Utility of ITS sequence data for phylogenetic reconstruction of Italian Quercus spp.

Abstract

Nuclear ribosomal DNA sequences encoding the 5.8S RNA and the Xanking internal transcribed spacers (ITS1 and ITS2) were used to test the phylogenetic relationships within 12 Italian Quercus taxa (Fagaceae). Hypotheses of sequence orthology are tested by detailed inspection of some basic features of oak ITS sequences (i.e., general patterns of conserved domains, thermodynamic stability and predicted conformation of the secondary structure of transcripts) that also allowed more accurate sequence alignment. Analysis of ITS variation supported three monophyletic groups, corresponding to subg. Cerris, Schlerophyllodrys ( D Ilex group sensu Nixon) and Quercus, as proposed by Schwarz [Feddes Rep., Sonderbeih. D,. A derivation of the "Cerris group" from the "Ilex group" is suggested, with Q. cerris sister to the rest of the "Cerris group." Quercus pubescens was found to be sister to the rest of the "Quercus group." The status of hybrispecies of Q. crenata (Q. cerris £ Q. suber) and Q. morisii (Q. ilex £ Q. suber) was evaluated and discussed. Finally, the phylogenetic position of the Italian species in a broader context of the genus is presented. The utility of the ITS marker to assess the molecular systematics of oaks is therefore conWrmed. The importance of Italy as a region with a high degree of diversity at the population and genetic level is discussed. 

Genomics of Fagaceae

“…The wind-pollinated genus Quercus has been wellstudied using molecular phylogenetics and two major clades have been identified (Manos et al 1999;Bellarosa et al 2005;Oh and Manos 2008;Denk and Grimm 2010). The larger of the two clades has been referred to as the New World oaks with sections Lobatae (red and black oaks), Protobalanus (golden cup oaks), and Quercus s.s. (white oaks).…”

Morphological and molecular data from Madeira support the persistence of an ancient lineage ofTaxus baccataL. in Macaronesia and call for immediate conservation actions

“…sequences available in GenBank. Universal ITS primers and PCR conditions followed Bellarosa et al (2005). PCR products were cleaned with Illustra DNA and Gel Band Purification Kit (GE Healthcare), and eluted in 30 μl type 6 elution buffer.…”

Detection of hybrids in nature: application to oaks (Quercus suber and Q. ilex)

“…Putative hybrids with parental morphology (Toumi and Lumaret, 1998;Belahbib et al, 2001;Staudt et al, 2004), intermediate morphology (Toumi and Lumaret, 1998;Lumaret et al, 2002;Bellarosa et al, 2005) or leaf morphology skewed toward Q. ilex (Staudt et al, 2004) have been reported. Bark cannot be used as a discriminating feature because F1s are considered to lack cork and, thus, they could be confused with pure Q. ilex (Lumaret et al, 2002;Bellarosa et al, 2005). The existence of morphologically cryptic hybrids seems to be the only certainty.…”

“…Within the section Cerris (subgenus Quercus), Q. suber and Q. ilex belong to different clades (groups Cerris and Ilex, respectively), which are thought to have diverged during the middle Tertiary (Manos et al, 2001). Despite their deep phylogenetic divergence, clearly supported by internal transcribed spacer, amplified fragment length polymorphisms and isozyme variation (Manos et al, 1999;Toumi and Lumaret, 2001;Bellarosa et al, 2005;Ló pez de Heredia et al, 2007b), hybridization has been inferred on the basis of morphological and molecular markers (Elena-Rosselló et al, 1992;Toumi and Lumaret, 1998;Lumaret et al, 2002;Oliveira et al, 2003;Bellarosa et al, 2005). Furthermore, extensive surveys of chloroplast DNA diversity of both species and of other relatives (such as Q. coccifera) across the whole distribution range have demonstrated widespread cytoplasmic introgression, mainly localized along a northeast-southwest line, from French Catalonia and eastern Iberia to Morocco (reviewed in Lumaret et al, 2005).…”