Discussion

Dec. 18, 2012:

Dear Marc-Henri, Didier, Barbara and All-

One reason for voting now is that naming new taxa in this fungal group (and epitypifications etc.) cannot be done without a settlement for the rice blast.  Certain research and publications will be held up without knowing which name is accepted.  Another reason is that recent discussions on Magnaporthe/Pyricularia names started April 2012 during the CBS Amsterdam One Fungus Which Name symposium.  In the past 7 months, there have been 1,059 pageviews to the Magnaporthe blogger from 10 countries (ranked from most frequent: United States, Japan, France, Russia, India, Germany, Spain, China, Sweden, and South Korea), plus numerous email correspondence among this email group.

However, as you pointed out, a much broader community has not been reached.  I agree that the vote will be extended until after the March 2013 Fungal genetics meeting.  But I still suggest we forward the message through our networks as early as we can. I will send you the poll results next week, although it is not final, for your reference.  I temporarily set the new deadline to March 30, 2013.

Best Regards,

Ning

p.s., on March 13th, 2013 during the Fungal genetics meeting, a brief ad hoc session is planned (http://www.fungalgenetics.org/2013/pages/workshops.shtml) to discuss name changes for model systems. 
---------
Dec. 17, 2012:
 Dear Colleagues

I agree with Marc-Henri and Barbara that we should leave some time for discussion about such an important issue. Some meetings are coming where naming/renaming our favorite fungus could be discussed. Only part of the community had the opportunity to express. There's no hurry.

Regards
Didier



Dear Ning,

Thank you for taking the initiative on this important issue.  But I agree with Marc-Henri that Dec 23 is too short a time frame for a vote on the name of the blast fungus.  I for one am still grading finals and have not had a lot of time to focus on this during the last semester.  We have several key meetings coming up, including Asilomar and the International Rice Blast meeting in Korea, where we had planned discussions with the broader community.  Certainly, this distribution list is missing key people who must be involved in a final vote.

I had not understood that we MUST have an final answer by the end of the year.  What is the deadline for making this important decision and the critical factors that dictate that we meet this deadline?  I don't support a vote by Dec 23, less than a week from now.

Best regards,
Barbara

The 23 th of décember is a too early date for such a vote and it has been decided with out discussion within the community

I totally disagree with such methods
Which are not democratic at all
À shame

I propose to postpone this vote after
À discussion at asilomar

I Will contact The magna porte comittee
To have his advice on this

Mh lebrun
----------

From Yukio Tosa, 2 Dec. 2012:



Dear Magnaporthe researchers:

I agree with Dr. Oster, Dr. Chuma, Dr. Ning, Dr. Aoki, and Dr. Crouch. There is no doubt that Magnaporthaceae is composed of at least two separate clades to which different genus names should be given.

To adopt Magnaporthe as the genus name of blast fungi, therefore, several steps of procedures are needed as pointed out by Dr. Aoki and Dr. Crouch.
(1) To change the type species of Magnaporthe from M. salvinii to M. oryzae (or M. grisea).
(2) To transfer M. salvinii (and all other species in the M. salvinii clade) to a new genus.

They are not impossible, but require laborious works and extensive upheaval (as noted by Dr. Crouch). A simple solution is to adopt Pyricularia as the genus name of the blast fungi.

The genus names of this family should not be determined only by the blast researchers. We should consider opinions of researchers on M. salvinii, M. poae, Gaeumanomyces graminis etc.

Sincerely,


**********************************
Yukio TOSA
Graduate School of Agricultural Science
Kobe University
Nada, Kobe 657-8501, JAPAN
TEL: 078-803-6540
**********************************



From Dr. Jeff Oster on 12 November 2012:

I agree that stem rot and blast should not share the same genus name (I work with both diseases). Magnaporthe was established for the stem rot fungus, and so should be applied to that fungus. It is unfortunate that Magnaporthe has been applied to Pyricularia, but is untenable, despite common usage, since these fungi, based on molecular analysis, are not similar enough to be placed in the same genus. Even more common usage (and with longer precedent than Magnaporthe) is Pyricularia for the blast fungus. So, since taxonomy is moving to one name/one fungus (even though Pyricularia has been used to refer to the anamorph), Pyricularia should be used for blast fungi.
There has always been confusion over using perfect (sexual)/imperfect (asexual) names, and I guess, in practice, folks will use both names no matter what taxonomists do. Part of this is due to familiarity, and part due to the life stage that pathologists usually work with (i.e., Pyricularia because we all see the imperfect stage spores, but do not see the sexual stage).
Finally, P.oryzae  was segregated out from O. grisea since the two species cannot intermate, have genetic differences, and have different host ranges. So P. oryzae should be used for the rice-infecting pathogen. The fact that it goes to other hosts might create some confusion--it has with Fusarium fungi. But perhaps (assuming no discernable significant differentiation on each host similar to that for P. oryzae vs P. grisea) forma specialis could be used (not sure how in keeping this is with current taxonomic thinking).

Jeff Oster
Plant Pathologist
Rice Experiment Station
PO Box 306
955 Hwy 162
Biggs, CA 95917

530-868-5481
530-868-1730 (fax)
jjoster@crrf.org
 ---------------------
From:     Jin-rong Xu <jinrong@purdue.edu>
    Subject:     RE: Magnaporthe Names  http://magnaporthe.blogspot.com/
    Date:     October 18, 2012 8:46:08 AM EDT
     
Dear all,

I second Didier's opinion. 

I am copying this email to Dr. Steve Goodwin.  He also has done some phylogenetic analysis with the rice blast fungus. 

Sincerely,

Jin-Rong

*****************************************
Jin-Rong Xu, Ph.D.
Professor of Fungal Biology
Dept. of Botany and Plant Pathology
Purdue University
West Lafayette, IN47907
Tel: 765-496-6918
Fax: 765-494-5896
http://www.ag.purdue.edu/btny/Pages/jinrong.aspx
*****************************************


-----Original Message-----
From: Didier Tharreau [mailto:tharreau@cirad.fr]
Sent: Thursday, October 18, 2012 4:29 AM
To: 中馬 いづみ
Cc: Takayuki AOKI; Ning Zhang; JoAnne Crouch; Marc-Henri Lebrun; Sylvia Klaubauf; jing Luo; Elisabeth Fournier; Linda Kohn; Barbara Valent; Seogchan Kang; Xu, Jin-rong; dowalker@eden.rutgers.edu; Amy Rossman; Andrew Minnis; Scott Redhead; Lorelei Norvell
Subject: Re: Magnaporthe Names http://magnaporthe.blogspot.com/

Dear All,

We know that the genus Magnaporthe and Pyricularia need revision. This revision will require some changes in the names of some species, whatever the choice of the genus name.
As far as I understood the new nomenclature rules, the existence of the teleomorph for a given species is not really required. We know that some species of Magnaporthe/Pyricularia have a teleomorph and that the species in this group have probably lost the sexual reproduction but were sexually reproducing by the past. In addition, many fungal species thought to be asexual are shown to have a sexual stage.
If we consider historical facts to determine the name of rice blast and allies, then we should consider that since the 90s (more than 20 years) the rice blast community has adopted and used Magnaporthe and that there is an enormous literature that was produced during this period, probably more than during the 100 preceding years.

Sincerely
Didier



Le 18/10/2012 08:03, 中馬 いづみ a écrit :
Dear All,

I am Izumi Chuma, a Japanese researcher working on populations of
blast fungi. I have just made a phylogenetic tree of Pyricularia and
Magnaporthe, and want to share you my opinion.

I sequenced rDNA-ITS and RPB1 regions of 40 isolates belonging to 9
species of blast fungi, and added them to the phylogenetic tree
published by Zhang et al. (2011). This tree showed that two clades
(i.e. one including Pyricularia oryzae/grisea and the other including
Magnaporthe salvinii) are clearly separated with 99-100 % bootstrap
support. This result is consistent with Zhang et al. (2011).

I do not think that Magnaporthe is suitable as the genus name for
species of blast fungi with three reasons. First, there are several
blast species whose teleomorph have not been discovered, and
therefore, which do not have species names with Magnaporthe (e.g.
Pyricularia zizaniaecola, P. zingiberi, P. higginsii etc.). If
Magnaporthe is adopted as the genus name of blast fungi, several new
species must be described, which seems complicated.
Second, Pyricularia seems the best name for them because it represents
'pyriform', the common characteristics of conidia of blast fungi.
Third, historically, blast fungi have long been called as
“Pyricularia”, and “Pyricularia” is still familiar to agronomists in
Asian countries. In Japan, or probably in most asian countries too, we
have a long research history of rice blast disease and have used
“Pyricularia“. Most of researchers working on blast fungi know about
the story of their nomenclature. I do not want to erase the name
“Pyricularia“ and change the history.

I think that we should assign “Pyricularia” to the clade consisting of
blast fungi, and “Magnaporthe” to the other clade including
Magnaporthe salvinii, the type species of Magnaporthe. I hope that we
could choose the best name for blast fungi considering everyone's
opinion.

Sincerely,

Izumi Chuma

---------------------------------
Izumi Chuma Ph.D

Assistant Professor
Laboratory of plant pathology
Graduate school of Agricultural sciences Kobe university

1-1 Rokkodai cho, nada-ku
Kobe 657-8501, Japan
+81-78-803-6540
chuizm@kobe-u.ac.jp <mailto:chuizm@kobe-u.ac.jp>
---------------------------------





On 2012/10/17, at 8:29, Takayuki AOKI wrote:

Dear All,

I am feeling that the rice blast working groups are making really
constructive discussion on the theme.
I am honestly happy to monitor its progress.

Regards,

Takayuki

Subject: Re[2]: Magnaporthe Names http://magnaporthe.blogspot.com/
Ning Zhang wrote on Tue, 16 Oct 2012 09:40:03 -0400

Dear Takayuki,

Thanks very much for joining the discussion. I agree with you that
the rice blast workers/users should play a
major role in deciding which name to use. I personally also agree
with Jo Anne, Andrew Minnis and you, to simply follow the priority
and use Pyricularia for rice blast.

Hope the rice blast researchers/users will help making a decision soon.

Sincerely,

Ning


On Oct 16, 2012, at 5:08 AM, Takayuki AOKI wrote:

Dear Jo Anne-san, Didier-san, Ning and others,

I hope everthing goes well with you, at first.
My name is Takayuki AOKI, and I thank you very very much for your
inviting me to the so interesting discussion
on
rice blast nomenclature. I am very much happy to enjoy the process.

Because I am not a rice blast worker, but a taxonomist on Fusarium
species, a much complicated taxonomic group,
and
because I am considering that the rice blast problems should be
discussed and decided by rice blast workers, I
have
refrained to represent my own idea actively. But I was waching very
carefully about the progress of the discussion.

By obtaining the discussion from Jo Anne-san, I think now we have
both sides of opinions for Magnaporthe or for Pyricularia. Then, I
would also like to express my own idea on the matter from the view
point of a taxonomist, although I am still considering the rice
blast problems should be solved or descided by the rice blast
workers.

I am personally in favor of Jo Anne's idea. Consideting the
historical meaning of P. oryzae Cavara in 1892 is surely important,
I agree to this. But as a taxonomist, I am feeling that the current
requirement to achieve Magnaporthe as the unified rice blast name
is quite a complicated, laborious and unusual process. It is a
possible
way, but not so simple and easy to transfer the name, Magnaporthe
from its type species, M. salvinii to rice
blast
fungi. I recognized that we required at least three steps to
realize the renaming.

1) Recognistion of rice blast species (P. oryzae, P. grisea)
different from the type species of Magnaporthe,
i.e.
M. salvinii, required.

When both genera are phylogenetically identical, placing the name
Magnaporthe as their representative is
relatively
easy, although Pyricularia Sacc. (Michelia 2(no. 6): 20, 1880) has
its nomenclatural priority to Magnaporthe
R.A.
Krause & R.K. Webster (Mycologia 64(1): 110, 1972), based on simple
comparison of priority. But it is a
different
case. As indicated by Ning et al. (2011), Magnaporthe has its own
clade(s?; M. salvinii and M. poae + M.
rhizophila) and Pyricularia (P. grisea and related species) has its
own clade, and they should be recognized as different groups
(genera) phylogenetically.

2) Transfer of M. salvinii (and other species recognised as
Magnaporthe, except Pyricularia-connected species)
to
another genus (or other genera) required.

Based on the situation, and to transfer the name, Magnaporthe to
rice blast species, connection of the genus
name,
Magnaporthe with its type species should be cut and released. It
means that M. salvinii and probably all other Magnaporthe species,
except Pyricularia-connected ones, should be move to another genus
(or genera). Even if,
the
genus Magnaporthe is preexisting for its type species, M. salvinii,
another alternative genus (or genera)
should be
found or created. Former Magnaporthe species should be transferred
to the genus (or genera), otherwise the possible new Magnaporthe (=
Pyricularia) may still contain polyphyletic elements. (Or excluded
species from Magnaporthe may have no generic name for them.--- How
to call them???)

3) Change of the type species of Magnaporthe.
The type species of the genus name, Magnaporthe should be changed
nomenclaturally from M. salvinii to some rice blast species (P.
oryzae or P. grisea). All of the process should be discussed and
approved by NCF
(Nomenclature
Committee for Fungi) of IBC, and also by General Committee of IBC.
This change should probably be placed at Appendix of the Code.

After all of the process, we will firstly be able to call the rice
blast species Magnaporthe oryzae or M.
grisea as
the unified name, permanently. Pyricularia names for them will
become synonyms of them (not anamorphic names).

As a taxonomist, I feel the process was extremely complicated,
laborious and very unusual when compare with a normal taxonomic
process. However, when Magnaporthe (or rice blast) workers do not
mind to spend such effort, I have no wish to stop it but will admit
and encourage it. I hope it may go well, but I personally prefer to
call
rice blast species as Pyricularia, because of a simple new
discovery of the fact that the rice blast species
was
proved to be different from the type species of Magnaporthe, i.e.
M. salvinii. For me, personally it is much stable taxonomic
consequence to understand the fact.

I hope you could make fruitful discussion futher.

Sincerely yours,

Takayuki AOKI (a Fusarium worker)



Subject: Re[2]: Magnaporthe Names http://magnaporthe.blogspot.com/
Crouch, JoAnne wrote on Sun, 30 Sep 2012 17:30:45 +0000

Dear Ning et al.,

To extend Didier's discussion points about the rice blast pathogen
name:

As Didier states, the ICN might be petitioned to conserve the name
M. oryzae to accommodate community
preference
and the last decade of tradition. But, in practice, doing so would
trivialize the seminal contribution to
mycology
and plant pathology made by Fridiano Cavara with the original
description of this organism, as he was the first
to
collect and describe the rice blast pathogen as P. oryzae Cavara in
1892. This is an enduring contribution by
a
prominent mycologist. How can anyone justify stripping this away,
in favor of a name just ten years old? If
we
don't like the rules, should we be allowed to just set them aside
for convenience sake? Do we just throw out
names
(and the authors) and apply new ones? Should this sort of precedent
be established? Will we next replace
Koch's
Postulates with Monsanto's Postulates, in return for corporate
sponsorship? 100 years from now, will our own contributions to
science be similarly marginalized?

A further point to consider: Conservation of the name M. oryzae
over P. oryzae would be a complex undertaking,
and would require extensive upheaval to related species of
Magnaporthe, including several economically
important
plant pathogens. Of particular note are the recent findings of
Zhang and colleagues, where phylogenetic trees generated from a
large multilocus dataset showed that strains of P.
oryzae from rice and turfgrass form a
separate
linage relative to all other Magnaporthe, including the Magnaporthe
type species M. salvinii. This means that
P.
oryzae and P. grisea are not even true members of the genus
Magnaporthe! Consequently, conservation of M.
oryzae
would require that every true Magnaporthe species ィC including the
type species M. salvinii ィC would need to
be
renamed and placed into a new genus, and M. oryzae would need to
replace M. salvinii as the new type species
for
Magnaporthe. The entire generic concept of Magnaporthe would need
to be re-written ィC not based on
scientific
evidence, but to accommodate preference of a single research
community, and to give the Magnaporthe name to an organism that is
not even a member of that genus. Similarly, every true Pyricularia
species would need to be renamed as a Magnaporthe!

Confusion over the "correct" name for this organism has permeated
the literature throughout the 20th century,
and
even in recent years it is not uncommon to see the rice blast or
gray leaf spot pathogens referred to
incorrectly
as M./P. grisea. As someone outside of the Magnaporthe/Pyricularia
research community, I don't have an
investment
in any name, so it is perhaps easier for me to maintain distance
from the potential implications of a name
change.
Regardless of outcome, any transition is unlikely to please all
parties. But the current data is clear --
Couch
and Kohn showed that in 2002 that M. oryzae and M. grisea are
diagnosable as distinct species and M./P. grisea
are
limited to Digitaria hosts, and Zhang et al showed in 2012 that
Magnaporthe as typified by M. salvinii is diagnosable as distinct
from Pyricularia. In the end, why choose to rewrite history in an
elaborate,
artificial
manner when the rewrite would be inconsistent with the data?

Jo Anne

---
Jo Anne Crouch, Ph.D.
Research Molecular Biologist
Systematic Mycology & Microbiology Lab U.S. National Fungus
Collections (BPI) USDA-ARS
10300 Baltimore Avenue, Bldg 10A, Room 227 Beltsville, MD 20705
Cell: (609) 933-5496
Phone: (301) 504-5331
joanne.crouch@ars.usda.gov
<mailto:joanne.crouch@ars.usda.gov><mailto:joanne.crouch@ars.usda.
gov>

On Sep 26, 2012, at 10:28 AM, Didier Tharreau wrote:

Dear Ning,

I could not post the message below on the blog, so I send it to
the list directly.

"I agree with the idea that we should keep the genus name
/Magnaporthe/ for the different species from the
/Magnaporthe/Pyricularia/ clade that includes /M. grisea/ and /M.
oryzae/. This genus name has been adopted for more than 20 years by
a large community. The sexual stage of species in this group has
been produced at least
/in
vitro/. So, following previous Botanical code recommendations,, I
would be in favor of the use of the name of
the
sexual form. In my opinion, coming back to /Pyricularia/ as genus
mane has no major advantage and would rather
be
counter-productive. Then, we will have to discuss about species
names within this clade.

First, some species in this group do not yet have species name. As
much as possible, if the species is
pathogenic
to one host plant, we should try to use a fungal species name
derived from the host plant name. Second, I
suggest
that we change species names for /grisea/ and /oryzae/ because the
names have introduced some confusion. The
name
。ー/grisea/。ア was used in the past for the species that is now
called 。ー/oryzae/。ア, and。ア /oryzae/。ア
is confusing
because it suggests that the species is pathogenic to rice only,
which is not the case.

/Magnaporthe salvinii/, which belongs to a different clade, should
be renamed. /Sclerotium oryzae/ was already
used but /Sclerotium/ is likely polyphyletic (to be verified).
Other names exist: /Vakrabeeja sigmoidea/ var.
/irregularis/, /Nakataea sigmoidea/ (Cavara) Hara, (1939),
/Phragmaporthe salvinii/ (Catt.) M. Monod, (1983)
and
may be others. But it seems that /M. salvinii/ is part of the
Gaeumanomyces clade. So, renaming to
/Gaeumanomyces
salvinii/ is probably accurate.

//

/Magnaporthe poae/which belongs to another clade with/G.
incrustans /would also require renaming. Why not
using
/Magnaporthiopsis/ as proposed by N Zhang?

The Gaeumanomyces clade could stay /Gaeumanomyces."

/

Sincerely
Didier
//



Le 02/05/2012 23:59, Ning Zhang a ィヲcrit :
Dear Magnaporthe researchers,

As you might have known, the end of dual nomenclature for fungi
will have major impact on pleomorphic species.
For Magnaporthaceae, an important question that has to be addressed
is *which genus name should be used for the rice blast fungus*.

During and after the April 2012 CBS "One Fungus, Which Name"
symposium, I discussed this question with a
number
of mycologists, including Marc-Henri Lebrun (France), Sylvia
Klaubauf (CBS), Takayuki Aoki (Japan), Izumi Chuma (Japan),
Seogchan Kang (USA) and Amy Rossman (USA) etc. Several of you
encouraged me to initiate a discussion platform regarding
/Magnaporthe/ names. Therefore, I create a blog
(http://magnaporthe.blogspot.com/) for the purpose of discussion.
Please feel free to post any comments or information there, or send
any larger files to
me
to post for you.

If you have trouble opening the blog, or prefer other ways of
communication, please let me know. Meanwhile, we
can use the email list.

Sincerely,

Ning

Ning Zhang, Ph.D
Assistant Professor
Dept. of Plant Biology and Pathology Dept. of Biochemistry and
Microbiology Rutgers, The State University of New Jersey
59 Dudley Road, Foran Hall 201
New Brunswick, NJ 08901

phone: (848)932-6348
zhang@aesop.rutgers.edu
<mailto:zhang@aesop.rutgers.edu><mailto:zhang@aesop.rutgers.edu>
<mailto:zhang@aesop.rutgers.edu>
http://aesop.rutgers.edu/~plantbiopath/faculty/zhang/zhang.htm
<http://aesop.rutgers.edu/%7Eplantbiopath/faculty/zhang/zhang.htm>
<http://aesop.rutgers.edu/%7Eplantbiopath/faculty/zhang/zhang.htm>
http://aesop.rutgers.edu/~dbm/ningzhang.html
<http://aesop.rutgers.edu/%7Edbm/ningzhang.html>
<http://aesop.rutgers.edu/%7Edbm/ningzhang.html>
--

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UMR BGPI
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TA A 54 / K
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Batiment K, bureau 120

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[Tue, 16 Oct 2012 14:54:54 +0900]

Dr. Takayuki AOKI, Mycologist, Unit Leader

Classification and Evaluation Research Unit (responsible for
Microorganisms Section of the NIAS Genebank) Genetic Resources
Center (MAFF) National Institute of Agrobiological Sciences
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 JAPAN


[Wed, 17 Oct 2012 08:26:31 +0900]

Dr. Takayuki AOKI, Mycologist

Classification and Evaluation Research Unit Genetic Resources Center
(MAFF) National Institute of Agrobiological Sciences
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 JAPAN



--

***************************************************************
Didier THARREAU
UMR BGPI
CIRAD-BIOS
TA A 54 / K
Campus International de Baillarguet
34398 Montpellier Cedex 5

Batiment K, bureau 120