Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer

Table 1 Summary of tests applied to the final set of HGT candidates

HGT candidate	Number of homologous sequences used^a	BLAST identity threshold	BLAST coverage cut-off	Topology changes with different number of sequences^b	Topology changes after editing alignment	Best model	Topology tests (supporting HGT)^c	Similarities between ML and BI tree reconstruction (%)
HGT1	44	40	90	No	No	LG + I + G + F	ELW, SH	83
HGT2	42	35	85	Yes	No	LG + G + F	n.a.	92
HGT3	54	41	96	Yes	No	LG + G	ELW	100
HGT4	43	40	90	No	No	LG + G + F	n.a.	93
HGT5	53	54	97	No	No	LG+G+F	n.a.	96
HGT6	46	44	90	Yes	No	WAG + G + F	n.a.	95
HGT7	37	35	85	No	No	LG + I + G + F	ELW, SH	84
HGT8	47	28	92	No	No	LG + I + G + F	ELW, SH	93
HGT9	50	37	90	No	No	LG + G + F	ELW, SH	81
HGT10	39	30	75	No	No	LG + G + F	ELW, SH	97
HGT11	44	30	80	No	No	LG + G + F	ELW, SH	89

^aAll sequences used have less than 10% of ambiguous quartets in TREE-PUZZLE.
^bTaking into account only the relative position of horizontal transfer group into the donor group. Topology changes of branches that do not affect the HGT candidates are not reported.
^cELW = Expected Likelihood Weight, SH = Shimodaira and Hasegawa, n.a = not applicable. The groups with homologous sequence only in bacteria are not suitable for topology tests.

ISSN: 1471-2164