Macrophomina Petr., Annls mycol. 21: 314 (1923)

Species of Macrophomina are mostly pathogens that cause damping-off, seedling blight, collar rot, stem rot, charcoal rot, basal stem rot and root rot in many plant species (Arora et al. 2001; Pal et al. 2001; Gupta et al. 2002; Sarr et al. 2014; Wijayawardene et al. 2017). The type species, Macrophomina phaseolina (Tassi) Goid., is a seed-borne polyphagous pathogen that affects more than 500 crop and non-crop species, including economically important crops, such as soybean, sunflower, common bean, peanut, corn, sorghum, cowpea and cotton (Gupta et al. 2002; Ndiaye et al. 2010; Sarr et al. 2014).

ClassificationDothideomycetes, incertae sedis, Botryosphaeriales, Botryosphaeriaceae

Type speciesMacrophomina phaseolina (Tassi) Goid., Annali Sper. agr., N.S. 1(3): 457 (1947)

Distribution – Worldwide

Disease symptoms – Charcoal rot, collar rot, damping-off, root rot, seedling blight, stem rot, wilt

        Seedling damage can occur when infected seeds are planted. Infected plants may produce slightly smaller leaflets than healthy plants and have reduced vigor. As the disease advances, leaflets turn yellow, wilt and turn brown (Adorada et al. 2018). A grey/silver discoloration can be observed in the roots and lower stem when the plants split open (Romero et al. 2017; Koehler and Shew 2018; Meena et al. 2018). In charcoal rot, the abundant production of minute black sclerotia by the fungus causes the rotted tissues to become blackened. Infections on soybean lead to early maturation and incomplete pod filling (ElAraby et al. 2003; Yang and Navi 2005; Sarr et al. 2014). In peanut, it causes seed and seedling rots, wilt, root and stem rots, leaf spot and rotting of developing pods and seeds (Gupta et al. 2002; Deshwal et al. 2003).

Hosts – This soil-borne fungus can infect more than 500 agricultural crops and weed species including, Fragaria, Glycine, Helianthus, Sorghum, and Zea.


Morphological based identification and diversity

Eight species names are recorded in Index Fungorum (2019), however, sequences are available for only two species Macrophomina phaseolina and M. pseudophaseolina (Sarr et al. 2014). Morphological characteristics of M. phaseolina are mostly similar to M. pseudophaseolina, except that conidia of the latter are shorter.

Colony and conidial morphology are the primary characters used to identify species within this genus (Ellis 1971, 1976; Simmons 1992). However, the connectivity of sexual and asexual morphs is not proven, as no sexual morph has been obtained from nature or culture (Crous et al. 2006; Wijayawardene et al. 2016, 2017). According to the morphological identifications, Macrophomina phaseolina has conidia with apical mucoid appendages as found in Tiarosporella (Sutton and Marasas 1976). Nevertheless, it can be distinguished from Tiarosporella in having conidia with apical mucoid appendages, per currently proliferating conidiogenous cells and dark brown (at maturity) conidia (Crous et al. 2006; Phillips et al. 2013). Morphologically M. phaseolina is similar to M. pseudophaseolina, except that conidia of the latter are shorter.


Molecular based identification and diversity

Phillips et al. (2013) suggested that phylogenetic analysis of combined SSU, LSU, ITS, tef1 and TUB2 genes provide better resolution. Sarr et al. (2014) used ITS, tef1, ACT, CAL and TUB2 sequence data representing a large sample of Macrophomina isolates from many hosts. According to the multi-gene analysis of SSU, LSU, ITS, tef1 and TUB2 genes in this study (Fig. 16), the two species cluster in a well-supported clade with high bootstrap values (100% ML, 1.00 BYPP). The overall topology of our phylogeny tree is similar to previous studies.


Recommended genetic markers (genus level) – LSU and SSU

Recommended genetic markers (species level) – ITS, tef1, ACT, CAL and TUB2


The accepted number of species: There are eight epithets in Index Fungorum (2019) However, two species have molecular data.


References: Crous et al. 2006; Phillips et al. 2013; Sarr et al. 2014, Wijayawardene et al. 2016 (morphology, phylogeny).


Table. Details of Macrophomina and Sphaeropsis isolates used in the phylogenetic analyses. Ex-type (or ex-epitype) strains are in bold and marked with an asterisk* and voucher strains are in bold.

Species Isolate/Voucher no SSU ITS LSU tef1 TUB2
Barriopsis fusca CBS 174.26* EU673182 EU673330 DQ377857 EU673296 EU673109
Botryobambusa fusicoccum CBS 134113* JX646826 JX646792 JX646809 JX646857 N/A
MFLUCC 11-0657 JX646827 JX646793 JX646810 JX646858 N/A
Botryosphaeria agaves CBS 133992* JX646825 JX646791 JX646808 JX646856 JX646841
MFLUCC 10-0051 JX646824 JX646790 JX646807 JX646855 JX646840
B. corticis CBS 119047* EU673175 DQ299245 EU673244 EU017539 EU673107
ATCC 22927 EU673176 DQ299247 EU673245 EU673291 EU673108
B. dothidea CBS 115476 * EU673173 AY236949 AY928047 AY236898 AY236927
CBS 110302 EU673174 AY259092 EU673243 AY573218 EU673106
Cophinforma atrovirens MFLUCC 11-0425* JX646833 JX646800 JX646817 JX646865 JX646848
MFLUCC 11-0655 JX646834 JX646801 JX646818 JX646866 JX646849
Dothiorella iberica CBS 115041* EU673155 AY573202 AY928053 AY573222 EU673096
CBS 113188 EU673156 AY573198 EU673230 EU673278 EU673097
Diplodia allocellula CBS 130408* N/A JQ239397 JQ239410 JQ239384 JQ239378
CBS 130410 N/A JQ239399 JQ239412 JQ239386 JQ239380
D. agrifolia CBS 132777* N/A JN693507 N/A JQ517317 JQ411459
UCROK 1429 N/A JQ411412 N/A JQ512121 JQ411443
Lasiodiplodia gonubiensis CBS 115812* EU673193 AY639595 DQ377902 DQ103566 DQ458860
CBS 116355 EU673194 AY639594 EU673252 DQ103567 EU673126
L. lignicola CBS 134112* JX646830 JX646797 JX646814 JX646862 JX646845
MFLUCC 11-0656 JX646831 JX646798 JX646815 JX646863 JX646846
Neoscytalidium hyalinum CBS 499.66 KF531818 KF531820 DQ377925 KF531798 KF531800
CBS 251.49 KF531817 KF531819 DQ377923 KF531797 KF531799
Neodeightonia subglobosa CBS 448.81* EU673202 EU673337 DQ377866 EU673306 EU673137
N. phoenicum CBS 122528* EU673205 EU673340 EU673261 EU673309 EU673116
Macrophomina phaseolina CBS 227.33 KF531823 KF531825 DQ377906 KF531804 KF531806
CBS 162.25 KF531824 KF531826 DQ377905 KF951996 KF531805
M. pseudophaseolina CPC 21422 N/A KF951792 N/A KF952154 KF952234
CPC 21417* N/A KF951791 N/A KF952153 KF952233
CPC 21524 N/A KF951799 N/A KF952161 KF952240
Phaeobotryon mamane CBS 122980* EU673184 EU673332 EU673248 EU673298 EU673121
CPC 12442 EU673185 EU673333 DQ377899 EU673299 EU673124
Oblongocollomyces variabilis CMW 25420 N/A EU101313 N/A EU101358 N/A
CMW 25421, CBS 121775 N/A EU101314 N/A EU101359 N/A
CMW 25422, CBS 121776 N/A EU101326 N/A EU101371 N/A
CMW 25423 N/A EU101327 N/A EU101372 N/A
Sphaeropsis citrigena ICMP 16812* EU673180 EU673328 EU673246 EU673294 EU673140
ICMP 16818 EU673181 EU673329 EU673247 EU673295 EU673141
S. eucalypticola CBS 133993* JX646835 JX646802 JX646819 JX646867 JX646850
MFLUCC 11-0654 JX646836 JX646803 JX646820 JX646868 JX646851
S. porosa CBS 110496* EU673179 AY343379 DQ377894 AY343340 EU673130
CBS 110574 N/A AY343378 N/A AY343339 N/A
S. visci CBS 122526 * N/A EU673324 N/A EU673292 N/A
  CBS 186.97 EU673178 EU673325 DQ377868 EU673293 EU673128

Fig Phylogenetic tree generated by maximum likelihood analysis of combined ITS, LSU, SSU, tef1 and TUB2 sequences. Related sequences were obtained from GenBank. Forty-four strains are included in the analyses, which comprise 3477 characters including gaps. Single gene analyses were carried out and compared with each species, to compare the topology of the tree and clade stability. The tree was rooted with Dothiorella iberica (CBS 113188 and CBS 115041). The tree topology of the ML analysis was similar to the MP and BI. The best scoring RAxML tree with a final likelihood value of -12764.659013 is presented. The matrix had 898 distinct alignment patterns, with 28.31% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.238049, C = 0.253522, G = 0.272022, T = 0.236408; substitution rates AC = 1.121500, AG = 2.393284, AT = 1.053637, CG = 1.711098, CT = 4.682724, GT = 1.000000; gamma distribution shape parameter α = 0.545763. The maximum parsimonious dataset consisted of constant 2820, 575 parsimony-informative and 82 parsimony-uninformative characters. The parsimony analysis of the data matrix resulted in the maximum of two equally most parsimonious trees with a length of 1490 steps (CI = 0.626, RI = 0.861, RC = 0.539, HI = 0.374) in the first tree. RAxML, maximum parsimony bootstrap support values ≥65% and Bayesian posterior probabilities ≥0.95 (BYPP) are shown respectively near the nodes. Ex-type strains are in bold.

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