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Title: The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion}
Article:
Abstract:
The ascomycetous fungus Nectria haematococca,( asexual name Fusarium solani), is a member of a group of >50 species known as the “Fusarium solani species complex”. Members of this complex have diverse biological properties including the ability to cause disease on >100 genera of plants and opportunistic infections in humans. The current research analyzed the most extensively studied member of this complex, N. haematococca mating population VI( MPVI). Several genes controlling the ability of individual isolates of this species to colonize specific habitats are located on supernumerary chromosomes. Optical mapping revealed that the sequenced isolate has 17 chromosomes ranging from 530 kb to 6. 52 Mb and that the physical size of the genome, 54. 43 Mb, and the number of predicted genes, 15, 707, are among the largest reported for ascomycetes. Two classes of genes have contributed to gene expansion: specific genes that are not found in other fungi including its closest sequenced relative, Fusarium graminearum; and genes that commonly occur as single copies in other fungi but are present as multiple copies in N. haematococca MPVI. Some of these additional genes appear to have resulted from gene duplication events, while others may have been acquired through horizontal gene transfer. The supernumerary nature of three chromosomes, 14, 15, and 17, was confirmed by their absence in pulsed field gel electrophoresis experiments of some isolates and by demonstrating that these isolates lacked chromosome-specific sequences found on the ends of these chromosomes. These supernumerary chromosomes contain more repeat sequences, are enriched in unique and duplicated genes, and have a lower G+C content in comparison to the other chromosomes. Although the origin( s) of the extra genes and the supernumerary chromosomes is not known, the gene expansion and its large genome size are consistent with this species' diverse range of habitats. Furthermore, the presence of unique genes on supernumerary chromosomes might account for individual isolates having different environmental niches.
Introduction:
The fungus Nectria haematococca, commonly referred to by its asexual name Fusarium solani, is a member of a monophyletic clade that includes over 50 phylogenetic species known as the “Fusarium solani species complex”[1],[2]. Members of the F. solani species complex are able to colonize an impressive variety of environments. As saprobes, they are present in agricultural and non-cultivated habitats, such as forests, scrub communities, savannahs, prairies, swamps, littoral zones, coastal zones, and deserts[3]. As pathogens, members of this complex are responsible for disease on ∼100 genera of plants[4], and they represent one of the most important group of pathogens associated with opportunistic fungal infections and keratitis in humans[2],[5]–[8]. Because of their diverse host range, some members have been proposed for the biological control of weeds and other pathogens[9]–[11]. Extreme environments are not beyond the reach of these fungi. F. solani is among the fungal species recovered from the highly radioactive inner parts of the damaged nuclear reactor at Chernobyl[12]. These fungi are capable of growing in anaerobic conditions in the soil[13] and are tolerant to many compounds shown to be toxic to other fungi[14],[15]. F. solani also has been found growing in the caves at Lascaux, France where it is damaging the 15, 000 year-old paintings[16]. The ability of these fungi to adapt to so many different environments reflects their genetic plasticity and metabolic diversity. Individual members of this species complex can degrade hydrocarbons, organofluorine compounds, lignin, metal cyanides, and pesticides in the soil[17]–[29]. The most extensively studied species of the F. solani complex is “mating population”( MP) VI of N. haematococca( also called Haematonectria haematococca[30]). The term “mating population” defines a group of isolates that are sexually fertile with one another, indicating that they are a biological species. Like other F. solani species, N. haematococcaa MPVI isolates can live in many habitats[31] and classical and molecular genetic analyses have demonstrated that the genes controlling the ability of individual isolates to colonize specific habitats are located on conditionally-dispensable supernumerary chromosomes( “CD chromosomes”), which were first described in fungi in 1991 using N. haematococca MPVI[32]. CD chromosomes are defined as supernumerary chromosomes that are not required for growth under all conditions but confer an adaptive advantage in certain habitats[33]. Subsequent research has demonstrated that in N. haematococca MPVI, genes on these chromosomes are involved in resistance to plant antimicrobials, utilization of specific carbon and nitrogen sources, and in host-specific pathogenicity[33]–[35]. In addition, the properties of the chromosomes and the properties of the genes on these chromosomes, suggest that some of these genes and perhaps even the entire chromosome( s) might have been acquired through horizontal gene transfer( HGT) and have properties similar to the genomic islands of bacteria[36]. The genomic sequence of N. haematococca MPVI has not only the potential to reveal a multitude of metabolic pathways involved in inhabiting many different types of environments, but also to expand on our understanding of the impact of gene flow on fungal evolution.
Discussion:
N. haematococca MPVI has a particularly large genome compared to most sequenced ascomycetes. The large number of genes is consistent with its metabolic, ecological, and biological diversity[31],[34]. Among the factors that have contributed to its large size are the supernumeary chromosomes( chromosomes 14, 15, and 17). The mapped portions of these chromosomes contain 418 genes( Table S10). Based on the sizes of these chromosomes as determined by the optical map, 1. 5 of 3. 5 Mb( approximately 40%) of these chromosomes remains unassigned. One of the unmapped scaffolds contains a gene( MAK1) known to be on a 1. 6-Mb CD chromosome in another isolate, 156-30-6[63]. Thus, there are probably substantially more than 418 genes on these chromosomes. It has been verified experimentally that at least three N. haematococca MPVI chromosomes( chromosomes 14, 15, and 17) are dispensable( Figures 6 and 7). These supernumerary chromosomes also have relatively few F. graminearum orthologs, but contain unique genes, a disproportionate number of possible pseudoparalogs, a lower G+C content, and a high amount of repetitive DNA with an enrichment of specific types of repeats. Chromosome 14 is a CD chromosome because genes on chromosome 14 increase the habitats available for N. haematococca MPVI[34]. Whether chromosomes 15 and 17 also contribute to the ability of this fungus to occupy more niches and are thereby CD chromosomes, is yet to be established. BLAST searches of the genes on chromosomes 14, 15, and 17 revealed similarity to genes involved in a variety of activities, e. g., biofilm formation, utilization of unique nutrients, etc.( data not shown), which are consistent with the involvement of these genes in habitat specialization. Like chromosome 14, the genes on chromosomes 15 and 17 differ in size from those on the other chromosomes( Table S10). B chromosomes, a well-known type of supernumerary chromosome[64],[65], also have large amounts of repetitive DNA. However, classical B chromosomes are highly heterochromatic, have very few, if any, active genes, and are for the most part transcriptionally inactive[64]–[66]. In contrast to classical B chromosomes, the CD chromosomes of N. haematococca MPVI contain functional genes for pathogenicity, antibiotic resistance, and the utilization of unique carbon/nitrogen sources[34]. In addition, based on ESTs[67], about 10% of the genes on the small chromosomes are expressed during growth in defined media, even though the BLAST searches did not detect genes involved in essential core functions( data not shown). The origin of the supernumerary chromosomes is unknown. B chromosomes are often proposed to be derived from A chromosomes( ‘normal’ chromosomes)[64]–[66]. However, restriction patterns used to construct the optical map did not reveal regions of similarity between any of N. haematococca MPVI three supernumerary chromosomes and the other chromosomes. Attempts to demonstrate synteny within the N. haematococca MPVI genome by identifying three-gene pairs in the same order and orientation failed to demonstrate any large-scale segmental duplications. However, six paired regions of up to 50 kb were found. Although three of these regions are on chromosome 14, two of the regions are similar to DNA on unmapped scaffolds and one is on chromosome 6, which appears to be part of the main genome complement. The RIP system of N. haematococca MPVI acting on ancient genome duplications in combination with gene loss might conceal any large-scale duplications, if they occurred[68]. It also has been proposed that B chromosomes could arise from A chromosomes following interspecific hybridization in sexual crosses[66]. In this situation, it is possible that the B chromosome would be the only remnants of an original A chromosome. Extending the mechanism of hybridization to include the well-known parasexual cycle that occurs in some fungi provides another explanation of the origin of supernumerary chromosomes in N. haematococca MPVI. As with sexual hybridization there are numerous barriers between vegetative fusion of different fungal species with the major one being vegetative incompatibility[69], which acts at the intraspecies level. However, as recently pointed out by Sanders[70], it would seem unlikely that the barriers to vegetative fusion are so efficient as to prevent entirely the fusion of fungal cells and the subsequent exchange of DNA. Such an event of DNA exchange need not be common; in principle it need happen only once, particularly if the transferred genetic material provided a selective advantage. The exchange of supernumerary chromosomes has been demonstrated in the laboratory, but thus far only between members of the same species[71],[72]. Supernumerary chromosomes do not explain entirely the large size of the N. haematococca MPVI genome. Unique genes on non-supernumerary chromosomes with atypical G+C content and codon preference are also potential pseudoparalogs obtained by HGT[41],[44],[46],[47]. Although HGT has not been considered to be a common mechanism of gene acquisition in fungi[73], there is an increasing number of examples of apparent HGT[74]–[76]. However, the data are often inconclusive and subject to different interpretations[77]. For example, genes may be classified as pseudoparalogs because of lineage-specific gene loss, poor phylogenetic taxon sampling, artifacts due to long branch attraction, and other variables that obfuscate gene origins via DDL or HGT[42],[43]. Many of the properties of the supernumerary chromosomes are similar to genomic islands of A. fumigatus[42]. These species-specific regions of DNA can be as large as 400 kb, and contain A. fumigatus-specific genes and large amounts of repetitive DNA. Genomic islands have smaller genes with fewer exons than the core genes found in Aspergillus species. The genes on these genomic islands, like those on the supernumerary chromosomes, encode metabolic processes that appear to be involved in the adaptation to different ecological niches. The origin of the genes on these islands was originally attributed to HGT, but after comparisons to genomes of additional Aspergillus species, Fedorova et al.[42] proposed that the genes on the genomic islands of Aspergillus arose by DDL. Nevertheless, the ability of N. haematococca MPVI to acquire genes by HGT or a similar mechanism would bypass the evolutionary restraint that an active RIP system places on a fungus by hindering the utility of gene duplications as a means to create new genes functions[50]. The genomic islands of A. fumigatus tend to be located in the sub-telomeric regions of chromosomes. In other fungi, genes involved in specific habitat associations, including pathogenicity, also are often located in the sub-telomeric regions[78]. In N. haematococca MPVI, gene placements differ among the chromosomes. Chromosomes 1, 4, 5, and 9 have most of their unique genes in the sub-telomeric regions( Figure 9). On the other large chromosomes, the unique genes are distributed in clusters throughout the chromosome. Chromosome 7 is unusual in that it is a large chromosome( 3. 0 Mb) that has some properties of the smaller chromosomes. For example, the majority of the genes on chromosome 7 are unique to N. haematococca MPVI( Figure 9). Chromosome 7 also has the largest number of possible pseudoparalogs( 159) of all the chromosomes( Figure 4). Only one isolate of N. haematococca MPVI( 77-13-4) was sequenced in the current study and it is a third generation progeny from a laboratory cross between two field isolates. In N. crassa, where RIP was first defined, both RIP and the translocation of chromosomal fragments occur during the sexual cycle[79]. Thus, the crossing of the original isolates of N. haematococca MPVI might have increased the degree of RIP and/or affected the locations of genes in 77-13-4. An examination of field isolates of this fungus has revealed a high degree of chromosomal polymorphism and differences in the locations of studied genes[80]. Thus, it would be of great interest to determine the sequence of field isolates of N. haematococca MPVI and other species within the F. solani species complex and to compare the sizes and organization of their genomes to F. graminearum and to other fusaria in the Gibberella clade.
Nectria haematococca MPVI occurs as a saprophyte in diverse habitats and as a plant and animal pathogen . It also was the first fungus shown to contain supernumerary chromosomes with unique habitat-defining genes . The current study reveals that it has one of the largest fungal genomes ( 15 , 707 genes ) , which may be related to its habitat diversity , and describes two additional supernumerary chromosomes . Two classes of genes were identified that have contributed to gene expansion: 1 ) specific genes that are not found in other fungi , and 2 ) genes that are present as multiple copies in N . haematococca but commonly occur as a single copy in other fungi . Some of these genes have properties suggesting their acquisition by horizontal gene transfer . We show that the three supernumerary chromosomes are different from the normal chromosomes; they contain more repeat sequences , are particularly enriched in unique and duplicated genes , and have a lower G+C content . Additionally , the biochemical functions of genes on these chromosomes suggest they may be involved in niche adaptation . The dispensable nature and possession of habitat-determining genes by these chromosomes make them the biological equivalent of bacterial plasmids . We believe they contribute to microbial diversity and have been overlooked in models of fungal evolution .