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BEN # 262

Adolf Ceska aceska at victoria.tc.ca
Sat Dec 23 12:41:53 EST 2000

BBBBB    EEEEEE   NN   N             ISSN 1188-603X
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BBBBB    EEEEEE   NN   N             NEWS

No. 262                              December 23, 2000

aceska at victoria.tc.ca                Victoria, B.C.
 Dr. A. Ceska, P.O.Box 8546, Victoria, B.C. Canada V8W 3S2


The  first  BOTANY  BC in the new decade, century and millennium
will take place in Smithers, BC (54 deg. 45' N, 127 deg. 10' W).
The activities will start on Thursday, July 26 (late  afternoon)
and end on Sunday, July 29, 2001. We will explore a wide variety
of  habitats  from  the valley bottom to alpine areas, from open
dry scrub-steppe to wetlands and old moist forests.  Illustrated
talks  will  include:  "Natural  history  of Bulkley Valley" (R.
Pojar); "Wetlands of British Columbia"  (W.  Mackenzie);  "Moon-
worts  by  daylight" (P. Williston); and "The all-embracing web:
mycorrhizae, mushrooms, and  you"  (M.  Kranabetter).  Look  for
details  and registration forms in an upcoming issue of BEN, and
mark those days in your calendar!

From: Scott Russell [srussell at ou.edu]

Scientists announced in _Nature_ that the  first  plant  genome,
that   of   _Arabidopsis   thaliana_   (aka   Mouse-ear   cress,
Brassicaceae), has been entirely sequenced as part of a monumen-
tal five country project that has involved  hundreds  of  scien-
tists, marking the culmination of research that was initiated in
1994.  This  was completed under budget and ahead of schedule by
four years. Completion of chromosomes 2 and 4  was  reported  at
the  end  of  last  year,  and with the release of sequences for
chromosomes 1, 3 and 5, the _Arabidopsis_ genome  is  completed.
The  announcement  was  made  in the December 14 issue of Nature
(released at 6 pm EST December 13 in North America).

The _Arabidopsis_ genome contains 130  Megabases,  encoding  ap-
proximately  25,500  nuclear  genes, 80 chloroplast genes and 60
mitochondrial genes. About 70 percent of the nuclear  genes  are
duplicated  within  the  code,  so there are about 15,000 unique
genes. The genome meets the same standard as the human genome of
having no more than one  mistake  per  10,000  base  pairs.  The
entire  genomic  sequence  is completed, annotated, released and
available in the public domain, on the  Internet.  As  with  the
human genome, no one has any proprietary right on the sequence.

The  significance of these data is that the _Arabidopsis_ genome
includes  all  of  the  information  needed  to   construct   an
_Arabidopsis_  plant. No matter that the plant is simple, incon-
spicuous and has never had economic impact outside of  its  role
as  a  genetic  model,  it still is representative of all of the
flowering plants, including crop plants. The major difference is
that the size  and  quick  generational  time  of  _Arabidopsis_
allows  a lot of plants to be grown and the results of any cross
to be available within less than two months. Further, the genome
size is among the smallest of flowering plants. The small genome
size also makes this plant among the easiest to transform, since
there are fewer redundant genes than a lot  of  organisms  have.
The  most  important  genes  in crop plants are expected to have
homologues in _Arabidopsis_ and vice versa.

Of course to all botanists and plant biologists, the  importance
is  obvious:  oxygen-breathing  animals  owe  their existence to
photosynthetic organisms. We now know how plants are made in the
barest (ACGT basepair) sense, but this is just the beginning  of
understanding  plant  complexity  and  variability.  As with all
science, what we do not know is more than what we do know (don't
tell legislators, they don't want to know this).  The  next  in-
itiative  in  this,  now, post-genomic period is NSF's so-called
"2010  Project"  to  determine  the  function  of   all   25,500
_Arabidopsis_  genes  over the next decade. This project is also
part of a worldwide effort and will be coordinated in a  similar
manner  to the genome sequencing project, with results similarly
publicly available.

Groups are currently working to establish _Arabidopsis_ microar-
rays -- glass slides with representatives of thousands of  genes
that  can  be  tested  against mRNA of different tissue types to
decipher the genes that are  active  at  a  given  developmental
stage  or  in  a  given  tissue. Another group is establishing a
collection of "gene knock-out" plants in which a single gene  is
genetically silenced in each of 25,500 plant lines so that there
is  a  knock-out  line  for  each  plant gene. Each promoter and
enhancer will also  be  identified  and  characterized.  Another
obvious  part  of  this project is proteomics -- the categoriza-
tion, identification and characterization  of  each  polypeptide
product  produced  by _Arabidopsis_. The current annual research
output on _Arabidopsis_ is nearly 2000 papers per  year  and  is
likely  to  accelerate.  I  presume that cryptographers are also
investigating genome sequences for hidden information  as  well,
as  is  underway  for  the  human  genome (a code is a code is a

Although this could be compared to Gray's  "Human  Anatomy,"  as
the  genome  will be the starting point for many future genetics
projects, it could also be rightly compared to a Rosetta  Stone,
which will require a lot of translation to reach its full poten-
tial.  Even  once  we understand of the genes, how they are con-
trolled will be as important as what the genes do.  Elements  of
how  plants control their genes will be held in common with crop
plants, other model animal systems  (like  nematodes  and  fruit
flies) and humans as well.

In  the  future,  are  possibilities  of using plants to produce
crops that have not yet been dreamed of. These could include for
instance higher yield crops for energy or amino acids  essential
to animals, crops with inborn disease and insect resistance that
will  reduce the need for pesticides and fungicides, plants that
can (perhaps in  combination  with  microbes)  metabolize  toxic
compounds,  and there are many other possibilities. Animal genes
could be introduced into plants, for example, to  cause  bananas
to  produce  vaccines  for the third world, or to produce animal
products (insulin?, human growth hormone?) in  plant  laticifers
for  mass  harvest  without  sacrificing  animals.  Genetically-
modified organisms will likely replace the chance experiments of
plant breeders that used to produce hybrid  seeds  in  the  past
through  crosses  of  entire  genomes,  but  can be more tightly
focussed to specific plant characteristics.

Some news stories and original press releases  are  as  follows:
-Nature:   http://www.nature.com/genomics/papers/a_thaliana.html
(includes a slide show describing the importance  of  the  work)
-NSF:   http://www.nsf.gov/od/lpa/news/press/00/pr0094.htm  
-San Francisco Chronicle:
-TAIR:  http://www.arabidopsis.org/genome_release.html 
(TAIR=The Arabidopsis Information Resource) (The links from TAIR 
allow the data to be accessed directly.)

For considerably more data on the project,  see  "Deciphering  a
Weed.  Genomic Sequencing of Arabidopsis" by Nancy Federspiel in
Plant Physiology (Plant Physiol, December 2000,  Vol.  124,  pp.
1456-1459), online at URL:
Her  account  provides a strategic view and provides information
about the molecular strategies used at each point in time.

The entire current issue of Plant Physiology is on _Arabidopsis_
and is currently available for free at URL:

From: Adolf Ceska [aceska at victoria.tc.ca]

_Bubbia  perrieri_  was  described  in 1963 based on a herbarium
specimen collected in Madagascar in 1909. Later  examination  of
the  type  specimen  led  to  the  description  of  a  new genus
_Takhtajania_ and the transfer of _Bubbia  perrieri_  into  this
new  genus in 1978. All we knew about _Takhtajania perrieri_ was
based on the 1909 herbarium collection. Since  1909  nobody  saw
one  living  plant  of this species, until in 1994, the Malagasy
plant collector Fanja Rasoavimbahoaka collected a flowering tree
in the Anjahanaribe-Sud Special Reserve southwest of Andapa. The
specimens were identified as _Takhtajania_ in late May  of  1997
by  Missouri Botanical Garden botanist George E. Schatz. The new
locality is 150 km from the original type locality.

_Takhtajania perrieri_ is the only member  of  the  family  Win-
teraceae in the Afro-Madagascan flora. The rediscovery of living
plants  of  _Takhtajania_  started  a multidisciplinary study of
this genus and its relatives from the  family  Winteraceae.  The
results  of  these  studies were published in a special issue of
the Annals of Missouri Botanical Garden 87(3)  with  eleven  ar-
ticles  on  various aspects of _Takhtajania_ and the Winteraceae

This single issue of the Annals of the Missouri Botanical Garden
87(3) is  available  from  the  MO  Botanical  Garden  Press  is
US$35.00  (plus US$6.00 to customers in Canada). All orders must 
be prepaid,  please contact  Brian Gardner  with  a credit  card 
number or send a check.

   Brian Gardner
   MO Botanical Garden Press
   4344 Shaw
   St. Louis MO 63110
   phone: 314-577-9534
   fax: 314-577-9591
   e-mail: mbgpress at mobot.org
   web site: http://www.mobot.org


I would like to thank all of you who  submitted  notes  and  ar-
ticles  to BEN in 2000. My thanks also go to all BEN readers for
their patience, to all BEN subscribers for remaining faithful to
BEN, and to all those, who know how and when to use  the  delete
button (although they may be gone by now). I have to thank to my 
ghost  writers whose English  is better than mine.  The Victoria 
Freenet Association has provided the Internet services that keep 
BEN alive, and  Dr. Scott Russell  has faithfully  served as the 
Chief Web Master. Poor man, he has to read every BEN issue  from
the beginning to the end.  Many thanks to all of you and all the 
best in the coming year.

                                               Adolf Ceska

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