Journal ArticleDOI
Comparison of two short DNA barcoding loci (COI and COII) and two longer ribosomal DNA genes (SSU & LSU rRNA) for specimen identification among quarantine root-knot nematodes ( Meloidogyne spp.) and their close relatives
Sebastian Kiewnick,Martijn Holterman,Sven van den Elsen,Hanny van Megen,Juerg Ernst Frey,Johannes Helder +5 more
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TLDR
None of the four markers distinguished between the tropical species Meloidogyne incognita, M. javanica and M. arenaria, although the high level of mitochondrial heteroplasmy recently reported for M. chitwoodi was not found in the populations under investigation, suggesting this could be a regional phenomenon.Abstract:
Root-knot nematodes (Meloidogyne spp.) are important pests of numerous crops worldwide. Some members of this genus have a quarantine status, and accurate species identification is required to prevent further spreading. DNA barcoding is a method for organism identification in non-complex DNA backgrounds based on informative motifs in short DNA stretches (≈600 bp). As part of the EU 7th Framework project QBOL, 15 Meloidogyne species were chosen to compare the resolutions offered by two typical DNA barcoding loci, COI and COII, with the distinguishing signals produced by two ribosomal DNA genes (small and large subunit rDNA; SSU ≈ 1,700 and LSU ≈ 3,400 bp). None of the four markers distinguished between the tropical species Meloidogyne incognita, M. javanica and M. arenaria. Taking P ID (Liberal) values ≥0.93 as a measure for species delimitation, the four mtDNA and rDNA markers performed well for the tropical Meloidogyne species complex, M. enterolobii, M. hapla, and M. maritima. Within cluster III A (Holterman et al. Phytopathology, 99, 227–235, 2009), SSU rDNA did not offer resolution at species level. Both mtDNA loci COI and COII did, whereas for LSU rDNA a longer fragment (≥700 bp) is required. The high level of mitochondrial heteroplasmy recently reported for M. chitwoodi (Humphreys-Pereira and Elling Nematology, 15, 315–327, 2013) was not found in the populations under investigation, suggesting this could be a regional phenomenon. For identification of RKNs, we suggest the combined use of SSU rDNA with one of three other markers presented here.read more
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Fungal DNA barcoding.
TL;DR: Three broad areas of research are suggested to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community.
Journal ArticleDOI
Mitochondrial coding genome analysis of tropical root-knot nematodes (Meloidogyne) supports haplotype based diagnostics and reveals evidence of recent reticulate evolution
TL;DR: It is indicated that the barcode region Nad5 can reliably identify the major lineages of tropical root-knot nematodes and mitochondrial haplotypes are strongly linked and consistent with traditional esterase isozyme patterns, suggesting that different parthenogenetic lineages can be reliably identified using mitochondrial haplotype patterns.
Journal ArticleDOI
Evolution of plant parasitism in the phylum Nematoda.
TL;DR: Ribosomal DNA frameworks with sequence data from more than 2,700 nematode taxa combined with detailed morphological information allow for explicit hypotheses on the origin of agronomically important plant parasites, such as root-knot, cyst, and lesion nematodes.
Journal ArticleDOI
Distribution of root-knot nematode species and their virulence on vegetables in northern temperate agro-ecosystems of the Pakistani-administered territories of Azad Jammu and Kashmir
TL;DR: This is the first comprehensive study on the presence of tropical RKN species in the temperate region of Azad Jammu and Kashmir, Pakistan, and their virulence on vegetable crops.
References
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Bioedit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/ nt
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Biological identifications through DNA barcodes
TL;DR: It is established that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals and will provide a reliable, cost–effective and accessible solution to the current problem of species identification.
Journal ArticleDOI
BOLD: The Barcode of Life Data System: Barcoding
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