Identification of Phytophthora species infecting citrus in Vietnam

In a survey aimed at identifying Phytophthora species infecting fruit crops in Viet Nam, P. citrophthora and P. nicotianae were the species most commonly recovered from soil and trees in citrus plantations. P. nicotianae was prevalent in citrus groves in the Ben Tre and Tien Giang provinces (southern Viet Nam). Interestingly, both A1 and A2 mating types of the latter species were found, while in other citrus-growing areas of the world, such as the Mediterranean region, South Africa, Australia and the Americas, A1 is the only mating type occurring in citrus groves, suggesting southern-east Asia could be a centre of origin of this Phytophthora species. Mixed infections of three Phytophthora s…

MOLECULAR ANALYSIS OF COLLETOTRICHUM SPECIES ASSOCIATED TO OLIVE IN CALABRIA.

A new molecular approach based on the use of genus-specific primers targeting the internal transcribed spacer (ITS) regions of rDNA, was developed and used to study the diversity of Colletotrichum species associated with the olive canopy in the Gioia Tauro plain (Calabria, southern Italy). Representative symptomatic and symptomless samples of leaves, flowers and fruits were collected during 2012 and analyzed by extracting total DNA and amplifying the target region with the genus-specific primers. Amplicons were cloned and sequenced in order to use the ITS as a barcode gene. No Colletotrichum species were detected in the first sampling period (May 28, 2012), whereas around 15% of the analyze…

MOLECULAR ANALYSIS OF PHYTOPHTHORA DIVERSITY IN ORNAMENTAL NURSERIES.

A molecular approach based on the use of genus-specific nested-PCR primers (Scibetta et al., 2012; J. Microbiol. Meth. 88: 356-368) was utilized to detect Phytophthora species in soil and root samples of potted ornamentals, collected across Apulia and Calabria, Southern Italy. Analyzed samples comprised many plant species with different levels of symptoms of decline on the canopy and root rots. Extraction protocols were optimized to obtain DNA samples of appropriate quality from soil and roots. The analysis of sequences after cloning of nested-PCR amplicons enabled the identification of different Phytophthora species including P. nicotianae, P. cinnamomi, P. cryptogea, P. palmivora and P. n…

Whither the species? Phytophthora taxa, MOTUs and barcodes in the world of metagenomics

The study of ecosystem diversity is being transformed by high throughput sequencing technology that allows an unparalleled depth of sampling of DNA barcode sequences. The opportunities are great at this fascinating interface of pathology, ecology, taxonomy and molecular biology but there are pitfalls. It is important to consider the potential for bias at all steps in the process from sampling through to data analysis. Increasingly Phytophthora diversity is being examined by metabarcoding of the PCR amplified rDNA ITS regions from soil, water or plant sample DNA. We have applied baiting and isolation, cloning and Sanger sequencing and Illumina MiSeq analysis to a time-series of filtered wate…

Metagenomic strategies to assess genetic diversity in Phytophthora species

Molecular analysis ofPhytophthoradiversity in nursery-grown ornamental and fruit plants

The genetic diversity of Phytophthora spp. was investigated in potted ornamental and fruit tree species. A metabarcoding approach was used, based on a semi-nested PCR with Phytophthora genus-specific primers targeting the ITS1 region of the rDNA. More than 50 ITS1 sequence types representing at least 15 distinct Phytophthora taxa were detected. Nine had ITS sequences that grouped them in defined taxonomic groups (P. nicotianae, P. citrophthora, P. meadii, P. taxon Pgchlamydo, P. cinnamomi, P. parvispora, P. cambivora, P. niederhauserii and P. lateralis) whereas three phylotypes were associated to two or more taxa (P. citricola taxon E or III; P. pseudosyringae, P. ilicis or P. nemorosa; and…