e-journal

Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity

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The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in
plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode.
Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S
sequences of Plantae and Fungi from GenBank, we designed new universal and plant-specific PCR primers for
amplifying the whole ITS region and a part of it (ITS1 or ITS2) of plants. In silico analyses of the new and the existing ITS primers based on these highly representative data sets indicated that (i) the newly designed universal primers are suitable for over 95% of plants in most groups; and (ii) the plant-specific primers are suitable for over 85% of plants in most groups without amplification of fungi. A total of 335 samples from 219 angiosperm families, 11 gymnosperm families, 24 fern and lycophyte families, 16 moss families and 17 fungus families were used to test the performances of these primers. In vitro PCR produced similar results to those from the in silico analyses. Our new primer pairs gave PCR improvements up to 30% compared with common-used ones. The new universal ITS primers will find wide application in both plant and fungal biology, and the new plant-specific ITS primers will, by eliminating PCR amplification of nonplant templates, significantly improve the quality of ITS sequence information collections in plant molecular systematics and DNA barcoding.

Keywords: barcoding, internal transcribed spacer, PCR, plant-specific, primer

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Ketersediaan

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Informasi Detail

Judul Seri

Molecular Ecology Resources

No. Panggil

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Penerbit

: John Wiley & Sons., 2016

Deskripsi Fisik

Molecular Ecology Resources (2016) 16, 138–149

Bahasa

English

ISBN/ISSN

doi: 10.1111/1755-09

Klasifikasi

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Tipe Isi

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Tipe Media

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Tipe Pembawa

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Edisi

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Subjek

BIOLOGI

Info Detail Spesifik

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Pernyataan Tanggungjawab

Wati/Agus

Versi lain/terkait

Lampiran Berkas

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