Evaluation of six candidate DNA barcode loci for identification of five important invasive grasses in eastern Australia.

Aisuo Wang,Hanwen Wu,Brendan Lepschi,David Gopurenko,Shilin Chen

doi:10.1371/journal.pone.0175338

Abstract

Invasive grass weeds reduce farm productivity, threaten biodiversity, and increase weed control costs. Identification of invasive grasses from native grasses has generally relied on the morphological examination of grass floral material. DNA barcoding may provide an alternative means to identify co-occurring native and invasive grasses, particularly during early growth stages when floral characters are unavailable for analysis. However, there are no universal loci available for grass barcoding. We herein evaluated the utility of six candidate loci (atpF intron, matK, ndhK-ndhC, psbE—petL, ETS and ITS) for barcode identification of several economically important invasive grass species frequently found among native grasses in eastern Australia. We evaluated these loci in 66 specimens representing five invasive grass species (Chloris gayana, Eragrostis curvula, Hyparrhenia hirta, Nassella neesiana, Nassella trichotoma) and seven native grass species. Our results indicated that, while no single locus can be universally used as a DNA barcode for distinguishing the grass species examined in this study, two plastid loci (atpF and matK) showed good distinguishing power to separate most of the taxa examined, and could be used as a dual locus to distinguish several of the invasive from the native species. Low PCR success rates were evidenced among two nuclear loci (ETS and ITS), and few species were amplified at these loci, however ETS was able to genetically distinguish the two important invasive Nassella species. Multiple loci analyses also suggested that ETS played a crucial role in allowing identification of the two Nassella species in the multiple loci combinations.

Highlights

We tested six loci for their utility as DNA barcode targets to distinguish five invasive grass species from seven native grasses which frequently co-occur in eastern Australia
Our results (DNA barcode gap analysis, NJ and Maximum Likelihood (ML) phylogenetic analyses) indicated that maturase K (matK) was suitable for distinguishing invasive H. hirta and E. curvula from native grasses (M. stipoides, A. scabra, T. triandra, P. sieberiana), but provided no or weak support for distinguishing N. neesiana from N. trichotoma, which are two important invasive grasses
In contrast highest Polymerase Chain Reaction (PCR) success was achieved at atpF, and most of the examined taxa were distinguished by this locus, indicating its potentials as a promising DNA barcode locus for the grasses of concern

Summary

Introduction

The application of DNA barcoding technology in weeds science environment and agricultural industry [1] Both N. trichotoma and N. neesiana are native to South American countries (Argentina, Uruguay, Peru etc.), and have become naturalised weeds in Australia ( in eastern states such as New South Wales, Australian Capital Territory, Victoria and Tasmania)[2, 3]. Et al (2014) [1] screened 18 loci for the possibility of using DNA barcoding technology to identify invasive weeds and native grasses (up to 29 grass species) collected from eastern Australia. We evaluated the chloroplast and nuclear loci (ITS, matK, ndhk and psbE), which were recommended by previous studies, on five major invasive grasses (N. trichotoma, N. neesiana, E. curvula, H. hirtai, C. gayana) and several co-occurring native grasses. We hope the availability of robust DNA barcoding loci will help weeds abatement officers to identify the five invasive weeds at early growth stages, which is important to Australian biosecurity (including border entry points for quarantine purposes) and weed control agencies as early detection in bio-surveillance for weed control will ensure an early intervention by control agencies

Materials and methods

Results

Discussion