Coffea is a large genus that belongs to the Rubiaceae family, the fourth largest family of angiosperms, in term of species number. To date, this genus encompasses 103 perennial species, all native to Africa, Madagascar, the Mascarene Islands and the Comoros Islands [
1]. It includes two economically important species:
C. arabica L. and
C. canephora Pierre, which represent a major agricultural commodity in world trade and one of the main sources of foreign exchange for Southern countries. The Rubiaceae is related to the Solanaceae family that contains numerous economically important crop species such as the tomato, the potato, the pepper, the eggplant, the tobacco and the petunia, all of these being annual. Both families belong to the Asterid I clade of dicotyledonous plants, and diverged from their common ancestor approximately 83-89 million years ago (MYA) (Figure ) [
2]. Besides phylogenetic considerations, Rubiaceae and Solanaceae are frequently considered as "sister" plant families based on genetic similarities observed between
C. canephora (hereafter referred to as "coffee tree") and the tomato,
Solanum lycopersicum, such as the genome size, 704 Mpb for the coffee tree [
3] and 950 Mbp for the tomato [
4], the basic chromosome number (11 and 12 for the coffee tree and the tomato, respectively), the cytogenetic chromosome architecture [
5,
6], the absence of polyploidization [
7] and expressed gene repertoires in the seed and the cherry [
8].
Based on available Expressed Sequences Tags (EST) databases [
9], a large set of conserved single-copy genes, designated as putative orthologous genes or COSII, were selected
in silico between Asterid plant species (eight species including
C. canephora and
S. lycopersicum) and the Rosid model plant
Arabidopsis thaliana [
7]
. These COSII were used as valuable markers to construct genetic maps [
10-
12] to perform comparative mapping and to study chromosomal evolution in the Solanaceae [
13]. Recently, using 257 COSII markers, a genetic map for the coffee tree was constructed and compared to that of the tomato [
14]. Comparative mapping revealed that despite extensive rearrangements, a high level of conservation was detected between the coffee tree and the tomato, reinforcing the assessment of Rubiaceae and Solanaceae as "sister" plant families [
14].
The Vitaceae family is another economically important family of angiosperms since it includes the
Vitis vinifera species, known as the grapevine, a perennial plant, cultivated to be used as fruit or for beverage production. Recent phylogenetic analyses have placed the Vitaceae family as the earliest diverging lineage of the Rosid clade, which allows us to consider this family as the "sister" group of all other
Rosid plant species [
15]. Despite a fairly small genome size of about 475 Mbp [
16] the presence of a high chromosome number (x = 19) suggested an ancestral polyploidy event of the grapevine genome [
17]. Analysis of the draft sequence of the grapevine genome indicated both a complete absence of recent whole genome duplications and the contribution of ancient duplication events to the genome organization of the grapevine as well as to all of the Rosid species [
18].
The grapevine and the coffee tree diverged from their last common ancestor approximately 114-125 MYA (Figure ) [
2], a long period of divergent evolution that should permit numerous chromosomal rearrangements to accumulate, allowing the genomes to reorganize significantly. So far, very few comparative mappings have been performed between very distantly related species belonging to two different clades, dicotyledonous or monocotyledonous [
19-
21]. Using genetic maps based on Expressed-Sequence Tags (EST) markers, four dicotyledonous crop species were compared to Arabidopsis, revealing common genome segments in a complex fragmented arrangement probably due to successive whole genome duplication in Arabidopsis [
22]. In a pilot case study, Salse and coworkers [
21] evaluated the synteny relationships between monocotyledonous and dicotyledonous species, which had diverged 146-161 MYA, using rice (
Oryza sativa) and Arabidopsis genomes as models. In accordance with the relatively long period of evolution reinforced by successive whole genome duplications in both lineages, a very low level of synteny was observed between these two species.
Pairwise comparative mapping studies have been performed within the Solanaceae [
12] and between the tomato and the coffee tree [
8,
14,
23], all species belonging to the Asterid I clade. However, no multiple comparisons have been conducted using Solanaceae, the coffee tree and the distantly related grapevine species, from the basal Rosid clade, to detect synteny, or to study the pattern of chromosomal evolution between species that have not experienced recent polyploidization. Recently, extensive conservation of the microsynteny was described at the
EIN4 locus between the coffee tree and the grapevine [
23], suggesting that genome microstructure may be preserved over a long period of evolution. Such intriguing microsynteny raised the question of the extent of genome microstructure conservation and the possible presence of macrostructure conservation between the distantly related coffee tree and grapevine genomes.
Here, to better understand the structural relationships between coffee tree, tomato and grapevine genomes, and then to evaluate the genome conservation and evolution over the past 114-125 MY, we combined comparative mapping at the macro and micro-scale levels. Using a set of genetically mapped COSII sequences in the coffee tree and in the tomato, we identified numerous syntenic blocks in the grapevine genome sequence, providing evidence that segmental rearrangements have occurred since the divergence between the coffee tree and the tomato. Using a BAC clone sequence at the ovate locus, we investigated conservation at the macro- and micro-scale levels of the ovate region between Rubiaceae, Solanaceae and Vitaceae plant families.
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