c8.7.6 – Comparative analysis of the chloroplast genomes of Fagaceae species

Pinzauti F* (1), Sebastiani F (1), Ranalli N (2), Bruschi P (2), Petit RJ (3), Vendramin GG (1)

(1) Plant Genetics Institute, Division of Florence, National Research Council, via Madonna del Piano 10, I50019 Sesto Fiorentino (FI), Italy; (2) Department of Agricultural Biotechnology, Piazzale delle Cascine 18, 50134 Firenze, Italy; (3) INRA – UMR BIOGECO, 69 route d’Arcachon, 33612 Cestas Cedex, France
Collocazione: c8.7.6 – Tipo Comunicazione: Presentazione orale
8° Congresso SISEF *
Sessione 7: “Biodiversità e Risorse genetiche forestali” *

Contatto: Giovanni Giuseppe Vendramin (giovanni.vendramin@igv.cnr.it)

Abstract: Knowledge about the chloroplast(cp)DNA sequence variations represents a great opportunity to provide new insights into phylogenetic relationships among plants. The size and complexity of the cp genome is well suited to short sequencing by synthesis reads. At this regard, during the past decade the availability of complete organellar genome sequences increased significantly, largely fuelled by advances in HT sequencing technology and the significant reduction in time and cost, resulting in more than 100 publicly available angiosperm chloroplast complete genomes at NCBI database (http://www.ncbi.nlm.nih.gov/genomes/), among which only that of Castanea mollissima belongs to a species of the Fagaceae family. Here we report the complete nucleotide sequence of three Fagaceae species, Quercus robur, Castanea sativa and Fagus sylvatica and the sequencing results of 32 chloroplast genomes, including different populations of Q. robur and some related species (Q. trojana, Q. calliprinos, Q. suber, Q. ilex, Q. pubescens, Q. petraea, Q. dalechampii, Q. lusitanica, Q. crenata, Q. virginiana, Q. macrolepis). Using traditional Sanger approach, the full chloroplast genomes of Quercus robur, Fagus sylvatica and Castanea sativa (reference genomes) were generated. Multiple long PCR reactions were used to isolate chloroplast DNAs. Conserved primer pairs (Grivet et al., 2001; Sebastiani, unpublished) were used to amplify most part of the cpDNA genome (about 140 kbp out of ca. 160 kbp). PCR fragments were pooled, nebulized in smaller fragments (ca. 900 bp), polished and used to construct the libraries. Using HT sequencing approaches (Illumina) and the reference genomes, the chloroplast genomes of European Quercus species and oak haplotypes (Q. robur and Q. petraea) were produced and assembled. Genomes annotation was performed using the package Geneious Pro 4.8.2 and Castanea mollissima cpDNA as reference. As expected, the gene order and content of the newly sequenced chloroplast genomes are highly conserved. However, some unique differences exist: for example, presence, absence and different length of repeated sequences and structural differences were detected at four genes: infA, accD, rps18, rpl22 and petA. The comparative analysis of the complete chloroplast sequences were used to identify useful polymorphism to be used in population genetic studies. By comparing Fagaceae cp genome sequences about 1200 diversities, including SPNs, in/del andSSRs were detected. The usefulness of the detected polymorphisms for evolutionary studies and for possible application for DNA barcoding is discussed.

Parole chiave: Chloroplast Genome, Fagaceae, Cp Evolution, Dna Barcoding

Citazione: Pinzauti F , Sebastiani F , Ranalli N , Bruschi P , Petit RJ , Vendramin GG (2011). Comparative analysis of the chloroplast genomes of Fagaceae species . 8° Congresso Nazionale SISEF, Rende (CS), 04 – 07 Ott 2011, Contributo no. #c8.7.6