The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.

Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae.

In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. Due to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast DNA sequences have long been used as choice markers for plant phylogeny reconstruction. The main objectives of this study are: 1) to gain insight in chloroplast genome evolution in the Rubiaceae (Ixoroideae) through efficient methodology for de novo assembly of plastid genomes; and, 2) to test the efficiency of mining SNPs in the nuclear genome of Ixoroideae based on the use of a coffee reference genome to produce well-supported nuclear trees. We assembled whole chloroplast genome sequences for 27 species of the Rubiaceae subfamily Ixoroideae using next-generation sequences. Analysis of the plastid genome structure reveals a relatively good conservation of gene content and order. Generally, low variation was observed between taxa in the boundary regions with the exception of the inverted repeat at both the large and short single copy junctions for some taxa. An average of 79% of the SNP determined in the Coffea genus are transferable to Ixoroideae, with variation ranging from 35% to 96%. In general, the plastid and the nuclear genome phylogenies are congruent with each other. They are well-resolved with well-supported branches. Generally, the tribes form well-identified clades but the tribe Sherbournieae is shown to be polyphyletic. The results are discussed relative to the methodology used and the chloroplast genome features in Rubiaceae and compared to previous Rubiaceae phylogenies.

Optimización de un medio de cultivo para plantas micropropagadas de dioscorea alata L / Optimization of a culture medium for micropropagated plants of dioscorea alata L

La propagación de material de ñame de buena calidad es esencial para incrementar la producción sostenible de este cultivo. El presente trabajo tuvo como propósito optimizar el medio de cultivo de micropropagación de Dioscorea alata L. clon Caraqueño a través de los siguientes objetivos: determinar el efecto de diferentes antioxidantes (carbón activado 0,5 g/L-1 ; carbón activado 1,0 g/L-1; cisteína 10 mg/L-1, 20 mg/L-1 y 30 mg/L-1) y concentraciones de sales de Murashige y Skoog (MS) (25, 50, 75 y 100 %) en el medio de cultivo durante el establecimiento y la multiplicación de las plantas in vitro, y evaluar la utilización de distintas combinaciones de ácido naftalenacético (0,01; 0,1 mg/L-1) y bencilaminopurina (0,01; 0,1 mg/L-1) en el mejor medio de cultivo de multiplicación obtenido en el experimento anterior. A los 35 días se seleccionaron 40 plantas in vitro, a las cuales se les determinaron las siguientes variables: longitud en cm del vástago; número de nudos de novo por explantes; número de hojas por explante y porcentaje de fenolización. Se evaluó además, en el experimento con los reguladores de crecimiento, el número de raíces y longitud de la raíz de mayor tamaño. Se aplicó un diseño experimental completamente aleatorio con análisis de varianza bifactorial y clasificación simple. Se realizó la prueba de comparación de medias de Tukey para un nivel de significación del 5%. Los resultados obtenidos mostraron que las sales MS al 75% de su concentración, el carbón activado (0,5 g/L-1) o la cisteína (10 mg/L-1), en combinación con los reguladores de crecimiento ANA/BAP (0,01/0,01 mg/L-1) en el medio de cultivo MS, incrementaron los indicadores de desarrollo de las plantas in vitro tales como número de nudos de novo (3,5), longitud del vástago (4,1 cm), número de hojas (3,8), número de raíces (5,7) y longitud de las raíces (6 cm).

The material propagation of good quality yam is essential to increase the sustainable production of this cultivation. In the present work the optimization of culture medium of Dioscorea alata L. clone Caraqueño micropropagation was carried out through the following objectives: to determine the effect of different anti-oxydants (activated charcoal 0,5 g.L-1; activated charcoal 1,0 g.L-1; cysteine 10 mg.L-1, 20 mg.L-1 and 30 mg.L-1) and Murashige and Skoog salts concentrations (25, 50, 75 and 100%) in the culture medium during the in vitro plants establishment and the multiplication, and to evaluate the use of different combinations of naftalenacetic acid (0,01; 0,1 mg.L-1) and benzylaminopurine (0,01; 0,1 mg.L-1) in the best multiplication medium obtained in the above experiment. At 35 days, 40 in vitro plants were selected. The following variables were determined in these plants: shoot length, cm; leaf and bud explant number; and oxydation phenolic percentage. In the experiment of plant growth regulators was also evaluated, the roots number and greater size root length. A totally randomized experimental design with one and two factor variance analysis and the Tukey test for means comparison at 5% significance level were applied. The obtained results showed that the salts MS at 75% concentration, the activated charcoal (0,5 g. L-1) or the cysteine (10 mg. L-1), in combination with the growth regulators ANA/BAP (0,01/0,01 mg.L-1) in the MS culture medium, increase the development of the in vitro plants, number of novo buds (3,5), shoot length (4,1 cm), number of leaves (3,8), number of roots (5,7) and greater size root length (6 cm).

Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes.

BACKGROUND: Coffea canephora, also called Robusta, belongs to the Rubiaceae, the fourth largest angiosperm family. This diploid species (2x = 2n = 22) has a fairly small genome size of approximately 690 Mb and despite its extreme economic importance, particularly for developing countries, knowledge on the genome composition, structure and evolution remain very limited. Here, we report the 160 kb of the first C. canephora Bacterial Artificial Chromosome (BAC) clone ever sequenced and its fine analysis. RESULTS: This clone contains the CcEIN4 gene, encoding an ethylene receptor, and twenty other predicted genes showing a high gene density of one gene per 7.8 kb. Most of them display perfect matches with C. canephora expressed sequence tags or show transcriptional activities through PCR amplifications on cDNA libraries. Twenty-three transposable elements, mainly Class II transposon derivatives, were identified at this locus. Most of these Class II elements are Miniature Inverted-repeat Transposable Elements (MITE) known to be closely associated with plant genes. This BAC composition gives a pattern similar to those found in gene rich regions of Solanum lycopersicum and Medicago truncatula genomes indicating that the CcEIN4 regions may belong to a gene rich region in the C. canephora genome. Comparative sequence analysis indicated an extensive conservation between C. canephora and most of the reference dicotyledonous genomes studied in this work, such as tomato (S. lycopersicum), grapevine (V. vinifera), barrel medic M. truncatula, black cottonwood (Populus trichocarpa) and Arabidopsis thaliana. The higher degree of microcollinearity was found between C. canephora and V. vinifera, which belong respectively to the Asterids and Rosids, two clades that diverged more than 114 million years ago. CONCLUSION: This study provides a first glimpse of C. canephora genome composition and evolution. Our data revealed a remarkable conservation of the microcollinearity between C. canephora and V. vinifera and a high conservation with other distant dicotyledonous reference genomes. Altogether, these results provide valuable information to identify candidate genes in C. canephora genome and serve as a foundation to establish strategies for whole genome sequencing. Future large-scale sequence comparison between C. canephora and reference sequenced genomes will help in understanding the evolutionary history of dicotyledonous plants.