Diversity Evaluation of Xylella fastidiosa from Infected Olive Trees in Apulia (Southern Italy)

Abstract

Olive culture is very important in the Mediterranean Basin. A severe outbreak of Olive Quick Decline Syndrome (OQDS) caused by Xylella fastidiosa infection was first noticed in 2013 on olive trees in the southern part of Apulia region (Lecce province, southern Italy). Studies were carried out for detection and diversity evaluation of the Apulian strain of Xylella fastidiosa. The presence of the pathogen in olive samples was detected by PCR amplifying the 16S rDNA, gyrase B subunit (gyrB) and HL hypothetical protein genes and single nucleotide polymorphisms (SNPs) assessment was performed to genotype X. fastidiosa. Twelve SNPs were recorded over gyrB and six SNPs were found for HL gene. Less variations were detected on 16S rDNA gene. Only gyrB and HL provided sufficient information for dividing the Apulian X. fastidiosa olive strains into subspecies. Using HL nucleotide sequences was possible to separate X. fastidiosa into subspecies pauca and fastidiosa. Whereas, nucleotide variation present on gyrB gene allowed separation of X. fastidiosa subsp. pauca from the other subspecies multiplex and fastidiosa. The X. fastidiosa strain from Apulia region was included into the subspecies pauca based on three genes phylogenetic analyses.

Keywords: 16S rDNA gene; Olea europea; genetic variation; gyrase B; hypothetical protein.

Fig. 1

Neighbor-joining tree generated in MEGA6 from the 383 bp length alignment of 16S rDNA gene sequences of 31 Xylella fastidiosa specimens, using the Kimura-2 parameter model with uniform rates among sites, complete deletion gap handling and 1000-replication bootstrapping. Nodes with bootstrap values < 60% were eliminated. Bootstrap values are indicated next to relevant nodes. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree.

Fig. 2

Neighbor-joining tree generated in MEGA6 from the 382 bp length alignment of gyrase B subunit gene sequences of 30 Xylella fastidiosa specimens, using the Kimura-2 parameter model with uniform rates among sites, complete deletion gap handling and 1000-replication bootstrapping. Nodes with bootstrap values inferior to 70% were eliminated. Bootstrap values are indicated next to relevant nodes. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree.

Fig. 3

Neighbor-joining tree generated in MEGA6 from the 216 bp length alignment of hypothetical protein HL gene sequences of 14 Xylella fastidiosa specimens, using the Kimura 2-parameter model with uniform rates among sites, complete deletion gap handling and 1000-replication bootstrapping. Nodes with bootstrap values inferior to 30% were eliminated. Bootstrap values are indicated next to relevant nodes. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree.