Molecular analyses of the genus Ilex (Aquifoliaceae) in southern South America, evidence from AFLP and ITS sequence data

Abstract

In order to clarify the relationships among southern South American (sSA) representatives of the genus Ilex, an amplified fragment length polymorphism (AFLP) analysis was accomplished. In addition, the phylogenetic relationships of the species were studied using ribosomal internal transcribed spacer (ITS) sequence data alone and in combination with AFLP data, taking into account the possible existence of paralogous sequences and the influence of alignment parameters. To explore stability of phylogenetic hypotheses, a sensitivity analysis was performed using 15 indel-substitution models. Within each species assayed, the AFLPs allowed the recognition of several diagnostic bands. Furthermore, the AFLP analysis revealed that individuals belonging to the same morpho-species formed coherent clades. In addition, some cases of geographical association were noted. Studies on ITS sequences revealed divergence between data obtained herein and sequence data downloaded from GenBank. The sensitivity analyses yielded different interspecific hypotheses of relationships. Notwithstanding, analyses of the ITS data alone and in combination with AFLPs, rendered clades stable to variation in the analytical parameters. Topologies obtained for the AFLPs, the ITS data alone and the combined analyses, demonstrated the existence of a group formed by I. argentina, I. brasiliensis, I. brevicuspis, I. integerrima, and I. theezans, and that I. dumosa and I. paraguariensis were distantly related to the former. Incongruence with traditional taxonomical treatments was found.

Phytochemistry and biology of Ilex pharmaceutical resources

“…The above findings agree with the molecular analysis of amplified fragment length polymorphism (AFLP; Gottleib et al, 2005). Based on the above study, 1-D-and 2-D-NMR-based metabolomics were used to classify 11 South American Ilex species .…”

Genomic screening in dioecious “yerba mate” tree (Ilex paraguariensis A. St. Hill., Aquifoliaceae) through representational difference analysis

“…As DNA templates we used 15 additional samples that were previously obtained (Gottlieb et al 2005) and correspond to EEINTA CA accessions No 1 #; 1 $; 34 $; 34 #; 37 #; 1-74 $ (Guaraní, Misiones, Argentina); 100 $ (Paraná, Brazil); 138 $ (Rio Grande do Sul, Brazil); 28 $; 28 #; 27$(Santa Catarina, Brazil); and SI-16 #; SI-19 $; SI-49 #; Y383 $ from the Establecimiento Las Marías (Misiones, Argentina). PCRs were done using 1 ll of DNA, 2.5 ll buffer 10X (Invitrogen), 0.2 mM of each dNTP (Invitrogen), 1.5 mM MgCl 2 (Invitrogen), 60 ng of each right and left primer, 0.5 U of Taq polymerase (Invitrogen) in a final volume of 25 ll.…”

“…is an economically important crop widely employed in several South American countries, like Argentina, Brazil, Paraguay and Uruguay, to prepare a stimulating beverage called ''mate''. The species shows a basal phylogenetic position, relative to other Ilex species, that contradicts its current classification (Gottlieb et al 2005). The ''yerba mate'' tree is functionally dioecious, exhibiting diclinous flowers in which one of the sexes is sterile or abortive (Giberti 2001).…”

Molecular characterization of Colletotrichum species causing soybean anthracnose in Argentina

“…Polyacrylamide gel electrophoresis conditions were conducted as in Gottlieb et al (2005). A 30-330-bp AFLP ® DNA Ladder (Invitrogen) size marker was included twice in each electrophoresis run.…”

“…The AFLP methodology was carried out on 250 ng of genomic DNA using the AFLP® Analysis System for Microorganisms Primer Kit (Invitrogen) as described in the instructions manual with minor modifications (Gottlieb et al 2005). Selective primers used herein, containing one, two or three additional bases, were combined as in Table 2.…”