Calonectria De Not., Comm. Soc. Crittog. Ital. 2(fasc.3): 477 (1867)

For synonyms see Index Fungorum (2018)



Calonectria was first introduced based on C. daldiniana in 1867. Calonectria species are pathogenic to a wide range of woody and herbaceous plant hosts in tropical and subtropical areas (Chen et al. 2011; Crous 2002; Lechat et al. 2010; Lombard et al. 2010 a,b; Li et al. 2017). The sexual morphs of Calonectria are characterised by yellow to dark red ascomata, with scaly to warty walls, and clavate, 4–8-spored asci. They produce Cylindrocladium asexual morphs with branched conidiophores, cylindrical, septate conidia, and stipe extensions with terminal vesicles (Crous 2002; Lombard et al. 2010b, 2016; Li et al. 2017).


ClassificationSordariomycetes, Hypocreaomycetidae, Hypocreales, Nectriaceae

Type speciesCalonectria pyrochroa (Desm.) Sacc., Michelia 1(no. 3): 308 (1878)

Distribution –– Worldwide

Disease Symptoms – Box blight, Cutting rot, Damping off, Canker, Leaf spots, leaf and shoot blights, Red crown rot, Root rot

Species of Calonectria are capable of causing diseases in all plant parts. Most diseases have been recorded from young plants or recent field plantings. Symptoms vary according to host species, host age or developmental stage, environmental conditions and the Calonectria species itself (Barnes and Linderman 2001). Leaf spots (caused by C. colhounii, C. ilicola, C. indusiata and C. pteridis) first appear as water-soaked lesions turning tan to dark brown, circular or irregular in shape surrounded by a red, dark brown or purple border with a chlorotic zone. Root necrosis is the main symptom of root rot caused by species such as C. crotalariae and C. ilicola (Lombard et al. 2010a, 2011). On conifers, there is necrosis of lateral and primary roots accompanied with blacking and splitting of the root cortex while on hardwoods, there is blackening of the root cortex with longitudinal cracking (Cordell et al. 1975). Lesions may coalesce and completely destroy the root. Crown infection can occur with the spread of root infection leading to stunting, discolouration of foliage, defoliation and plant death (Lombard et al. 2010a; Lombard et al. 2011).

HostsCalonectria species are soil-borne pathogens and are mainly associated with forestry, agricultural and horticultural plants, on more than 100 plant families (Chen et al. 2011; Crous et al. 1991; Crous 2002, Gehesquiére et al. 2016; Lombard et al. 2010a, b; Li et al. 2017; Lopes et al. 2018). Calonectria species are less commonly associated with fruit rot as compared to leaf spot and root rot (Diaz et al. 2013; Lopes et al. 2018).

Morphological based identification and diversity

Calonectria species were known by Cylindrocladium names for many years. Cylindrocladium species were commonly found in nature and well-known plant pathogens. Later Calonectria was conserved (Hawksworth 2011; McNeill et al. 2012) over Cylindrocladium by Rossman et al. (2013). Most isolates were identified based on morphology. Later, polyphasic approaches based on morphology and sexual compatibility was used to delimit cryptic species (Schoch et al. 2001; Lombard et al. 2010a, b, 2016) and these studies have revealed that there are many species of Calonectria yet to be discovered (Lombard et al. 2016). Calonectria has been subjected to numerous taxonomic studies and 129 species have been recognized based on both morphological and molecular approaches (Crous and Wingfield 1994; Crous 2002; Lechat et al. 2010; Li et al. 2017; Lombard et al. 2010a, b, 2016; Maharachchikumbura et al. 2015, 2016; Lopes et al. 2018).

Macroconidial dimensions and septation, and shape of the vesicle are the best diagnostic characters for identification of Calonectria (Schoch et al. 2000; Crous 2002; Li et al. 2017). Perithecial colour, ascospore number within the asci, and ascospore septation and dimensions are also important for sexual morph identification (Lombard et al. 2010a). However, perithecia of Calonectria species are morphologically very similar, hence are not useful in identification (Crous and Wingfield 1994; Crous 2002). However, intraspecific variation in vesicle shape and conidial dimensions are commonly used in the identification of Calonectria, which can result in taxonomic confusion (Crous et al. 1998; Lombard et al. 2010b).

Molecular based identification and diversity

Morphological data are essential to supplement DNA sequence data for accurate species identification (Lombard et al. 2016). Earlier studies used ITS gene alone to separate Cylindrocladium species, however, the ITS region contains few informative characters (Crous et al. 1999; Schoch et al. 2001; Lombard et al. 2010b). A genus-wide phylogeny can be inferred using TUB, TEF1-α, cmdA and His3 (Lombard et al. 2016; Crous et al. 2002). The LSU gene also provides little information in resolving species of the genus (Lombard et al. 2010b). This study reconstructs the phylogeny of Calonectria based on analyses of a combined TEF1-α, TUB, cmdA and His3 sequence data. After Lombard et al (2010a), this is the first multigene analysis for all the available Calonectria species. Calonectria species formed two major clades in our phylogenetic analysis, which define morphologically similar groups. Similar results were obtained in the previous study by Lombard et al. (2010b) employing seven gene regions (including additional LSU, ITS and ACT sequence data). However, insufficient data are available for the His3 gene region in GenBank. Therefore, it is difficult to have comparative phylogenetic analyses.

Recommended genetic markers (genus level) – LSU and ITS

Recommended genetic markers (species level) – TUB, TEF1-α, cmdA, His3, ACT

Accepted number of species: There are 399 species epithets in Index Fungorum (2018) under this genus. However, only 283 are accepted.

References: Lombard et al. 2010a, b, c, d, 2016, Maharachchikumbura et al. 2015, 2016 (morphology and phylogeny)

Table Calonectria. Details of the isolates used in the phylogenetic tree. Ex-type (ex-epitype) strains are in bold and marked with an * and voucher strains are in bold.

Species Isolate TEF1- α His3 cmdA TUB
Calonectria acicola CBS 114812* GQ267291 DQ190692 GQ267359 DQ190590
C. aciculata CMW 47645*; CERC 5342; CBS 142883
5342; CBS 142883
MF442644 MF442759 MF442874 MF442989
C. aconidialis CBS 136086* KJ462785 KJ463133 KJ463017
C. amazonica CBS 116250*; CPC 3534 KX784682 KX784555 KX784612
C. amazoniensis CBS 115440*; CPC 3885 KX784685 KX784558 KX784615
C. angustata CBS 109065*; CPC 2347; CBS 114544 FJ918551 DQ190696 GQ267361 AF207543
C. arbusta CBS 136079*; CMW 31370; CERC1705 KJ462787 KJ463135 KJ463018
Ca. asiatica CBS 114073*; CMW 23782; CBS 112954
SFE 726; CPC

AY725705 AY725658 AY725741 AY725616
C. australiensis CBS 112954* GQ267293 DQ190699 GQ267363 DQ190596
C. avesiculata CBS 313.92*; CMW 23670; CPC 2373; ATCC 38226 GQ267294 GQ267364
C. blephiliae CBS136425*; CPC21859 KF777243 KF777246
C. brachiatica CBS 123700*; CMW 25298 GQ267296 FJ696396 GQ267366 FJ696388
C. brasiliensis CBS 230.51*; CMW 23670; CPC 2390 GQ267328 GQ267259 GQ267421 GQ267241
C. brassiana CBS 134855*; CBS 13485 KM395883 KM396057 KM395970
C. brassicae CBS 111869*; CMW 30982; CPC 2409; PC 551197 FJ918566 DQ190720 GQ267382 AF232857
C. brassicicola CBS 112841*; CPC 4552 KX784689 KX784561 KX784619
C. brevistipitata CBS 115671*; CPC 94 KX784693 KX784565 KX784623
C. canadiana CBS 110817*; CPC 499 GQ267297 AY725743 AF348212
C. candelabrum CPC 1675 FJ972525 GQ267367 FJ972426
C. cerciana CBS 123693*; CMW 25309 FJ918559 FJ918528 GQ267369 FJ918510
C. chinensis CBS 114827*; CMW 23674; CPC 4101 AY725710 AY725661 AY725747 AY725619
C. citri CBS 186.36*; CMW 23675 GQ267299 GQ267371 GQ267247 AF333393
C. clavata CBS 114557*; ATCC 66389; CPC 2536 GQ267305 DQ190623 GQ267377 AF333396
C. cliffordiicola CBS 111812*; CPC 2631 KX784694 KX784566 KX784624
C. colhounii CBS 293.79*; CMW 30999 GQ267301 DQ190639 GQ267373 DQ190564
C. colombiana CBS 115127*; CMW 30871; CPC 1160 FJ972492 FJ972442 GQ267455 FJ972423
C. colombiensis CBS 112220*; CMW 23676; CPC 723 AY725711 AY725662 AY725748 GQ267207
C. crousiana CBS 127198*; CMW 27249 HQ285822 HQ285794
C. curvispora CBS 116159*; CMW 23693 GQ267302 AY725664 GQ267374 AF333394
C. cylindrospora CBS 110666; CPC 496 FJ918557 FJ918527 GQ267423 FJ918509
C. densa CBS 125261*; CMW 31182 GQ267352 GQ267444 GQ267232
C. duoramosa CBS 134656*; LPF434 KM395853 KM396110 KM396027 KM395940
C. ecuadorensis  CBS 111706* KX784747 KX784604 KX784674
C. ecuadoriae CBS 111406*; CPC 1635 GQ267303 DQ190705 GQ267375 DQ190600
C. ericae CBS 114458*; CPC 2019 KX784699 KX784571 KX784629
C. eucalypti CBS 125275* GQ267338 GQ267267 GQ267430 GQ267218
C. eucalypticola CBS 134847* KM395877 KM396051 KM395964
C. expansa CBS 136247*; CMW 31392; CERC 1727 KJ462798 KJ463146 KJ463029 KJ462914
C. foliicola CBS 136641*; CMW 31393; CERC 1728 KJ462800 KJ463031 KJ462916
C. fujianensis CBS 127201*; CMW 27257 HQ285820 HQ285806 HQ285792
C. glaebicola CBS 134852* KM395879 KM396136 KM396053 KM395966
C. gordoniae CBS 112142*; CPC 3136; ATCC 201837 GQ267309 DQ190708 GQ267381 AF449449
C. gracilipes CBS 111141* GQ267311 DQ190644 GQ267385 DQ190566
C. gracilis CBS 111807* GQ267323 DQ190646 GQ267407 AF232858
C. guangxiensis CBS 136092*; CMW 35409; CERC 1900; CPC 23506 KJ462803 KJ463151 KJ463034 KJ462919
C. hainanensis CBS 136248*; CMW 35187; CERC 1863 KJ462805 KJ463152 KJ463036
C. hawksworthii CBS 111870*; CPC 2405; MUCL 30866 FJ918558 DQ190649 GQ267386 AF333407
C. henricotiae CBS 138102*; CB045 KF815185 KF815157 JX535308
C. hodgesii CBS 133609*; LPF 245 KC491225 KC491222 KC491228
C. honghensis  CMW 476695*; CERC 5572; CBS 142885 MF442665 MF442780 MF442895 MF442997
C. hongkongensis CBS 114828*; CPC 4670 AY725717 AY725667 AY725755 AY725622
C. humicola CBS 125251* GQ267353 GQ267282 GQ267445 GQ267233
C. hurae CBS 114551, CMW 16720 ; CPC 2344 FJ918548 DQ190728 GQ267387 AF333408
C. ilicicola CBS 190.50*; CMW 30998; IMI 299389 AY725726 AY725676 AY725764 AY725631
C. indonesiae CBS 112823*; CMW 23683; CPC 4508 AY725718 AY725668 AY725756 AY725623
C. indonesiana CBS 112936* KX784701 KX784573 KX784631
C. indusiata CBS 144.36* GQ267332 DQ190653 GQ267453 GQ267239
C. insularis CBS 114558*; CPC 768 FJ918556 GQ267389 AF210861
C. kyotensis CBS 114525* AY725713 AY725750 AF348215
C. lageniformis CBS 111324*; CPC 1473 KX784702 KX784574 KX784632
C. lantauensis CMW 47252*; CERC 3302; CBS 142888 MF442677 MF442792 MF442907
C. lateralis CBS 136629*; CMW 31412; CERC 1747 KJ462840 KJ463186 KJ463070 KJ462955
C. lauri CBS 749.70* GQ267312 GQ267250 GQ267388 GQ267210
C. leguminum CBS 728.68* FJ918547 DQ190654 GQ267391 AF389837
C. leucothoes CBS 109166*; CPC 2385; ATCC 64824 FJ918553 FJ918523 GQ267392 FJ918508
C. lichi CERC 8866* MF527039 MF527055 MF527071 MF527097
C. longiramosa CBS 116319* KX784705 KX784577 KX784635
C. machaerinae CBS 123183*; CPC 15378 KX784706 KX784636
C. macroconidialis CBS 114880*; CPC 307 GQ267313 GQ267393
C. madagascariensis CBS 114572*; CPC 2252 GQ267314 DQ190658 GQ267394 DQ190572
C. magnispora CBS 136249*; CMW 35184; CERC 1860 KJ462841 KJ463187 KJ463071 KJ462956
C. malesiana CBS 112752*; CPC 4223 AY725722 AY725672 AY725760 AY725627
C. maranhensis CBS 134811* KM395861 KM396118 KM396035 KM395948
C. metrosideri CBS 133603* KC294310 KC294308 KC294304 KC294313
C. mexicana CBS 110918* FJ972526 FJ972460 GQ267396 AF210863
C. microconidialis CBS 136638*; CMW 31487; CERC 1822 KJ462845 KJ463191 KJ463075 KJ462960
C. montana CERC 8952* MF527049 MF527065 MF527081 MF527107
C. monticola CBS 140645*; CPC 28835 KT964773 KT964771 KT964769
C. morganii CBS 119670; CPC 12766; DISTEF-GP1 GQ421797 DQ521602 DQ521600
C. mossambicensis CMW 36327* JX570718 JX570726 JX570722
C. multilateralis CBS 110932*; CPC 957 KX784712 KX784580 KX784642
C. multinaviculata CBS 134858*; LPF233 KM395898 KM396155 KM396072 KM395985
C. multiphialidica CBS 112678* AY725723 AY725673 AY725761 AY725628
C. multiseptata CBS 112682* FJ918535 DQ190659 GQ267397 DQ190573
C. naviculata CBS 101121 GQ267317 GQ267252 GQ267399 GQ267211
C. nemoralis CBS 116249* KX784752 KX784609 KX784679
C. nemoricola CBS 134837* KM395892 KM396149 KM396066 KM395979
C. nymphaeae CBS 131802*; HGUP 100003 KC555273 JN984864
C. octoramosa CBS 111423* KX784746 KX784603 KX784673
C. orientalis CBS 125260* GQ267356 GQ267285 GQ267448 GQ267236
C. ovata CBS 111299* GQ267318 GQ267253 GQ267400 GQ267212
C. pacifica CBS 109063*; CMW 16726; IMI 354528 AY725724 GQ267255 AY725762 GQ267213
C. papillata CBS 136097*; CMW 37976; CERC 1939 KJ462849 KJ463195 KJ463079 KJ462964
C. paracolhounii CBS 14679*; CPC 2445 KX784714 KX784582 KX784644
C. paraensis CBS 134669*; LPF430 KM395837 KM396094 KM396011 KM395924
C. parakyotensis CBS 136085*; CMW 35169; CERC 1845 KJ462851 KJ463197 KJ463081
C. parva CBS 110798*; CPC 410 KX784716 KX784583 KX784646
C. parvispora CBS 111465* KX784717 KX784584 DQ190607
C. pauciramosa CMW 5683*; CPC 971 FJ918565 FJ918531 GQ267405 FJ918514
C. penicilloides CBS 174.55*; IMI 299375 GQ267322 GQ267257 GQ267406 AF333414
C. pentaseptata CBS 136087*; CMW 35177; CERC 1853 KJ462853 KJ463199 KJ463083 KJ462966
C. piauiensis CBS 134850* KM395886 KM396143 KM396060 KM395973
C. pini CBS 123698* GQ267344 GQ267436 GQ267224
C. plurilateralis CBS 111401*; CPC 1637 KX784719 KX784586 KX784648
C. pluriramosa CBS 136976*; CMW 31440; CERC 1774 KJ462882 KJ463228 KJ463112 KJ462995
C. polizzii CBS 123402* FJ972488 FJ972438 FJ972419
C. propaginicola CBS 134815*; LPF220 KM395866 KM396129 KM396040 KM395953
C. pseudobrassicae CBS 134662*; LPF280 KM395849 KM396106 KM396023 KM395936
C. pseudocerciana CBS 134824* KM395875 KM396132 KM396049 KM395962
C. pseudocolhounii CBS 127195*; CMW 27209 HQ285816 HQ285802 HQ285788
C. pseudoecuadoriae CBS 111402*; CPC 1639 KX784723 KX784589 KX784652
C. pseudohodgesii CBS 134818* KM395817 KM395991 KM395905
C. pseudokyotensis CBS 137332*; CMW 31439; CERC 1774 KJ462881 KJ463227 KJ463111 KJ462994
C. pseudometrosideri CBS 134845* KM395821 KM395995 KM395909
C. pseudomexicana CBS 130354*; DISTEF-TCROU1 JN607296 JN607266 JN607281
C. pseudonaviculata CBS 114417*; CPC 10926 GQ267325 GQ267409 GQ267214
C. pseudopteridis CBS 163.28*; IMI 299579 a KM395902 KM396076
C. pseudoreteaudii CBS 123694*; CMW 25310 FJ918541 FJ918519 GQ267411 FJ918504
C. pseudoscoparia CBS 125257* GQ267349 GQ267278 GQ267441 GQ267229
C. pseudospathiphylli CBS 109165*; CPC 1623 FJ918562 AF348241 GQ267412 FJ918513
C. pseudospathulata CBS 134841* KM395896 KM396153 KM396070 KM395983
C. pseudoturangicola CMW 474965*; CERC 7126; CBS 142890 MF442750 MF442865 MF442980 MF443080
C. pseudouxmalensis CBS 110924*; CPC 942 KX784726 KX784654
C. pseudovata CBS 134675*; LPF285 KM395859 KM396116 KM396033 KM395946
C. pseudoyunnanensis CMW 476555*; CERC 5376; CBS 142892 MF442753 MF442868 MF442983 MF443083
C. pteridis CBS 111793*; ATCC 34395; CPC 2372 FJ918563 DQ190679 GQ267413 DQ190578
C. putriramosa CBS 111449*; CPC 1951 KX784728 KX784591 KX784656
C. queenslandica CBS 112146*; CPC 3213 FJ918543 FJ918521 GQ267415 AF389835
C. quinqueramosa CBS 134654*; LPF065 KM395855 KM396112 KM396029 KM395942
C. reteaudii CBS 112144*; CMW 30984; CPC 3201 FJ918537 DQ190661 GQ267417 AF389833
C. robigophila CBS 134652* KM395850 KM396107 KM396024 KM395937
C. rumohrae CBS 111431*; CPC 1716 FJ918549 DQ190675 GQ267419 AF232871
C. seminaria CBS 136632*; CMW 31450; CERC 1785; CPC 23488 KJ462885 KJ463231 KJ463115 KJ462998
C. silvicola CBS 135237* KM395891 KM396065 KM395978
C. spathiphylli CBS 114540; ATCC 44730; CPC 2378 GQ267330 GQ267424 AF348214
C. spathulata CBS 555.92* GQ267331 GQ267261 GQ267427 GQ267215
C. sphaeropedunculata CBS 136081*; CMW 31390; CERC 1725 KJ462890 KJ463236 KJ463120 KJ463003
C. stipitata CBS 112513*; CPC 3851 KX784734 KX784596 KX784661
C. sulawesiensis CBS 125277* GQ267342 GQ267434 GQ267222
C. sumatrensis CBS 112829*; CMW 23698; CPC 4518 AY725733 AY725696 AY725771 AY725649
C. syzygiicola CBS 112831*; CPC 4511 KX784736 KX784663
C. telluricola CBS 134664*; LPF217 KM395843 KM396100 KM396017 KM395930
C. tereticornis CBS 111301*; CPC 1429 KX784737 KX784664
C. terrae-reginae CBS 112151*; CPC 3202 FJ918545 FJ918522 GQ267451 FJ918506
C. terrestris CBS 136642*; CMW 35180; CERC 1856 KJ462891 KJ463237 KJ463121 KJ463004
C. terricola CBS 116247*; CPC 3583 KX784738 KX784665
C. tetraramosa CBS 136635*; CMW 31474*; CERC 1809*; CPC 23489 KJ462898 KJ463244 KJ463128 KJ463011
C. trifurcata CBS 112753* KX784740 KX784598 KX784667
C. tropicalis CBS 116271; CPC 3559 KX784742 KX784599 KX784669
C. tucuruiensis CBS 114755* KX784743 KX784600 KX784670
C. tunisiana CBS 130357* JN607291 JN607261 JN607276
C. turangicola CBS 136077*; CMW 31411; CERC 1746; CPC23479 KJ462900 KJ463246 KJ463013
C. uniseptata CBS 413.67* GQ267307 GQ267248 GQ267379 GQ267208
C. uxmalensis CBS 110925*; CPC 945 KX784708 KX784638
C. variabilis CBS 112691; CPC 2506 GQ267335 GQ267264 GQ267458 GQ267240
C. venezuelana CBS 111052*; CPC 1183 KX784744 KX784601 KX784671
C. vietnamensis CBS 112152* KX784745 KX784602 KX784672
C. yunnanensis CMW 476445*; CERC 5339; CBS 14289 MF442758 MF442873 MF442988 MF443088
C. zuluensis CBS 125268; CMW 9188 FJ972483 FJ972433 GQ267459 FJ972414
Curvicladiella cignea CBS 109167*; CPC 1595; MUCL 40269 KM231867 KM231461 KM231287 KM232002



























Fig Phylogenetic tree generated by maximum likelihood analysis of combined TEF1-α, TUB, cmdA and His3 sequence data of Calonectria species. Related sequences were obtained from GenBank. One hundred sixty strains are included in the analyses, which comprise 1946 characters including gaps. Tree topology of the ML analysis was similar to the one generated from BI (Figure not shown). The best scoring RAxML tree with a final likelihood value of – 35122.522366 is presented. The matrix had 1231distinct alignment patterns, with 15.02% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.219321, C = 0.325516, G = 0.222910, T = 0.232253; substitution rates AC = 1.329187, AG = 3.755831, AT = 1.528969, CG = 0.930598, CT = 4.519462, GT = 1.000000; gamma distribution shape parameter α = 0.749195. Maximum likelihood bootstrap support (MLBT≥65%) and posterior probabilities (BIPP≥0.90) from Bayesian inference analysis are indicated respectively near the nodes. The ex-type strains are in bold and new isolates in blue. The scale bar indicates 0.06 nucleotide changes per site. The tree is rooted to Curvicladiella cignea.

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