Abstract
BackgroundCoffee trees (Rubiaceae) and tomato (Solanaceae) belong to the Asterid clade, while grapevine (Vitaceae) belongs to the Rosid clade. Coffee and tomato separated from grapevine 125 million years ago, while coffee and tomato diverged 83-89 million years ago. These long periods of divergent evolution should have permitted the genomes to reorganize significantly. So far, very few comparative mappings have been performed between very distantly related species belonging to different clades. We report the first multiple comparison between species from Asterid and Rosid clades, to examine both macro-and microsynteny relationships.ResultsThanks to a set of 867 COSII markers, macrosynteny was detected between coffee, tomato and grapevine. While coffee and tomato genomes share 318 orthologous markers and 27 conserved syntenic segments (CSSs), coffee and grapevine also share a similar number of syntenic markers and CSSs: 299 and 29 respectively. Despite large genome macrostructure reorganization, several large chromosome segments showed outstanding macrosynteny shedding new insights into chromosome evolution between Asterids and Rosids. We also analyzed a sequence of 174 kb containing the ovate gene, conserved in a syntenic block between coffee, tomato and grapevine that showed a high-level of microstructure conservation. A higher level of conservation was observed between coffee and grapevine, both woody and long life-cycle plants, than between coffee and tomato. Out of 16 coffee genes of this syntenic segment, 7 and 14 showed complete synteny between coffee and tomato or grapevine, respectively.ConclusionsThese results show that significant conservation is found between distantly related species from the Asterid (Coffea canephora and Solanum sp.) and Rosid (Vitis vinifera) clades, at the genome macrostructure and microstructure levels. At the ovate locus, conservation did not decline in relation to increasing phylogenetic distance, suggesting that the time factor alone does not explain divergences. Our results are considerably useful for syntenic studies between supposedly remote species for the isolation of important genes for agronomy.
Highlights
Coffee trees (Rubiaceae) and tomato (Solanaceae) belong to the Asterid clade, while grapevine (Vitaceae) belongs to the Rosid clade
Macrosynteny between the coffee tree and the tomato using COSII mapping data A set of 867 Conserved Ortholog Set II (COSII) loci was selected including 430 and 755 sequences anchored on coffee and tomato genetic maps, respectively
The highest number of syntenic relationships was established between coffee Linkage Group (LG) G and tomato LG 2 with 16 COSII orthologous relationships
Summary
Coffee trees (Rubiaceae) and tomato (Solanaceae) belong to the Asterid clade, while grapevine (Vitaceae) belongs to the Rosid clade. 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]. 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 1) [2]. 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]
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