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 similar to 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.

We compare several types of evolutionary divergence of synteny blocks: sequence level divergence of the genes in the block, loss of genes affecting the length and structure of the blocks and spatial position of the block in relation to the chromosomal centromere, and suggest other dimensions, such as the predominant functional characteristic of the genes in the block. We focus on the evolutionary history of the allotetraploid Coffea arabica genome and its two progenitor genomes through three major genomic events spanning 120 million years.

Whole-genome doubling, tripling or replicating to a greater degree, due to fixation of polyploidization events, is attested in almost all lineages of the flowering plants, recurring in the ancestry of some plants two, three or more times in retracing their history to the earliest angiosperm. This major mechanism in plant genome evolution, which generally appears as instantaneous on the evolutionary time scale, sets in operation a compensatory process called fractionation, the loss of duplicate genes, initially rapid, but continuing at a diminishing rate over millions and tens of millions of years. We study this process by statistically comparing the distribution of duplicate gene pairs as a function of their time of creation through polyploidization, as measured by sequence similarity. The stochastic model that accounts for this distribution, though exceedingly simple, still has too many parameters to be estimated based only on the similarity distribution, while the computational procedures for compiling the distribution from annotated genomic data is heavily biased against earlier polyploidization events-syntenic 'crumble'. Other parameters, such as the size of the initial gene complement and the ploidy of the various events giving rise to duplicate gene pairs, are even more inaccessible to estimation. Here, we show how the frequency of unpaired genes, identified via their embedding in stretches of duplicate pairs, together with previously established constraints among some parameters, adds enormously to the range of successive polyploidization events that can be analysed. This also allows us to estimate the initial gene complement and to correct for the bias due to crumble. We explore the applicability of our methodology to four flowering plant genomes covering a range of different polyploidization histories.

Gene loss is the obverse of novel gene acquisition by a genome through a variety of evolutionary processes. It serves a number of functional and structural roles, compensating for the energy and material costs of gene complement expansion. A type of gene loss widespread in the lineages of plant genomes is “fractionation” after whole genome doubling or tripling, where one of a pair or triplet of paralogous genes in parallel syntenic contexts is discarded. The detailed syntenic mechanisms of gene loss, especially in fractionation, remain controversial. We focus on the the frequency distribution of gap lengths (number of deleted genes – not nucleotides) within syntenic blocks calculated during the comparison of chromosomes from two genomes. We mathematically characterize s simple model in some detail and show how it is an adequate description neither of the Coffea arabica subgenomes nor its two progenitor genomes. We find that a mixture of two models, a random, one-gene-at-a-time, model and a geometric-length distributed excision for removing a variable number of genes, fits well.

We take advantage of synteny blocks, the analytical construct enabled at the evolutionary moment of speciation or polyploidization, to follow the independent loss of duplicate genes in two sister species or the loss through fractionation of syntenic paralogs in a doubled genome. By examining how much sequence remains after a contiguous series of genes is deleted, we find that this residue remains at a constant low level independent of how many genes are lost—there are few if any relics of the missing sequence. Pseudogenes are rare or extremely transient in this context. The potential exceptions lie exclusively with a few examples of speciation, where the synteny blocks in some larger genomes tolerate degenerate sequence during genomic divergence of two species, but not after whole genome doubling in the same species where fractionation pressure eliminates virtually all non-coding sequence.

BACKGROUND:We propose a new, continuous model of the fractionation process (duplicate gene deletion after polyploidization) on the real line. The aim is to infer how much DNA is deleted at a time, based on segment lengths for alternating deleted (invisible) and undeleted (visible) regions.RESULTS:After deriving a number of analytical results for "one-sided" fractionation, we undertake a series of simulations that help us identify the distribution of segment lengths as a gamma with shape and rate parameters evolving over time. This leads to an inference procedure based on observed length distributions for visible and invisible segments.CONCLUSIONS:We suggest extensions of this mathematical and simulation work to biologically realistic discrete models, including two-sided fractionation.

The microbial residues, due to their closely connection with humic substances (HS), aroused our considerable interest. The method of shake-flask in liquid culture was adopt to accumulate them, in which the cellulose served as the sole C source. The microbial suspensions including Trichoderma viride (Tv), Aspergillus niger (An), Penicillium (P) and mixed strains (Ms) were inoculated into the cellulose culture fluid respectively. The incubation was performed for 70 days at a constant temperature of 28 degrees C. The results showed that different microbial treatments had different effects on the C turnover in the cellulose fluid, among which Ms performed the most effective role in accumulating microbial residue and consuming organic C of cell metabolic product, Tv followed. As compared to cellulose, large amounts of inorganic N in the fluid could be transferred into the organic N components of residue. In the mean time, the proportion of aromatic rings could be increased at the cost of losing O-containing groups. Specifically, the degrees of condensation were enhanced by Tv and An, however their degrees of oxidation were inhibited. On the contrary, the P and Ms treatments had a significant advantage in the oxydative degradation of cellulose. Although some intermediate products (polysaccharides, phenolic compounds, carboxylic groups and syringyl units etc.) of HS could be detected in the microbial residues treated by Tv and An, their organic molecules did not still achieve the polymerization degree of real HS.