20 Bevan Weir (via Web) Barcoding plant pathogens Bevan S. Weir Landcare Research, New Zealand, [email protected] Fungal and Bacterial plant pathogens present a major risk to trade and primary production in the relatively isolated ecosystems of the Pacific Island nations. A major obstacle to managing the risk of these pathogens is their rapid and accurate identification. Many pathogens are cryptic species that cannot easily be resolved by morphological identification. In addition new taxa are being described that can only be practically identified by DNA sequences. Colletotrichum fungi are considered to be one of the top ten important plant pathogens in the world, and have had a history of confusing taxonomy. Over the past five years a major taxonomic initiative was undertaken by several labs worldwide to clarify their taxonomy. DNA sequencing and voucher specimens were critical to this work, and now most of these fungi can be identified by non-specialists using DNA barcodes. DNA barcoding can even be useful by itself in taxa without recent taxonomic revisions. In New Zealand a study was made of all Phomopsis/Diaporthe fungal cultures in the national collection that were isolated from New Zealand. This DNA barcode database allows the rapid identification of fungal cultures isolated from imported plants, potentially identifying fungi that may be new to New Zealand. The quality and utility of online DNA Barcode databases will be discussed as well as the most useful barcoding genes. Biodiversity collections such as culture collections and herbaria that contain bacteria and fungi from the Pacific region are critical to biosecurity & sustainable development. Key Words: fungi, bacteria, barcoding, biosecurity, plant pathology. 11:20 – 11:40 Mark Blacket (via Web) DNA-based identifications reveal multiple introductions of the vegetable leafminer Liriomyza sativae (Diptera: Agromyzidae) into northern Australasia Mark J. Blacket1, Anthony D. Rice2, Linda Semeraro3, Mallik B. Malipatil4 1 Department of Environment and Primary Industries, Victoria Australia, [email protected] 2 Northern Australian Quarantine Strategy NAQS, Department of Agriculture Fisheries and Forestry DAFF, Queensland Australia, [email protected] 3 Department of Environment and Primary Industries, Victoria Australia, [email protected] 4 Department of Environment and Primary Industries / La Trobe University, Victoria Australia, [email protected] Leafmining flies (Agromyzidae) can be serious pests of vegetable crops. Some genera such as Liriomyza being particularly problematic with numerous species, some with a wide host range (i.e. polyphagous), that are difficult to morphologically identify from larvae, pupae and adult females. In the current study DNA sequence species identification (DNA barcoding) was employed to establish new locality and host records of the vegetable leafminer fly, Liriomyza sativae, from the Torres Strait (Queensland, Australia) and the central highlands of Papua New Guinea (PNG); documenting a significant range extension of this highly invasive plant pest. Immature leafminer specimens (from leaf mines) were collected during field surveys on FTA® filter paper cards, which proved a reliable means of preserving and transporting insect DNA under tropical conditions. Specimens were identified through sequencing two sections of the Cytochrome Oxidase I (COI) gene; the utility of each in the identification of species and intra-specific genetic lineages, was assessed. The current study indicates that multiple haplotypes of L. sativae occur in PNG, while a different haplotype is present in the Torres Strait. The DNA barcoding methods employed here appear generally applicable to the identification of other agromyzid leafminers (Phytomyzinae and Agromyzinae) and should decrease the likelihood of potentially co-amplifying internal hymenopteran parasitoids. Currently, L. sativae is still unknown from the Australian mainland; further sampling of leafminer flies from northern Australia and surrounding areas is required, both as surveillance for possible Liriomyza incursions, as well as to characterise endemic species with which Liriomyza species might be confused / misidentified. Key Words: Leafminer, Diptera, Agromyzidae, Liriomyza sativae; New records: Torres Strait Islands, Papua New Guinea (PNG); Quarantine / Biosecurity: invasive plant pest; DNA barcoding: COI gene; DNA preservation: FTA cards 11:40 – 12:00 John Hooper (via Web) Pumping Indo-west Pacific sponges through the taxonomic pipeline: The Sponge Barcoding and SpongeMaps Projects Hooper, J. N. A. 1,2, K. A. Hall 1, M. Ekins 1, S. Vargas 3, D. Erpenbeck 3, G. Wörheide 3,4& G. Jolley-Rogers 5 1Natural Environments Program, Queensland Museum, South Brisbane 4101, Australia 2Eskitis Institute for Cell and Molecular Therapies, Griffith University, Mt Gravatt Research Park, Nathan 4111, Australia 3Department of Earth and Environmental Sciences and GeoBio-CenterLMU, Ludwig-Maximilians Universität München, Richard-Wagner-Strasse 10, 80333 München, Germany 4Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Strasse 10, 80333 München, Germany 5CSIRO Plant Industry, Canberra 2601, Australia Phylum Porifera includes ~8,500 valid (named) species world-wide, distributed from ephemeral freshwater to deep-sea habitats, but, based on extensive surveys, this number represents potentially <30% of their actual diversity. Collections of these species from the Indo-west Pacific have escalated substantially over the past two decades due to pharmaceutical discovery and national bioregional planning (amongst others), such that for many bioregions they represent the most significant body of currently available knowledge. Yet most of these collections remain unidentified, or at best only partially processed (categorized only into operational taxonomic units, or OTUs).The collections now vastly outweigh the expertise available to resolve them taxonomically. Complicating this are the appalling problems associated with the traditional taxonomy of sponges (such as abundant phenotypic convergences, secondary character losses, etc), with independent datasets becoming increasingly important. Recent molecular and chemical analyses continue to discover growing numbers of cryptic species, previously undetected morphologically. In this way the Sponge Barcoding Project (www.spongebarcoding.org) – the first initiative to genetically barcode a non-bilaterian metazoan phylum – continues to build a comprehensive DNA database to facilitate the identification of unknown or partially identified specimens. DNA from approximately 20,000 museum specimens (predominantly from the western Pacific) is being extracted and amplified for the standard COI barcoding fragment besides other markers, so far with ~25% mean amplification success rate for the former. Not withstanding some sponge-specific problems (such as frequent co-amplification of non-target organisms), this methodology has already contributed considerably to the refinement of sponge systematics, evaluation of morphometric character importance, geographic phenotypic variability, and has demonstrated the utility of the standard barcoding fragment for Porifera (despite its conserved evolution within this basal metazoan phylum). To provide biological (morphometric) context to these molecular barcodes, particularly those from OTUs still unresolved within the Linnaean classification, we recently created SpongeMaps (www.spongemaps.org) as a means to ensure there is a biodiversity informatics legacy of knowledge and expertise gained from one project for future projects. SpongeMaps integrates diverse data (GIS specimen data; species and OTUs; images; molecular, chemical, and other datasets) through an online, password protected, two way iterative process. It provides an ability to interrogate existing data to better process new collections; a capacity to aggregate or differentiate populations across the Indo-west Pacific by creating new OTUs; automatic publication of online pages for individual species that contextualize GIS specimen data delivered by the online biodiversity databases (such as the Encyclopedia of Life and the Atlas of Living Australia); and to link external datasets for taxonomic hierarchy, specimen GIS and mapping, DNA sequence data, chemical structures, and images. This talk focuses mainly on the digitization and delivery of these sponge data using SpongeMaps. 12:00 – 12:20 Esperanza Maribel DNA Barcoding of Philippine Orchids Esperanza Maribel, G. Agoo & Glenn G. Oyong The Philippine orchid flora consists of about 1140 species and varieties in 152 genera of which at least 10 percent are endemic. Identification and documentation of this rich diversity pose a challenge to taxonomy and conservation. DNA barcoding can help address these challenges by using DNA sequence data for species-level identification, interspecific and intraspecific variation analysis and population genetic studies. The DNA barcodes determined by the Consortium of the Barcode of Life (CBOL) in achieving these goals are trnH-psbA, rbcL, matK, accD, rpoB,rpoc1, and trnL(UAA)-trnF(GAA). A barcoding project on Philippine plants is initiated to test the genes, trnH-psbA, rbcL, and matK, in identification and describing variation. DNA are extracted and processed using standard protocol set by the CBOL. The DNA are then kept in a cold storage facility in the DLSU-CENSER laboratory. Voucher specimens are also collected and are now deposited in the DLSU-Manila Herbarium. A living collection of the plants is also maintained. Results of this study show that rbcL and matK are the more useful barcodes based on robustness in PCR amplification and sequence alignment, gene length, ability to identify or define interspecific sequence differences in speciose genera, i.e. Eria, Bulbophyllum, Dendrobium, Dendrochilum, ability to distinguish intraspecific sequence differences, and nucleotide diversity or divergence. Keywords: DNA Barcoding, Philippine flora, taxonomy.
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