P. Hamon

Physical mapping of rDNA and heterochromatin in chromosomes of 16 Coffea species: A revised view of species differentiation

The chromosome organization among 15 wild diploid Coffea species and cultivated tetraploid C. arabica was determined by fluorochrome banding (CMA, DAPI) and double fluorescence in-situ hybridization (FISH) of 5S and 18S rDNA achieved on the same chromosome plates. Two to five chromosome pairs (plus one putative chromosome B) are marked. Overall, there are two SAT-chromosome pairs for East African species and one for the Malagasy and the West and Central African species. 18S rDNA loci are telomeric and strongly marked the SAT-chromosome pairs. Generally, only one pericentromeric 5S rDNA locus characterized East African species, while an additional minor locus co-localized with the 18S rDNA-SAT locus for the Malagasy species and West and Central African species. A combination of rDNA FISH plus CMA and DAPI banding patterns enables identification of almost all the species, even those for which the genetic or botanical status is still being discussed. C. arabica clearly appears to be an allotetraploid species, including one genome from East Africa and one from West and Central Africa. However, since the minor 5S rDNA-SAT locus present in West/Central African genomes is not detected, two evolutionary hypotheses could be put forward for C. arabica. Considering only the diploid species, global trends are obvious in rDNA signal patterns, genome size variations, and geographic distribution of the species, but there are no clear evolutionary trends. However, complex interactions between these factors and environmental growing conditions exist, which have resulted in loss and gain of rDNA loci and probably also in copy repeat number variations in each rDNA family.

Advances in Coffea Genomics

Abstract Coffee is the second most valuable commodity exported by developing countries. The Coffea genus comprises over 103 species but coffee production uses only two species throughout the tropics: Coffea canephora, which is self-sterile and diploid and better known as Robusta, and C. arabica, which is self-fertile and tetraploid. With the arrival of new analytical technologies and the start of genome sequencing projects, it was clearly time to review the state of the art of coffee genetics and genomics. In the first part of this chapter, we present the main results concerning genetic diversity and phylogeny – the most advanced fields – based on large molecular marker sets, such as random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), intersimple sequence repeat (ISSR), single sequence repeats (SSRs), or conserved orthologue set (COS), which are mainly polymerase chain reaction (PCR) based. These markers also enable the construction of genetic maps and the identification of quantitative trait loci (QTLs) for both morphological and biochemical traits. In the second part, after reviewing current knowledge on variation in coffee genome size and insights into cytogenetics, we focus on currently available genomic resources and web facilities. Large sets of expressed sequences tags (ESTs) and bacterial artificial chromosome (BAC) libraries for both C. canephora and C. arabica have been obtained along with information on genes and specific metabolic pathways. In the final section, we describe recently designed tools and their ultimate goal, which is to facilitate the sequencing, assembly and annotation of the first Coffea genome. We are at the gate of a new era of scientific approaches to coffee that should lead to a better understanding of phylogenetic relationships and genome evolution within the genus. Finally, taken together, this information should help develop improved varieties to meet the new challenges represented by ongoing radical changes in the environment.

Ancestral synteny shared between distantly-related plant species from the asterid (Coffea canephora and Solanum Sp.) and rosid (Vitis vinifera) clades

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.

Future prospects of the genetic integrity of two species of okra (Abelmoschus esculentus and A. caillei) cultivated in West Africa

SummaryA study of the geographical distribution of two species of okra, Abelmoschus esculentus and A. caillei, shows that both are cultivated in almost all villages from the Gulf of Guinea to the southern limit of the Sahel. If the cultivars of both species, collected in the same village, are sown simultaneously, as often is the case, study of flowering reveals the possibility of interspecific pollination during about 7 weeks to 2 months. Interspecific hybrids can be obtained artificially, but at experimental stations and in the field very low rates of cross fertilization are observed. In addition, the sterility of the F1 hybrids makes their genetic participation in subsequent generations unlikely. In this study, we show that: 1) although grown for the same purpose, the two species are clearly managed as two separate crops by local growers; 2) the conditions which allow gene flow between both crops exist, and 3) the rate of spontaneous introgressions is low. The genetic integrity of the two species does not, therefore, seem threatened and the relative balance between them is mainly tied to the choice of the growers.

Terminal-Repeat Retrotransposons with GAG Domain in Plant Genomes: A New Testimony on the Complex World of Transposable Elements

A novel structure of nonautonomous long terminal repeat (LTR) retrotransposons called terminal repeat with GAG domain (TR-GAG) has been described in plants, both in monocotyledonous, dicotyledonous and basal angiosperm genomes. TR-GAGs are relatively short elements in length (<4 kb) showing the typical features of LTR-retrotransposons. However, they carry only one open reading frame coding for the GAG precursor protein involved for instance in transposition, the assembly, and the packaging of the element into the virus-like particle. GAG precursors show similarities with both Copia and Gypsy GAG proteins, suggesting evolutionary relationships of TR-GAG elements with both families. Despite the lack of the enzymatic machinery required for their mobility, strong evidences suggest that TR-GAGs are still active. TR-GAGs represent ubiquitous nonautonomous structures that could be involved in the molecular diversities of plant genomes.

Microsatellite markers for Amborella (Amborellaceae), a monotypic genus endemic to New Caledonia

UNLABELLED PREMISE OF THE STUDY Informative markers are required for assessing the diversity of Amborella trichopoda, the only species of its order, endemic to New Caledonia and considered to be the sister species to all flowering plants. Therefore, expressed sequence tag (EST)-based microsatellite markers were developed. • METHODS AND RESULTS Fifty-five microsatellite loci were characterized in 14896 putative unigenes, which were generated by assembling A. trichopoda ESTs from the public sequence database. Seventeen markers revealed polymorphism in 80 adult shrubs from three populations. The number of alleles per locus ranged from two to 12, with a total of 132 alleles scored. The mean expected heterozygosity per population ranged from 0.336 to 0.567. • CONCLUSIONS These markers offer an appropriate amount of variation to investigate genetic diversity structure, gene flow, and other conservation issues.