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PLoS Genet
2009 Aug 01;58:e1000618. doi: 10.1371/journal.pgen.1000618.
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The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion.
Coleman JJ
,
Rounsley SD
,
Rodriguez-Carres M
,
Kuo A
,
Wasmann CC
,
Grimwood J
,
Schmutz J
,
Taga M
,
White GJ
,
Zhou S
,
Schwartz DC
,
Freitag M
,
Ma LJ
,
Danchin EG
,
Henrissat B
,
Coutinho PM
,
Nelson DR
,
Straney D
,
Napoli CA
,
Barker BM
,
Gribskov M
,
Rep M
,
Kroken S
,
Molnár I
,
Rensing C
,
Kennell JC
,
Zamora J
,
Farman ML
,
Selker EU
,
Salamov A
,
Shapiro H
,
Pangilinan J
,
Lindquist E
,
Lamers C
,
Grigoriev IV
,
Geiser DM
,
Covert SF
,
Temporini E
,
Vanetten HD
.
???displayArticle.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.
Figure 1. TBLASTN analysis of genes on each chromosome.The relative frequency of the best TBLASTN hits for proteins from each N. haematococca MPVI chromosome. The red line depicts hits to the F. graminearum genome, the yellow line depicts hits to one of the seven other fungal species, and the blue line represents hits to none of the fungal species included in the search.
Figure 2. Phylogenetic placement of paralogs in N. haematococca MPVI.
N. haematococca 1 is the ortholog. (A) Placement of a gene at this position implies a recent gene duplication. (B) Placement of a gene at this position indicates the gene may be a pseudoparalog.
Figure 3. The phylogenetic relationship of the ABC transporter YOR1 from selected fungal genomes.Maximum parsimony analysis was used to establish the phylogenetic relationship between the ortholog (Nh63546, red box) and the pseudoparalog (Nh73313, blue box) of N. haematococca MPVI.
Figure 4. Chromosomal locations of possible pseudoparalogs.The percentage for each chromosome is based on the number of possible pseudoparalogs out of the total number of genes on that chromosome.
Figure 5. G+C content of orthologs, possible pseudoparalogs, and unique genes.
Figure 6. Partial electrophoretic karyotypes of 77-13-7, 77-13-4, and two isolates, B33 and HT-1, derived from 77-13-7 and 77-13-4, respectively.Pulsed-Field Gel Electrophoresis conditions that allowed the resolution of the smaller chromosomes were used.
Figure 7. Detection of chromosome-specific sequences found on the ends of chromosomes 14, 15, and 17 in isolates 77-13-7, 77-13-4, and two isolates, B33 and HT-1, derived from 77-13-7 and 77-13-4, respectively.Primers from the scaffolds at the ends of the chromosomes were used to produce PCR products from the end of chromosome 14 (A), chromosome 15 (B), and chromosome 17 (C).
Figure 8. Distribution of repeat elements in the N. haematococca genome.The bar graphs show homologs of previously known or novel transposable elements (Class I, retrotransposons; Class II, DNA transposons; Duplications, repeated regions that are mutated duplicated genes, usually with TE fragments; unknown, repeats that do not match any known or hypothetical proteins). A t-test on the log odds ratio of repetitive and unique fractions of each chromosome revealed that chromosomes 14, 15, and 17 had a higher repetitive content than the other chromosomes (p = 0.01416).
Figure 9. Distribution of orthologs, possible pseudoparalogs, and unique genes on each of the chromosomes of N. haematococca MPVI.Compositional statistical analysis using an additive log-ratio transformation [102] reveals that the distribution of genes within the three classes is statistically different on chromosomes 14, 15, and 17 than on the other chromosomes (p = 1.05e-5).Compositional statistical analysis using an additive log-ratio transformation [102] reveals that the distribution of genes within the three classes is statistically different on chromosomes 14, 15, and 17 than on the other chromosomes (p = 1.05e-5).
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