China has two populations of
Lentinula edodes
sensu lato as follows:
L. edodes
sensu stricto and an unexcavated morphological species respectively designated as A and B. In a previous study, we found that the nuclear types of the two populations are distinct and that both have two branches (A1, A2, B1 and B2) based on the internal transcribed spacer 2 (ITS2) sequence. In this paper, their mitogenome types were studied by resequencing 20 of the strains. The results show that the mitogenome type (mt) of ITS2-A1 was mt-A1, that of ITS2-A2 was mt-A2, and those of ITS2-B1 and ITS2-B2 were mt-B. The strains with heterozygous ITS2 types had one mitogenome type, and some strains possessed a recombinant mitogenome. This indicated that there may be frequent genetic exchanges between the two populations and both nuclear and mitochondrial markers were necessary to identify the strains of
L. edodes
sensu lato. In addition, by screening SNP diversity and comparing four complete mitogenomes among mt-A1, mt-A2 and mt-B, the
cob
,
cox3
,
nad2
,
nad3
,
nad4
,
nad5
,
rps3
and
rrnS
genes could be used to identify mt-A and mt-B and that the
cox1, nad1
and
rrnL
genes could be used to identify mt-A1, mt-A2 and mt-B.