Xavier Argout,Jerome Salse,Jean-Marc Aury,Mark J Guiltinan,Gaetan Droc,Jerome Gouzy,Mathilde Allegre,Cristian Chaparro,Thierry Legavre,Siela N Maximova,Michael Abrouk,Florent Murat,Olivier Fouet,Julie Poulain,Manuel Ruiz,Yolande Roguet,Maguy Rodier-Goud,Jose Fernandes Barbosa-Neto,Francois Sabot,Dave Kudrna,Jetty Siva S Ammiraju,Stephan C Schuster,John E Carlson,Erika Sallet,Thomas Schiex，et al.
We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.
The genome of woodland strawberry (Fragaria vesca)
Vladimir Shulaev,Daniel J Sargent,Ross N Crowhurst,Todd C Mockler,Otto Folkerts,Arthur L Delcher,Pankaj Jaiswal,Keithanne Mockaitis,Aaron Liston,Shrinivasrao P Mane,Paul Burns,Thomas M Davis,Janet P Slovin,Nahla Bassil,Roger P Hellens,Clive Evans,Tim Harkins,Chinnappa Kodira,Brian Desany,Oswald R Crasta,Roderick V Jensen,Andrew C Allan,Todd P Michael,Joao Carlos Setubal,Jean-Marc Celton,et al.
The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted.
