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RATIONALE - The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. METHODS - We studied an individual of C. arabica 'Bourbon Vermelho'. A BAC library of 175,872 BAC clones was constructed and sequenced using an Illumina HiSeq2000. Each BAC pool was assembled independently with the tool ABySS and scaffolded with SSPACE. Genotyping by sequencing (GBS) was conducted using the restriction enzyme PstI followed by single-end sequencing on an Illumina HiSeq2000. SNP calling was performed using Stacks. Principal Component Analysis was performed using the R package ade4. A hierarchical study of the diversity has been conducted using a model-based clustering procedure with admixture as implemented in STRUCTURE. RESULTS - We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugenioides subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. CONCLUSIONS & PERSPECTIVES - We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distrib

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.

The necessity to adapt to climate change is even stronger for grapevine than for other crops, because grape berry composition—a key determinant of fruit and wine quality, typicity and market value— highly depends on “terroir” (complete natural environment), on vintage (annual climate variability), and on their interactions. In the same time, there is a strong demand to reduce the use of pesticides. Thus, the equation that breeders and grape growers must solve has three entries that cannot be dissociated: adaptation to climate change, reduction of pesticides, and maintenance of wine typicity. Although vineyard management may cope to some extent to the short–medium-term effects of climate change, genetic improvement is necessary to provide long-term sustainable solutions to these problems. Most vineyards over the world are planted using vines that harbor two grafted plants’ genomes. Although this makes the range of interactions (scion-atmosphere, rootstock-soil, scion-rootstock) more complex, it also opens up wider possibilities for the genetic improvement of either or both the grafted genotypes. Positive aspects related to grapevine breeding are as follows: (a) a wide genetic diversity of rootstocks and scions that has not been thoroughly explored yet; (b) progress in sequencing technologies that allows high-throughput sequencing of entire genomes, faster mapping of targeted traits and easier determination of genetic relationships; (c) progress in new breeding technologies that potentially permit precise modifications on resident genes; (d) automation of phenotyping that allows faster and more complete monitoring of many traits on relatively large plant populations; (e) functional characterization of an increasing number of genes involved in the control of development, berry metabolism, disease resistance, and adaptation to environment. Difficulties involve: (a) the perennial nature and the large size of the plant that makes field testing long and demanding in manpow

The grapevine reference genome was published by Jaillon et al. [1]. The sequence for the first version of the genome, called the 8X version, was obtained using a whole genome shotgun strategy and the Sanger sequencing technology and was assembled from reads representing 8X coverage. Soon after, the assembly was improved through the addition of 4X of additional coverage, including more Bacterial Artificial Chromosome end sequences that greatly improved the scaffolding of the sequence contigs [2], [3]. The corresponding scaffolds and raw sequences were deposited in European Molecular Biology Laboratory (EMBL) archives (FN594950-FN597014, 2065 entries, release 102). A new chromosome assembly was also developed, based on an improved version of the maps used for the 8X genome version [2], [3], [4], [5] and was also archived at EMBL (FN597015-FN597047, 33 entries, release 102): it is referenced in the grapevine community as the 12X.v0 version of the grapevine reference genome. The chromosome sequence scaffolding of this version still necessitated improvements as around 9% of the sequence was not anchored to chromosomes (with the corresponding scaffolds stacked in the “Unknown” chromosome) and 3.5% of the sequence could be assigned to a chromosome but without certain placement and orientation within the chromosome (stacked in additional “random” chromosomes).

In ancient DNA (aDNA) research, evolutionary and archaeological questions are often investigated using the genomic sequences of organelles: mitochondrial and chloroplast DNA. Organellar genomes are found in multiple copies per living cell, increasing their chance of recovery from archaeological samples, and are inherited from one parent without genetic recombination, simplifying analyses. While mitochondrial genomes have played a key role in many mammalian aDNA projects, including research focused on prehistoric humans and extinct hominins, it is unclear how useful plant chloroplast genomes (plastomes) may be at elucidating questions related to plant evolution, crop domestication, and the prehistoric movement of botanical products through trade and migration. Such analyses are particularly challenging for plant species whose genomes have highly repetitive sequences and that undergo frequent genomic reorganization, notably species with high retrotransposon activity. To address this question, we explored the research potential of the grape (Vitis vinifera L.) plastome using targeted-enrichment methods and high-throughput DNA sequencing on a collection of archaeological grape pip and vine specimens from sites across Eurasia dating ca. 4000 BCE-1500 CE. We demonstrate that due to unprecedented numbers of sequence insertions into the nuclear and mitochondrial genomes, the grape plastome provides limited intraspecific phylogenetic resolution. Nonetheless, we were able to assign archaeological specimens in the Italian peninsula, Sardinia, UK, and Armenia from pre-Roman to medieval times as belonging to all three major chlorotypes A, C, and D found in modern varieties of Western Europe. Analysis of nuclear genomic DNA from these samples reveals a much greater potential for understanding ancient viticulture, including domestication events, genetic introgression from local wild populations, and the origins and histories of varietal lineages.