Phylogeny of Meloidogyne spp. based on 18S rDNA and the intergenic region of mitochondrial DNA sequences

Abstract

Summary -The 18S rDNA of 19 populations of Meloidogyne spp. was amplified and directly sequenced. The region of mitochondrial DNA, located in the 3 portion of the gene that codes for cytochrome oxidase subunit II (COII) through a portion of the 16S rRNA (lRNA) gene, from 16 of these populations was cloned and sequenced. Heteroplasmic sequences were identified from both rDNA and mtDNA regions for several taxa. Several sequences sampled from nominal taxa differed from previously published accounts. Phylogenetic trees based on alignments of these sequences were constructed using distance, parsimony and likelihood optimality criteria. For 18S rDNA data, three main clades were identified. One well supported clade (86-91% bootstrap) included the most common and widely disseminated species, e.g., M. arenaria, M. javanica and M. incognita, some recently described or redescribed species (M. floridensis, M. paranaensis, and M. ethiopica) plus numerous unidentified isolates. All mitotic parthenogenetic species, except for M. oryzae, were included in this clade. Other, less well supported clades included the amphimictic and facultative meiotic species M. hapla, M. microtyla, M. maritima and M. duytsi. One such clade comprised three meiotic parthenogens (M. exigua, M. graminicola and M. chitwoodi) and M. oryzae. This clade was moderately supported (77% bootstrap) but the relationships within this clade were poor. For mitochondrial DNA data, only the species in clade I from rDNA analysis, and M. hapla were analysed. These species formed a well supported clade (100% bootstrap) to the exclusion of M. mayaguensis and M. hapla. The addition of taxa and mtDNA data to publicly available records improved the discrimination sensitivity of species and atypical, non-identified, isolates.

A new root‐knot nematode, Meloidogyne silvestris n. sp. (Nematoda: Meloidogynidae), parasitizing European holly in northern Spain

“…The trees obtained from MP analysis of different rDNA sequences agreed with those obtained in Neighbour Joining and MP analysis by Castillo et al (2003), Landa et al (2008), Palomares Rius et al (2007, and Tigano et al (2005). The addition of the sequences of this new species or additional sequences from the GenBank database to the maximum parsimony analyses caused small subtle changes in topology of the dendrograms shown in Fig.…”

“…The addition of the sequences of this new species or additional sequences from the GenBank database to the maximum parsimony analyses caused small subtle changes in topology of the dendrograms shown in Fig. 6 compared to that reported previously (Castillo et al, 2003;Tigano et al, 2005). MP analysis showed that the 18S, ITS1-5·8S-ITS2 and D2-D3 sequences of M. silvestris n. sp.…”

“…The different regions of rDNA were amplified as described by Castillo et al . (2003) and Tigano et al . (2005) using the following primer sets: MelF (5 ′ -TACGGACTGAGATAATGGT-3 ′ ) and MelR (5 ′ -GGTTCAAGCCACTGCGA-3 ′ ) for the 18S, 5367 (5 ′ -TTGATTACGTCCCTGCCCTTT-3 ′ ) and F195 (5 ′ -TCCTCCGCTAAATGATATG-3 ′ ) for the ITS1-5·8S-ITS2, and D2A (5 ′ -ACAAGTACCGTGAGGGAAAGTTG-3 ′ ) and D3B (5 ′ -TCGGAAGGAACCAGCTACTA-3 ′ ) for the D2-D3 region of 28S.…”

Detecção de Meloidogyne mayaguensis em goiabeira e mamoeiro no estado de Goiás, usando marcadores moleculares

“…Enquanto, para a amplificação da região do mtDNA foram utilizados os primers C2F3 (5´-GGTCAATGTTCAGAAATTTGTGG-3`) e 1108 (5`-TACCTTTGACCAATCACGCT-3`) (Powers & Harris, 1993 Esses marcadores permitiram a diferenciação de M. mayaguensis com relação a outras espécies comuns de Meloidogyne devido ao tamanho do produto de amplificação. Os resultados obtidos confirmaram a detecção de M. mayaguensis nas duas propriedades, pois os fragmentos de PCR obtidos foram os mesmos previamente descritos para essa espécie, isto é 780 pb para IGS (Block et al, 1997;Adam et al, 2007) e 705 pb para a região do DNA mitocondrial (Block et al, 2002;Brito et al, 2004;Tigano et al, 2005;Jeyaprakash et al, 2006) …”

Genetic diversity of the root‐knot nematode Meloidogyne ethiopica and development of a species‐specific SCAR marker for its diagnosis

“…This cluster was successfully separated on the basis of AFLP and RAPD data, suggesting that these three isolates may belong to the same, as yet undescribed, species. The same unidentified RKN have been compared to several of the most common species of Meloidogyne in a phylogenetic study based on mitochondrial DNA sequences, and were shown to be closely related (c. 85% bootstrap value) to isolates that have since been confirmed as M. inornata (Carneiro et al, 2008b) and M. ethiopica (Tigano et al, 2005). However, the SCAR marker developed here for M. ethiopica did not result in any PCR amplification for this Meloidogyne sp.…”