Diaporthe: a genus of endophytic, saprobic and plant pathogenic fungi

Abstract

Diaporthe (Phomopsis) species have often been reported as plant pathogens, non-pathogenic endophytes or saprobes, commonly isolated from a wide range of hosts. The primary aim of the present study was to resolve the taxonomy and phylogeny of a large collection of Diaporthe species occurring on diverse hosts, either as pathogens, saprobes, or as harmless endophytes. In the present study we investigated 243 isolates using multilocus DNA sequence data. Analyses of the rDNA internal transcribed spacer (ITS1, 5.8S, ITS2) region, and partial translation elongation factor 1-alpha (TEF1), beta-tubulin (TUB), histone H3 (HIS) and calmodulin (CAL) genes resolved 95 clades. Fifteen new species are described, namely Diaporthe arengae, D. brasiliensis, D. endophytica, D. hongkongensis, D. inconspicua, D. infecunda, D. mayteni, D. neoarctii, D. oxe, D. paranensis, D. pseudomangiferae, D. pseudophoenicicola, D. raonikayaporum, D. schini and D. terebinthifolii. A further 14 new combinations are introduced in Diaporthe, and D. anacardii is epitypified. Although species of Diaporthe have in the past chiefly been distinguished based on host association, results of this study confirm several taxa to have wide host ranges, suggesting that they move freely among hosts, frequently co-colonising diseased or dead tissue. In contrast, some plant pathogenic and endophytic taxa appear to be strictly host specific. Given this diverse ecological behaviour among members of Diaporthe, future species descriptions lacking molecular data (at least ITS and HIS or TUB) should be strongly discouraged.

Keywords: Diaporthales; Diaporthe; Multi-Locus Sequence Typing (MLST); Phomopsis; systematics.

Fig. 1

Consensus phylogram of 22 104 trees resulting from a Bayesian analysis of the combined 5-gene sequence alignment. Clades are numbered on the right of the boxes and Diaporthe species names in purple reflect new combinations and in red new species. Strain accession numbers are followed by the original species name (black, when applicable), the isolation source (green) and country of origin (blue). Accession numbers and names in bold represent strains known to be ex-type strains or are considered to be authentic for the species. Red dots indicate strains from medicinal plants and yellow dots from humans. Bayesian posterior probabilities are shown at the nodes and the scale bar represents the expected changes per site. The tree was rooted to Diaporthella corylina (strain CBS 121124).

Fig. 1

Consensus phylogram of 22 104 trees resulting from a Bayesian analysis of the combined 5-gene sequence alignment. Clades are numbered on the right of the boxes and Diaporthe species names in purple reflect new combinations and in red new species. Strain accession numbers are followed by the original species name (black, when applicable), the isolation source (green) and country of origin (blue). Accession numbers and names in bold represent strains known to be ex-type strains or are considered to be authentic for the species. Red dots indicate strains from medicinal plants and yellow dots from humans. Bayesian posterior probabilities are shown at the nodes and the scale bar represents the expected changes per site. The tree was rooted to Diaporthella corylina (strain CBS 121124).

Fig. 1

Consensus phylogram of 22 104 trees resulting from a Bayesian analysis of the combined 5-gene sequence alignment. Clades are numbered on the right of the boxes and Diaporthe species names in purple reflect new combinations and in red new species. Strain accession numbers are followed by the original species name (black, when applicable), the isolation source (green) and country of origin (blue). Accession numbers and names in bold represent strains known to be ex-type strains or are considered to be authentic for the species. Red dots indicate strains from medicinal plants and yellow dots from humans. Bayesian posterior probabilities are shown at the nodes and the scale bar represents the expected changes per site. The tree was rooted to Diaporthella corylina (strain CBS 121124).

Fig. 1

Consensus phylogram of 22 104 trees resulting from a Bayesian analysis of the combined 5-gene sequence alignment. Clades are numbered on the right of the boxes and Diaporthe species names in purple reflect new combinations and in red new species. Strain accession numbers are followed by the original species name (black, when applicable), the isolation source (green) and country of origin (blue). Accession numbers and names in bold represent strains known to be ex-type strains or are considered to be authentic for the species. Red dots indicate strains from medicinal plants and yellow dots from humans. Bayesian posterior probabilities are shown at the nodes and the scale bar represents the expected changes per site. The tree was rooted to Diaporthella corylina (strain CBS 121124).

Fig. 1

Consensus phylogram of 22 104 trees resulting from a Bayesian analysis of the combined 5-gene sequence alignment. Clades are numbered on the right of the boxes and Diaporthe species names in purple reflect new combinations and in red new species. Strain accession numbers are followed by the original species name (black, when applicable), the isolation source (green) and country of origin (blue). Accession numbers and names in bold represent strains known to be ex-type strains or are considered to be authentic for the species. Red dots indicate strains from medicinal plants and yellow dots from humans. Bayesian posterior probabilities are shown at the nodes and the scale bar represents the expected changes per site. The tree was rooted to Diaporthella corylina (strain CBS 121124).

Fig. 2

Diaporthe anacardii (CBS 720.97). a. Conidiomata sporulating on PNA; b. conidiomata sporulating on PDA; c, d. conidiogenous cells; e. beta conidia; f. alpha conidia. — Scale bars = 10 μm.

Fig. 3

Diaporthe angelicae (CBS 111591). a, b. Transverse section through conidiomata, showing conidiomatal wall; c, d. conidiogenous cells; e. alpha and beta conidia; f. conidiogenous cells giving rise to beta conidia; g. beta conidia. — Scale bars: a = 140 μm, all others = 10 μm.

Fig. 4

Diaporthe arengae (CBS 114979). a. Conidiomata sporulating on PNA; b, c. conidiogenous cells; d. beta conidia; e, f. alpha conidia. — Scale bars = 10 μm.

Fig. 5

Diaporthe brasiliensis (CBS 133183). a. Conidiomata sporulating on PDA; b, c. transverse section through conidiomata, showing conidiomatal wall; d, e. conidiogenous cells; f, g. alpha conidia. — Scale bars: b = 80 μm, all others = 10 μm.

Fig. 6

Diaporthe chamaeropis (CBS 454.81). a. Conidiomata sporulating on PDA; b. conidiomata sporulating on PNA; c–e. conidiogenous cells; f. alpha conidia; g. beta conidia. — Scale bars = 10 μm.

Fig. 7

Diaporthe cinerascens (CBS 719.96). a. Conidiomata sporulating on PDA; b, c. conidiogenous cells; d. alpha conidia. — Scale bars = 10 μm.

Fig. 8

Diaporthe elaeagni (CBS 504.72). a. Conidiomata sporulating on PNA; b. conidiomata sporulating on PDA; c, d. conidiogenous cells; e. beta conidia. — Scale bars = 10 μm.

Fig. 9

Diaporthe foeniculacea (CBS 111554). a. Conidiomata sporulating on PDA; b, c. transverse section through conidiomata, showing conidiomatal wall; d–f. conidiogenous cells; g. beta conidia; h. alpha conidia. — Scale bars: b = 250 μm, all others = 10 μm.

Fig. 10

Diaporthe hongkongensis (CBS 115448). a, b. Conidiomata sporulating on PDA; c, d. conidiogenous cells; e. beta conidia; f. alpha conidia. — Scale bars = 10 μm.

Fig. 11

Diaporthe mayteni (CBS 133185). a. Conidiomata sporulating on PNA; b, c. transverse section through conidiomata, showing conidiomatal wall; d, e. conidiogenous cells; f. beta conidia; g. alpha conidia. — Scale bars: b = 85 μm, all others = 10 μm.

Fig. 12

Diaporthe neoarctii (CBS 109490). a. Conidiomata sporulating on PDA; b, c. transverse section through conidiomata, showing conidiomatal wall; d–f. conidiogenous cells; g. alpha conidia. — Scale bars: b = 225 μm, all others = 10 μm.

Fig. 13

Diaporthe nomurai (CBS 157.29). a. Conidiomata sporulating on PDA; b–e. conidiogenous cells; f. alpha conidia; g. beta conidia. — Scale bars = 10 μm.

Fig. 14

Diaporthe oncostoma (CBS 100454). a. Conidiomata sporulating on OA; b, c. transverse section through conidiomata, showing conidiomatal wall; d–f. conidiogenous cells; g. alpha conidia. — Scale bars: b = 225 μm, all others = 10 μm.

Fig. 15

Diaporthe oxe (CBS 133186). a. Conidiomata sporulating on PDA; b, c. transverse section through conidiomata, showing conidiomatal wall; d, e. conidiogenous cells; f. beta conidia; g. alpha conidia. — Scale bars: b = 100 μm, all others = 10 μm.

Fig. 16

Diaporthe paranensis (CBS 133184). a. Conidiomata sporulating on PDA; b, c. transverse section through conidiomata, showing conidiomatal wall; d, e. conidiogenous cells; f. alpha and beta conidia. — Scale bars: b = 100 μm, all others = 10 μm.

Fig. 17

Diaporthe perseae (CBS 151.73). a. Conidiomata sporulating on PDA; b–d. conidiogenous cells; e. alpha and beta conidia. — Scale bars = 10 μm.

Fig. 18

Diaporthe pseudomangiferae (CBS 101339). a. Conidiomata sporulating on PNA; b. conidiomata sporulating on PDA; c, d. conidiogenous cells; e. beta conidia; f. alpha conidia. — Scale bars = 10 μm.

Fig. 19

Diaporthe pseudophoenicicola (CBS 462.69). a, b. Conidiomata sporulating on PDA; c, d. conidiogenous cells; e. alpha conidia. — Scale bars = 10 μm.

Fig. 20

Diaporthe raonikayaporum (CBS 133182). a. Conidiomata sporulating on PNA; b, c. transverse section through conidiomata, showing conidiomatal wall; d. conidiogenous cells; e. beta with a few alpha conidia; f. alpha conidia. — Scale bars: b = 100 μm, all others = 10 μm.

Fig. 21

Diaporthe schini (CBS 133181). a. Conidiomata sporulating on PDA; b, c. transverse section through conidiomata, showing conidiomatal wall; d, e. conidiogenous cells; f. beta conidia. — Scale bars: b = 135 μm, all others = 10 μm.

Fig. 22

Diaporthe tecomae (CBS 100547). a. Conidiomata forming on PNA; b, c. conidiogenous cells; d. beta conidia. — Scale bars = 10 μm.

Fig. 23

Diaporthe terebinthifolii (CBS 133180). a. Conidiomata sporulating on PNA; b, c. transverse section through conidiomata, showing conidiomatal wall; d, e. conidiogenous cells; f. beta conidia. — Scale bars: b = 100 μm, c = 25 μm, all others = 10 μm.