species based on morphological identification are now considered to be species
complexes composed of many species [33, 36, 37].
Phylogenetic analyses of Fusarium isolates are being performed based on numerous diagnostic marker sequences. Among them the most common are calmodulin
(cmd) [38], histone 3 (HIS3), Tri101 [39], mating-type (MAT) locus [36], internally
transcribed spacer regions in the ribosomal repeat region (ITS1 and ITS2) [40, 41],
the intergenic spacer region (IGS) [42], the nuclear ribosomal RNA large subunit
(28S or LSU rDNA), and the mitochondrial small subunit (mtSSU rDNA) [27].
Protein-coding genes are also in use, such as RNA polymerase (RPB2), β-tubulin
(tub2) [43], translation elongation factor (EF-1α) [43–45], and ATP citrate lyase
(ACL1) [46]. Notably, not all of these sequences work equally well showing
significant polymorphism for all Fusarium species. For instance, the ITS regions
have shown its limited usefulness within many Fusarium species, such as
F. avenaceum, F. arthrosporioides/F. tricinctum, F. sporotrichioides/F. langsethiae,
and the lineages of F. graminearum species complex, due to the occurrence of
non-orthologous copies [25, 38]. Correspondingly, β-tubulin gene is not discriminative for genotypes from the Fusarium solani species complex [47]. Nevertheless,
EF-1α, RPB1, and/or RPB2 gene fragments have gained the most of the researcher’s
interest for the following reasons: (i) highly informative at the species level, (ii) nonorthologous copies, (iii) amplified from all species of the genus using single pairs of
universal primers, and (iv) sequences from these three genes are well represented in
the reference database (i.e., FUSARIUM-ID, Fusarium MLST, and NCBI GenBank)
[48–50].
Phylogenetical characterization based on genealogical concordance (GCPSR),
a robust method for determined species boundaries [31], has shown the severe
limitations of morphological and biological species identification in Fusarium and
accelerated species discovery inside the genus. To date, approximately two-thirds
of the 300 phylogenetically distinct species-level Fusaria were discovered using
GCPSR-based studies [51]. Moreover, continuous research investments have provided tremendous insight into evolutionary relationships within the Fusarium genus
inferred from partial RPB1 and RPB2 sequences. The study determined 20 monophyletic species complexes and 9 monotypic lineages, which were named informally
to facilitate the communication of an isolate’s clade membership and genetic
diversity [24, 52]. Based on newly discovered species, two of these monotypic
lineages are currently considered as species complexes [24, 53, 54].
5
Secondary Metabolism Biosynthetic Pathways
Recently, it appeared that genomic regions involved in secondary metabolism
present similarly useful or sometimes better targets for designing phylogenetic
markers and their analysis [3]. The weak side of such approach is that only some
of Fusarium species may possess the gene cluster of interest but the resolution of
the genotypes obtained with SM biosynthetic sequences may be higher than that
10 Fusarium Secondary Metabolism Biosynthetic Pathways: So Close but So. . .
217
complexes composed of many species [33, 36, 37].
Phylogenetic analyses of Fusarium isolates are being performed based on numerous diagnostic marker sequences. Among them the most common are calmodulin
(cmd) [38], histone 3 (HIS3), Tri101 [39], mating-type (MAT) locus [36], internally
transcribed spacer regions in the ribosomal repeat region (ITS1 and ITS2) [40, 41],
the intergenic spacer region (IGS) [42], the nuclear ribosomal RNA large subunit
(28S or LSU rDNA), and the mitochondrial small subunit (mtSSU rDNA) [27].
Protein-coding genes are also in use, such as RNA polymerase (RPB2), β-tubulin
(tub2) [43], translation elongation factor (EF-1α) [43–45], and ATP citrate lyase
(ACL1) [46]. Notably, not all of these sequences work equally well showing
significant polymorphism for all Fusarium species. For instance, the ITS regions
have shown its limited usefulness within many Fusarium species, such as
F. avenaceum, F. arthrosporioides/F. tricinctum, F. sporotrichioides/F. langsethiae,
and the lineages of F. graminearum species complex, due to the occurrence of
non-orthologous copies [25, 38]. Correspondingly, β-tubulin gene is not discriminative for genotypes from the Fusarium solani species complex [47]. Nevertheless,
EF-1α, RPB1, and/or RPB2 gene fragments have gained the most of the researcher’s
interest for the following reasons: (i) highly informative at the species level, (ii) nonorthologous copies, (iii) amplified from all species of the genus using single pairs of
universal primers, and (iv) sequences from these three genes are well represented in
the reference database (i.e., FUSARIUM-ID, Fusarium MLST, and NCBI GenBank)
[48–50].
Phylogenetical characterization based on genealogical concordance (GCPSR),
a robust method for determined species boundaries [31], has shown the severe
limitations of morphological and biological species identification in Fusarium and
accelerated species discovery inside the genus. To date, approximately two-thirds
of the 300 phylogenetically distinct species-level Fusaria were discovered using
GCPSR-based studies [51]. Moreover, continuous research investments have provided tremendous insight into evolutionary relationships within the Fusarium genus
inferred from partial RPB1 and RPB2 sequences. The study determined 20 monophyletic species complexes and 9 monotypic lineages, which were named informally
to facilitate the communication of an isolate’s clade membership and genetic
diversity [24, 52]. Based on newly discovered species, two of these monotypic
lineages are currently considered as species complexes [24, 53, 54].
5
Secondary Metabolism Biosynthetic Pathways
Recently, it appeared that genomic regions involved in secondary metabolism
present similarly useful or sometimes better targets for designing phylogenetic
markers and their analysis [3]. The weak side of such approach is that only some
of Fusarium species may possess the gene cluster of interest but the resolution of
the genotypes obtained with SM biosynthetic sequences may be higher than that
10 Fusarium Secondary Metabolism Biosynthetic Pathways: So Close but So. . .
217