Frequent gain and loss of introns in fungal cytochrome b genes

Abstract

In this study, all available cytochrome b (Cyt b) genes from the GOBASE database were compiled and the evolutionary dynamics of the Cyt b gene introns was assessed. Cyt b gene introns were frequently present in the fungal kingdom and some lower plants, but generally absent or rare in Chromista, Protozoa, and Animalia. Fungal Cyt b introns were found at 35 positions in Cyt b genes and the number of introns varied at individual positions from a single representative to 32 different introns at position 131, showing a wide and patchy distribution. Many homologous introns were present at the same position in distantly related species but absent in closely related species, suggesting that introns of the Cyt b genes were frequently lost. On the other hand, highly similar intron sequences were observed in some distantly related species rather than in closely related species, suggesting that these introns were gained independently, likely through lateral transfers. The intron loss-and-gain events could be mediated by transpositions that might have occurred between nuclear and mitochondria. Southern hybridization analysis confirmed that some introns contained repetitive sequences and might be transposable elements. An intron gain in Botryotinia fuckeliana prevented the development of QoI fungicide resistance, suggesting that intron loss-and-gain events were not necessarily beneficial to their host organisms.

Figure 1. Maximum parsimony (MP) phylogenetic trees and schemata of intron gains in Botryotinia and Monilinia spp.

(A) and (B), MP phylogenetic trees based on cDNA sequences and intron sequences at position 164 of the Cyt b gene from Botryotinia and Monilinia spp. The numbers at each node indicate the bootstrap (BS) values (N = 500) supporting individual branches. (C) Schemata of position 164 intron gains from lateral transfers in Monilinia species M. fructicola, M. yunnanensis and M. mumecola. Intron names are shown in parenthesis after the species name. The GenBank accession nos. of Cyt b genes in Botryotinia and Monilinia spp were AB428335 (B. fuckeliana), GQ304941 (M. fructicola), GU952817 (M. laxa), HM149254 (M. fructigena), HQ908793 (M. yunnanensis) and JN204425 (M. mumecola) which include the cDNA sequences and intron sequences at position 164.

Figure 2. Identification of the Cyt b gene intron in Monilinia spp.

Two restriction enzymes EcoR I and Hind III were used to generate the restriction profiles. Digested genomic DNA was separated in 0.8% agarose gel, and the blot was hybridized with the My3 (A) and My4 (B) fragments. White and black arrows in (A) indicate the expected bands for EcoR I and Hind III digestions. Lanes 1, 11 and 2, 12: M. yunnanensis isolates YKG10-64a and SM09-7c; 3, 13 and 4, 14: M. fructigena isolates SL10 and Mfg2-GE-A; 5, 15 and 6, 16: M. laxa isolates BEK-SZ and EBR ba11b; 7, 17 and 8, 18: M. mumecola isolates HWL10-11a and HWL10-20a; 9, 19 and 10, 20: M. fructicola isolates MPA14 and BM09-4a. The sizes (in kilobases) of marker DNA fragments are indicated on both sides (Wide Range DNA Marker on the left and DL 2000 DNA Marker on the right, TaKaRa Biotechnology (Dalin) Co., Ltd).