DOI: 10.5061/dryad.4q4kf
title: Data from: “Direct PCR” optimization yields a rapid, cost-effective, non-destructive, and efficient method for obtaining DNA barcodes without DNA extraction

description: 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 (&gt;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. 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
 (&gt;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.
description: Direct PCR
 DatasheetAligned Sequences Direct
 PCR