CONNECTIVITY OF CORAL POPULATIONS WITHIN THE SINGAPORE STRAIT

Ph.DDOCTOR OF PHILOSOPH

Effects of macroalgal morphology on marine epifaunal diversity

10.1017/S0025315419000900Journal of the Marine Biological Association of the United Kingdom9981697-170

Effects of macroalgal morphology on marine epifaunal diversity

Sequence data, community datasets and R script

'Direct PCR' optimization yields a rapid, cost-effective, nondestructive and efficient method for obtaining DNA barcodes without DNA extraction

Macroinvertebrates that are collected in large numbers pose major problems in basic and applied biodiversity research: identification to species via morphology is often difficult, slow and/or expensive. DNA barcodes are an attractive alternative or complementary source of information. Unfortunately, obtaining DNA barcodes from specimens requires many steps and thus time and money. Here, we promote a short cut to DNA barcoding, that is, a nondestructive PCR method that skips DNA extraction ('direct PCR') and that can be used for a broad range of invertebrate taxa. We demonstrate how direct PCR can be optimized for the larvae and adults of nonbiting midges (Diptera: Chironomidae), a typical invertebrate group that is abundant, contains important bioindicator species, but is difficult to identify based on morphological features. After optimization, direct PCR yields high PCR success rates (>90%), preserves delicate morphological features (e.g. details of genitalia, and larval head capsules) while allowing for the recovery of genomic DNA. We also document that direct PCR can be successfully optimized for a wide range of other invertebrate taxa that need routine barcoding (flies: Culicidae, Drosophilidae, Dolichopodidae, Sepsidae; sea stars: Oreasteridae). Key for obtaining high PCR success rates is optimizing (i) tissue quantity, (ii) body part, (iii) primer pair and (iv) type of Taq polymerase. Unfortunately, not all invertebrates appear suitable because direct PCR has low success rates for other taxa that were tested (e.g. Coleoptera: Dytiscidae, Copepoda, Hymenoptera: Formicidae and Odonata). It appears that the technique is less successful for heavily sclerotized insects and/or those with many exocrine glands

Data from: “Direct PCR” optimization yields a rapid, cost-effective, non-destructive, and efficient method for obtaining DNA barcodes without DNA extraction

Macroinvertebrates that are collected in large numbers pose major problems in basic and applied biodiversity research: identification to species via morphology is often difficult, slow, and/or expensive. DNA barcodes are an attractive alternative or complementary source of information. Unfortunately obtaining DNA barcodes from specimens requires many steps and thus time and money. Here, we promote a short-cut to DNA barcoding; i.e., a non-destructive PCR method that skips DNA extraction (“direct PCR”) and that can be used for a broad range of invertebrate taxa. We demonstrate how direct PCR can be optimized for the larvae and adults of non-biting midges (Diptera: Chironomidae), a typical invertebrate group that is abundant, contains important bioindicator species, but is difficult to identify based on morphological features. After optimization, direct PCR yields high PCR success rates (>90%), preserves delicate morphological features (e.g., details of genitalia, and larval head capsules) while allowing for the recovery of genomic DNA. We also document that direct PCR can be successfully optimized for a wide range of other invertebrate taxa that need routine barcoding (flies: Culicidae, Drosophilidae, Dolichopodidae, Sepsidae; sea stars: Oreasteridae). Key for obtaining high PCR success rates is optimizing (1) tissue quantity, (2) body part, (3) primer pair, and (4) type of Taq polymerase. Unfortunately, not all invertebrates appear suitable because direct PCR has low success rates for other taxa that were tested (e.g., Coleoptera: Dytiscidae, Copepoda, Hymenoptera: Formicidae and Odonata). It appears that the technique is less successful for heavily sclerotized insects and/or those with many exocrine glands

Next-Generation Sequencing Identification Tools for Nee Soon freshwater swamp forest, Singapore

10.26492/gbs70(suppl.1).2018-08The Gardens's Bulletin Singapore70Supplement 1155-174ISSN 0374-785

Environmental DNA detection of the invasive mussel Mytella strigata as a surveillance tool

10.3391/mbi.2021.12.3.05Management of Biological Invasions123578-59

Aligned Sequences Direct PCR

Aligned Sequences Direct PC

Direct PCR Datasheet

Direct PCR Datashee