A novel and unexpected mode of chromosome-level sequence conservation, which we have called mesosynteny, has been detected between species of filamentous Ascomycetes, and in particular the Dothideomycetes. Mesosynteny implies the conservation of gene content within chromosomes but without conservation of gene order or orientation. It contrasts markedly with the macrosynteny observed commonly in plants and animals and the absence of synteny seen in other eukaryotes such as distantly related yeast species. The cause of mesosyntenic chromosomal evolution is not known. However, a mesosyntenic pattern would be expected to occur if intra-chromosomal recombination (including inversions) occurred significantly more frequently than inter-chromosomal recombinational events such as translocations.
Mesosynteny is distinct from macrosynteny. Macrosynteny would be expected to arise when the predominant modes of chromosomal evolution are inter-chromosomal recombination and gene loss. These considerations suggest that different patterns of mutagenic events can lead either to mesosynteny or to macrosynteny as chromosomes evolve following a speciation event.
Mesosynteny also is distinct from microsynteny, which is characterized by co-linearity between clusters of two to about ten genes with both order and orientation conserved. Earlier comparisons of synteny in related filamentous fungi frequently found clusters of genes with related functions but without retention of gene order or orientation. An example is the quinate cluster, which is conserved across species of the Ascomycetes [21
]. This pattern of shuffled cluster retention is akin to what we observe at the whole-chromosome level.
Our results suggest that mesosyntenic chromosomal conservation is restricted to the Pezizomycotina and is most pronounced in the Dothideomycetes [45
]. The Dothideomycetes are the only group to exhibit non-degraded mesosynteny between species of the different genera (estimated to have diverged approximately 120 to 150 Mya) and orders (approximately 300 Mya). A recognizable yet degraded form of mesosynteny was found between many species of Pezizomycotina outside the Dothideomycetes. The estimated time of divergence within Dothideomycetes orders are comparable to other orders within the Pezizomycotina that exhibited either degraded mesosynteny or no detectable synteny (Table ) [38
]. No mesosynteny was observed in any of the fungal groups outside of the Pezizomycotina that were surveyed: yeasts, Basidiomycetes, Blastocladiomycetes and Chytridiomycetes. The evolutionary separation between these groups and the Dothideomycetes (500 to 650 Mya) [38
] may be so great that both mesosynteny and macrosynteny have decayed below the limit of detection. To our knowledge, mesosynteny has not been observed in non-fungal eukaryotes. Superficially similar dot-plots have been occasionally observed in comparisons of chordate genomes [45
] but appear to be due to the amplification of paralogous copies of genes within chromosomes. Overall, either macrosynteny or no synteny has been found outside the Pezizomycotina.
Chromosomal conservation akin to mesosynteny had been observed previously in a number of inter-species comparisons within the Pezizomycotina, but its full extent was not analyzed. These include comparisons between the Pezizomycetes Tuber melanosporum
and the Eurotiomycetes Coccidioides immitus
] and the Sordariomycetes P. anserina
and N. crassa
]. As N. crassa
and P. anserina
are heterothallic, the authors suggested that the observed conservation may be specific to out-crossing (heterothallic) fungi. However, evidence from this study suggests otherwise as mesosynteny was observed between both heterothallic and homothallic species (Table ; Additional files 3
). For example, two homothallic Sordariomycetes species, which diverged approximately 225 Mya [38
], exhibited degraded mesosynteny (Fusarium graminearum
and Chaetomium globosum
; Additional file 7
Mesosynteny was observed in species both with and without (F. oxysporum
] and Penicillium marneffei
]) a known sexual stage. It may be that sexual crossing has been lost relatively recently in these species. Nonetheless, this finding suggests that mesosyntenic relationships were not quickly lost in the absence of meiosis. Amongst the mesosyntenic Pezizomycotina, mesosynteny was weakest in comparisons against the M. oryzae
genome (Figures and ; Table ). M. oryzae
is believed to exist in nature in purely asexual lineages. The sequenced isolate of M. oryzae
was a fertile derivative of two asexual lineages [19
]. We speculate that a history of asexual reproduction and/or the process of laboratory domestication may have destroyed the remnants of mesosynteny in this isolate. This hypothesis could be tested by comparisons with genome sequences from additional isolates of M. oryzae
or related species in the Magnaporthales.
In some species there was an uneven distribution of syntenic relationships between different chromosomes. The genome of M. graminicola
has been finished [39
] and comprises 21 chromosomes, the eight smallest of which have been shown to be dispensable [49
]. These dispensable chromosomes displayed little sequence conservation with genes from any other species, and therefore no detectable synteny of any type (Figure ). In contrast, the M. graminicola
core chromosomes exhibited a typical mesosyntenic pattern in most comparisons with other Pezizomycotina species. Similarly, the conditionally dispensable chromosomes (CDCs) of F. oxysporum
(3, 6, 14 and 15) showed no synteny with almost all species tested. All of these supernumerary chromosomes are thought to have originated by lateral transfer from unknown donor species [39
]. Whether the lack of synteny of most supernumerary chromosomes is because they come from distantly related species or because they evolve more rapidly than core chromosomes is not known.
Surprisingly, CDC 14 of N. haematococca
was mesosyntenic to F. oxysporum
CDCs (chromosome 14 and the terminal end of chromosomes 3 and 6; Figure ; Additional file 4
). This is in contrast to the core chromosomes of each species, which exhibited macrosynteny and to previous comparisons that had indicated that these CDCs were non-syntenic. A comparison of the F. oxysporum
genome with the closely related Fusarium verticillioides
indicated that the F. oxysporum
CDCs were not syntenic [50
]. A possible explanation for this phenomenon is that mutations and rearrangements in supernumerary chromosomes accumulate more rapidly because these chromosomes are rarely required for survival. Faster accumulation of mutations potentially coupled with origins in distantly related donor species may allow the sequences of supernumerary chromosomes to diverge to the point where no sequence similarity remains (as in M. graminicola
). The occurrence of mesosyntenic rearrangement in F. oxysporum
and N. haematococca
may also be related to the origin of their CDCs. These may have arisen in their common ancestor from a single chromosome, which subsequently mutated and broke into smaller chromosomes. Alternatively, they may have been recently transferred laterally from a common (or closely related) donor.
Whole-genome shotgun sequencing involves the generation of many short DNA reads that are assembled into longer segments. Macrosyntenic relationships are commonly used to assist the assembly and finishing of fragmented genome sequences, particularly in prokaryotic genomes. Sequences that are macrosyntenic to a long sequence of a closely related genome can be confidently hypothesized to be joined physically. Mesosynteny between a new genome assembly with a reference genome also may be used to suggest which scaffolds are juxtaposed. This could significantly reduce the cost and complexity of assembling and finishing genomes. To test whether mesosynteny could be used to predict scaffold joins in genomic sequences, early and late assemblies of the M. graminicola
genome were analyzed to determine whether the joining of contigs or scaffolds in the finished genome could have been predicted by mesosyntenic relationships of the draft genome to P. nodorum
]. Mesosynteny was remarkably successful in predicting separate scaffolds that should be joined and for identifying mis-joins in the initial assembly. This approach has the potential to assist with assembly and finishing of other genomes within the Pezizomycotina.