Variation in secondary metabolite production potential in the Fusarium incarnatum-equiseti species complex revealed by comparative analysis of 13 genomes

Villani, Alessandra; Proctor, Robert H.; Kim, Hye-Seon; Brown, Daren W.; Logrieco, Antonio F.; Amatulli, Maria Teresa; Moretti, Antonio; Susca, Antonia

doi:10.1186/s12864-019-5567-7

Table 3 Putative horizontal gene transfer (HGT) events of NRPS and PKS genes between FIESC and other lineages of Fusarium. Grey highlighting indicates that results from all analyses were consistent with HGT

From: Variation in secondary metabolite production potential in the Fusarium incarnatum-equiseti species complex revealed by comparative analysis of 13 genomes

Gene	HGT Donor	HGT Recipient	Identification^a		Additional Evidence for HGT^b
Gene	HGT Donor	HGT Recipient	Manual Tree Comparison	NOTUNG	Bootstrap	SH-AU	d _S
HGT Events with FIESC Recipient
NRPS4	Tricinctum complex	FIESC (Incarnatum clade)	+	+	100	+	+
NRPS11	Sambucinum complex (or close relative)	FIESC	–	+	–	–	–
NRPS14	Sambucinum complex (or close relative)	FIESC	–	+	100^c	+	–
NRPS16	F. longipes (or close relative)	FIESC	+	+	77	–	±
NRPS22	Fujikuroi complex (African clade)	FIESC (Incarnatum clade)	+	+	100	+	+
PKS10	Tricinctum complex	F. scirpi (or recent ancestor)	+	+	100	+	+
PKS10	Sambucinum complex	FIESC (Incarnatum clade)	+	+	100	+	–
PKS22	F. torreyae relative	FIESC (Equiseti clade)	–	+	100	+	–
PKS23	Fujikuroi complex	FIESC (Incarnatum clade)	+	+	100^d	+	+
PKS48	Tricinctum complex (F. avenaceum relative)	FIESC (Incarnatum clade)	+	+	100	+	–
PKS62^e	Fujikuroi complex	FIESC	NA	NA	–	NA	+
PKS69^e	Fujikuroi complex	FIESC	+^f	NA	90	+	+
HGT Events with FIESC Donor
NRPS19	FIESC	Sambucinum complex	+	+	74	+	±
NRPS34	FIESC (Equiseti clade)	F. longipes	–	+	–	–	±
PKS22	FIESC (Equiseti clade)	Tricinctum complex	+	+	100	+	–
PKS42	FIESC (Equiseti clade)	Ancestor of Sambucinum and Chlamydosporum complexes	–	+	–	–	±
PKS43	FIESC (Incarnatum clade)	Sambucinum complex (F. sporotrichioides ancestor)	–	+	–	–	±
PKS43	FIESC (Equiseti clade)	F. avenaceum (or recent ancestor)	–	+	–	–	±
PKS43	FIESC5 (or close relative)	F. aywerte (or recent ancestor)	–	+	–	–	±

^aPutative HGT events were identified by manual comparison of individual NRPS and PKS gene trees to the species tree (Fig. 1) and by using the gene tree reconciliation program NOTUNG [76]. + indicates the method identified the putative HGT event, and – indicates the method did not identify the HGT event. For the Manual comparison column, ± indicates a branch conflict was identified, but that we considered an alternative hypothesis (i.e., an hypothesis that did not involved HGT to FIESC) was also plausible. NA indicates not applicable
^bThree analyses were done to further assess evidence for HGT: bootstrap analysis, SH- AU tests, and estimates of number of synonymous substitutions per synonymous site (d_S). In the Bootstrap column, numerical values correspond to the bootstrap values for the branch in the NRPS/PKS gene tree that conflicted with the species tree; and – indicates that the bootstrap value for the conflicting branch was < 70%, or that in our estimation the branch indicative of HGT in NOTUNG analysis did not conflict with the species tree. In the SH-AU column, + indicates that the constrained tree was significantly worse than the unconstrained tree; and – indicates that the constrained tree was not significantly worse than the unconstrained tree. In the d_S column, + indicates d_S ratio < 1; indicates d_S ratio > 1; and ± indicates comparisons for which d_S ratios < 1 may not be evidence of HGT, because over 50% of comparisons for the gene yielded d_S ratios < 1. NA indicates not applicable
^cThe bootstrap value of 100 was for a FIESC and Sambucinum complex branch that excluded F. aywerte (i.e., Chlamydosporum complex). From our manual comparison of the NRPS14 tree with the species tree, we considered that the topology of the NRPS14 tree could have resulted if the relationship of FIESC and Sambucinum complex sequences were concordant with the species tree, but the relationship of F. aywerte sequences to Sambucinum complex sequences was not concordant with the species tree
^dThis bootstrap value is for a clade that includes members of FIESC and the Fujikuroi and Nisikadoi complexes (See Additional file 5). The bootstrap value for the clade consisting of only FIESC and the Fujikuroi complex was < 70%, and therefore not significant. This in turn suggests that the donor of HGT of PKS23 may have been an ancestor or other relative of the Fujikuroi and Nisikadoi complexes
^eSome non-FIESC homologs used in the PKS62 and PKS69 analyses were not species included in the species tree inferred the current study. Fusarium agapanthi and F. dlaminii are members of the Fujikuroi complex [80], and Fusarium sp. NRRL 25184 (25184) is a member of the F. newnesense species complex, a lineage that is closely related to the Fujikuroi, Nisikadoi and Oxysporum complexes [81]
^fThis branch conflict was inferred by comparison of the PKS69 tree to previously reported species trees showing the relationships of FIESC and F. dlaminii to one another and/or other lineages of Fusarium [3, 29]. The previous studies indicate that F. dlaminii and F. fujikuroi are both members of the Fujikuroi complex. In the PKS69 tree, the F. dlaminii homolog is more closely related to FIESC homologs than to the F. fujikuroi homolog. Thus, the PKS69 tree conflicts with the relationships of species

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ISSN: 1471-2164

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