PAV – collection of plant pathogen microorganisms: fungi ... · EPPO- Q collection Rome 2015. The...
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PAV – collection of plant pathogen microorganisms:fungi, oomyctes, bacteria, viruses, and viroids
Council for Agricultural Research and Economics - Plant Pathology Research Center of Rome, Italy
EPPO- Q collection Rome 2015
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EPPO- Q collection Rome 2015
Before talking about the PAV-collection of living microorganisms just few words on the historical scientific roots of our Institute which harbors several Herbaria:The most famous is:the Herbarium of fungi of citrus of Otto Penzig a famous German mycologist
Herbarium Mycologicum RomanicumMycotheca Italica (of Saccardo)
Herbarium Crittogamico Italiano (of Anzi, Arcangeli, Carestia, Passerini, Spegazzini)
Herbarium of parasitic fungi of cultivated plants (of Cavara, Briosi, Pollacci).
Herbaria
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EPPO- Q collection Rome 2015
The PAV-collection of phytopathogenic microorganisms includes fungi, oomycetes, bacteria, viruses and viroids
It is a working collection and the microorganisms or infective entities here preserved derived from research or diagnostic activities
A group of core isolates have been included in a national collection project named COLMIA
Consultable on the web at:
www.colmia.it
This National project included 11 working units each with its in-situcollection of microorganisms associated with agricultural research fields (soil, diseases, entomopathogenic activity) or transformation processes (wine, cheese, table-olives)
http://www.colmia.it/
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EPPO- Q collection Rome 2015
Specimens listed in COLMIA are just few among hundreds of single-cell strains conserved in PAV
Most of them are characterized and subjected to phylogenetic and molecular studies
Table 1. List of main species or genera of the plant pathogen microorganisms or infective entities included in COLMIA (www.COLMIA.it) Microorganism or entity
N. of strains
Fungi 251 Alternaria spp. 7 Ascochyta rabiei 19 Bipolaris spp. (Of which 14 Bipolaris oryzae) 16 Drechslera teres 12 Drechslera graminea 23 Fusarium spp. 51 Fusarium lateritium 54 Marssonina juglandis 5 Monilia spp. 13 Monilia fructicola quarantine organism 6 Neotyphodium spp. 14 Phomopsis 4 Pyrenochaeta lycopersici 22 Tubakia dryina 5 Oomycetes 11 Phytophthora cactorum 1 Phytophthora cinnamomi 4 Phytophthora hedraiandra 2 Phytophthora megasperma 1 Phytophthora niederhauserii 3 Bacteria 62 Brenneria nigrifluens 4 Erwinia carotovora 5 Pseudomonas avellanae 10 Pseudomonas syringae 11 Xanhomonas arboricola 16 Xanthomonas campestris 6 Virus and viroids 35 Apple scar skin viroid 1 Hop stunt viroid 2 Peach latent mosaic viroid 3 Pear blister canker viroid 1 Beet pseudo yellow virus 1 Caper latent virus 2 Cucumber mosaic virus 1 Cucurbit aphid-borne yellows virus 2 Plum pox virus quarantine organism 23
Table 1. List of main species or genera of the plant pathogen microorganisms or infective entities included in COLMIA (www.COLMIA.it)
Microorganism or entity
N. of strains
Fungi
251
Alternaria spp.
7
Ascochyta rabiei
19
Bipolaris spp. (Of which 14 Bipolaris oryzae)
16
Drechslera teres
12
Drechslera graminea
23
Fusarium spp.
51
Fusarium lateritium
54
Marssonina juglandis
5
Monilia spp.
13
Monilia fructicola quarantine organism
6
Neotyphodium spp.
14
Phomopsis
4
Pyrenochaeta lycopersici
22
Tubakia dryina
5
Oomycetes
11
Phytophthora cactorum
1
Phytophthora cinnamomi
4
Phytophthora hedraiandra
2
Phytophthora megasperma
1
Phytophthora niederhauserii
3
Bacteria
62
Brenneria nigrifluens
4
Erwinia carotovora
5
Pseudomonas avellanae
10
Pseudomonas syringae
11
Xanhomonas arboricola
16
Xanthomonas campestris
6
Virus and viroids
35
Apple scar skin viroid
1
Hop stunt viroid
2
Peach latent mosaic viroid
3
Pear blister canker viroid
1
Beet pseudo yellow virus
1
Caper latent virus
2
Cucumber mosaic virus
1
Cucurbit aphid-borne yellows virus
2
Plum pox virus quarantine organism
23
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EPPO- Q collection Rome 2015
In our Institute are stored approximately:2500 Fungi130 Phytophthoras860 Bacteria300 Virus & viroids
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EPPO- Q collection Rome 2015
One of the purpose of a collection is to preserve biodiversity. In PAV-collection are maintained isolates of the same pathogenic species for preserving the variability within the population in terms of virulence, metabolite/toxin production, pesticide resistance, etc.
We have numerous strains that are used as reference in pathogenic tests
I will be giving some examples about fungi, bacteria, and viruses showing the information provided on the web site catalogue of COLMIA
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EPPO- Q collection Rome 2015
Fungi
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EPPO- Q collection Rome 2015
Fungi
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EPPO- Q collection Rome 2015
Bacteria
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EPPO- Q collection Rome 2015
Viruses
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EPPO- Q collection Rome 2015
Alternaria alternata complex or “small-spored catenulate A. alternata species groups pathogenic on nuts (walnut & hazelnut)
NGN
A. alternata complex strains
A. alternata A. tenuissima A. arborescensBAN
AFLP, ISSR, H4 polyphasic classification
Hong S. G., Maccaroni M., Figuli P. J., Pryor B. M., Belisario A., 2006. Polyphasic classification of Alternaria spp. isolated from hazelnut and walnut in Europe. Mycological Research, 110: 1290-1300.
A. infectoriaA. alternataalter ISPaVe1769 alter ISPaVe1796 alter ISPaVe1781 tenui ISPaVe1792 tenui ISPaVe1770 tenui ISPaVe1783 tenui ISPaVe1788 tenui ISPaVe1789 tenui ISPaVe1790 tenui ISPaVe1798 tenui ISPaVe1786 tenui ISPaVe1773 alter ISPaVe1779 A. tenuissimaalter ISPaVe1782 A. arborescensarbor ISPaVe1793 arbor ISPaVe1768 arbor ISPaVe1778 arbor ISPaVe1771 arbor ISPaVe1772 arbor ISPaVe1794 arbor ISPaVe1780 arbor ISPaVe1791 arbor ISPaVe1784 arbor ISPaVe1787 arbor ISPaVe1776 arbor ISPaVe1774 arbor ISPaVe1722 arbor ISPaVe1795 arbor ISPaVe1797 arbor ISPaVe1775
Coefficient0.00 0.25 0.50 0.75 1.00
Hong et al., Mycological Research
A. infectoriaA. alternataalter ISPaVe1769 alter ISPaVe1796 alter ISPaVe1781 tenui ISPaVe1792 tenui ISPaVe1770 tenui ISPaVe1783 tenui ISPaVe1788 tenui ISPaVe1789 tenui ISPaVe1790 tenui ISPaVe1798 tenui ISPaVe1786 tenui ISPaVe1773 alter ISPaVe1779 A. tenuissimaalter ISPaVe1782 A. arborescensarbor ISPaVe1793 arbor ISPaVe1768 arbor ISPaVe1778 arbor ISPaVe1771 arbor ISPaVe1772 arbor ISPaVe1794 arbor ISPaVe1780 arbor ISPaVe1791 arbor ISPaVe1784 arbor ISPaVe1787 arbor ISPaVe1776 arbor ISPaVe1774 arbor ISPaVe1722 arbor ISPaVe1795 arbor ISPaVe1797 arbor ISPaVe1775
Coefficient0.00 0.25 0.50 0.75 1.00
Hong et al., Mycological Research
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EPPO- Q collection Rome 2015
TEF-1α
RAPDForty (40) strains of Fusarium oxysporum f. sp. melonis (FOM) characterized by race, RAPD profile and phylogeny to distinguish the 4 races by UPGMA with the Neighbor-joining analysis
Luongo L., Ferrarini A., Haegi A., Vitale S., Polverari A., Belisario A., 2015. Genetic Diversity and Pathogenicity of Fusarium oxysporum f. sp. melonis Races from different areas of Italy. Journal of Phytopathology, 163: 73–83. doi: 10.1111/jph.12280. ISSN: 1439-0434.
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EPPO- Q collection Rome 2015
Neighbor-joining analysis of Simple
Sequence Repeats (SSR) of 315 Italian
Fusarium fujikuroi isolates
Valente M.T., Infantino A., Desiderio F., Aragona M., 2013 Analysis of Fusarium fujikuroi genetic structure by SSR markers. Proceedings of the 12th European Conference on fungal genetics, Seville, March 23-27, 2014, Poster 414, page 277
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EPPO- Q collection Rome 2015
SA
12_T
2SA
15_T
2SA
11_T
2
83
SA19
_T2
SA23
_T2
SA13
_T2
61
SA24
_T2
63
SA9_
T2SA
10_T
2
99
SA25
_T2
SA26
_T2
98
SA20
_T2
SA14
_T2
I19_
T2SA
1_T2
SA2_
T2
75
SA3_
T2SA
4_T2
76
I16_T
2
I4_T2
I5_T2
I20_T
2
I1_T2
I6_T2
I10_T2
70 I11_T2
I13_T259
RB16_T
2
RB17_T2
95RB13
_T2
RB1_T2
RB2_T2
RB3_T2RB4_T2RB5_T2RB6_T2RB7_T2RB8_T2RB9_T2RB10_T2RB11_T2RB12_T2
61
51
RB15_T2RA16_T2RA17_T2RA15_T2RA14_T2
99
RA1_T2RA10_T2RA11_T2
RA12_T2RA9_T2
RA8_T2RA2_T2
RA3_T2
RA4_T2
RA6_T2
RA7_T2
RA13_T2
52
87
76
R3-18_T2
Is1361_T1
Is1447_T1
Is1448_T1
Is1362_T1
Is1363_T1
71Is1347_T1
Is1360_T1
Is1364_T1
Is1346_T1
Is1384_T1Is1449_T1Is1385_T1Is1446_T1Is1444_T1Is1445_T1
52SD
7_T2
SD8_
T2SD
9_T2
SD14
_T2
SD15
_T2
SD10
_T2
SD13
_T2
SD21
_T2
SD24
_T2
SD25
_T2
SD6_
T2
SD12
_T2
SD1_
T2
SD2_
T255
SD4_
T2
R3-20
_T2
R3-11
_T2
R3-14
_T1
R3-5_
T2R3
-6_T2
R3-2_
T2R3
-9_T2R3-
3_T2
R3-12_
T2 52R3-1_T
2R3-1
3_T2 59R3-1
6_T2R3-7_T2R
3-8_T2R3-15_
T1SB2_T1P
11_T2R3-10_T2R3-17_T2 63
SD3_T1SD5_T1
57
SD11_T1
88
RB14_T1I18_T1
RA18_T1
SB10_T1
SB17_T1
SB16_T1
SB4_T1
SB9_T1
84
SB15_T1
SB8_T1
SB7_T1
SB13_T1
5469
SA8_T1
I14_T1
P16_T1
P17_T1
89
P10_T1SB3_T1
P12_T1P13_T1
93
P4_T1P3_T1
P15_T1P9_T1
P7_T1P8_T1
P14_T165
81
0
2
4
6
8
10
Evolutionary relationships of 139 Pyrenochaeta lycopersiciisolates inferred using the Neighbor-joining method after AFLP analyses
Infantino A., Pucci N., Aragona M., De Felice S., Rau D. Genetic structure of Italian populations of Pyrenochaeta lycopersici causal agent of corky root rot of tomato. Plant Pathology 64, 941–950
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AFLP analysis of Xanthomonas arboricola pv. juglandis pathogenic on walnut
(104 strains in PAV-collection)
Loreti S., Gallelli A., Belisario A., Wajnberg E. and Corazza L., 2001. Investigation of genomic variability of Xanthomonas arboricola pv. juglandis by AFLP analysis. European Journal of Plant Pathology, 107, 583-591
EPPO- Q collection Rome 2015
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Gene-sequence analysis of genes involved in plant - pathogen interaction for developing a diagnostic method ofPseudomonas syringae pv. actinidiae (241 strains in PAV-collection)
Gallelli A., L’Aurora A. and Loreti S. , 2011. Gene sequence analysis for the molecular detection of Pseudomonas syringae pv. actinidiae: developing diagnostic protocols. Journal of Plant Pathology 93 (2): 425-435
EPPO- Q collection Rome 2015
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More than 300 isolates of 70 viruses, viroids and phytoplasmas are collected in our Institute since the 90’s
These species are pathogens of the major agricultural crops: vegetables, fruit trees, grapevine
PAV viruses, viroids and phytoplasmas collection
EPPO- Q collection Rome 2015
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Plum Pox Virus: M, D, EA, Rec, C strains
Peach Latent Mosaic Viroid: severe, mild and calico isolates
Flavescence Dorée: C and D isolates
Potato Spindle Tuber Viroid: tomato, Solanum jasminoides, Cestrum spp. isolates
Potato Virus Y: O, N, NTN, W strains
Viral pathogens of particular interest
EPPO- Q collection Rome 2015
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EPPO- Q collection Rome 2015
Strains are preserved following several methods suitable to the type of organism
For fungi:
Tubes with agarized medium (slants)Mineral oilWaterLiquid nitrogenFilter paper
For bacteria:
Maintenance at -80°C in glycerolFreeze-drying
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EPPO- Q collection Rome 2015
For phytoplasmas:
DNA extract maintained at -80°C Plant tissue freeze-drying
For viruses and viroids:
RNA/DNA extract maintained at -80°CPlant tissue freeze-dryingPreservation on plants
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EPPO- Q collection Rome 2015
To develop a PAV-collection catalogue on the web
To reach a continuity in maintenance and implementation of the collection
To have a curator fully dedicated to PAV-collection
Last but not least to have stable funding to support all the activities
About the future
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Thank you for your
attention!!
EPPO- Q collection Rome 2015
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