Tempo news magazine 48/XXXVIII 18-24 January 2010, pages 47-48

** Creating identity cards for plants **

By: Kurniawan

  LIPI and Harvard researchers are identifying the plants of Gunung
  Palung National Park using DNA, then uploading these data to the
  Internet. This is the first step to sharing this information for all.

THREE women were gathered around the glass fumehood in a
laboratory. Their hands deftly filled small tubes with a liquid
dripped from a pipette. On the tubes were written reference numbers
from collections made at Gunung Palung National Park, West
Kalimantan. The researchers were extracting deoxyribonucleic acid
(DNA) from the samples.

Such activity was typical of work conducted at the Biosystematics
Laboratory, Center Research in Biology, Indonesian Institute of
Sciences, Cibinong, Bogor, on Tuesday last week.  The goal of the work
that day was to determine the DNA sequences from the plant
samples. "Having sequenced its DNA, the plant collection was stored in
the herbarium," said Teguh Triono, Head of Taxonomy and Systematics
Research in the Herbarium Bogoriense.

Herbarium Bogoriense now stores 2.5 million species of plants,
collected since 1817 by Caspar Georg Carl Reinwardt, founder of the
Botanical Gardens, Bogor. However, only 14,000 specimens have been
digitized and displayed on the site, http://ibis.biologi.lipi.go.id,
"because we have few staff and data entry is a slow process. Running
smoothly, one person might enter the data from 30 plants in one day,"
said Teguh.

At this time, Teguh is working with Campbell O. Webb, a senior
researcher at the Arnold Arboretum of Harvard University, on a
pioneering project to collect and create the DNA barcodes for the
whole flora of Gunung Palung. They are assisted by Rani Asmarayani, a
LIPI researcher who deals with DNA extraction and sequencing, and,
among others, students from IKAHIMBI (the Association of Indonesian
Biology Student Associations).

This inventory is important because Indonesia has the highest
biological diversity in the world. Teguh estimates that there are
31,000 types of higher plants in Indonesia, not including mushrooms
and mosses.

All the field findings from Gunung Palung and the collection at
Herbarium Bogoriense are converted to a digital form and published via
the Internet. "With the data on the web, scientists in other parts of
the world can study it too," said Teguh.

One difficulty in the inventory of plants in Indonesia, said Teguh, is
that species have not yet been collected and identified from many
areas. By sharing information through this web site, we hope
taxonomists or experts in different areas can complement each other's
work.

Webb and Teguh even propose the need for social networking site, or a
special Wiki, for biodiversity. On a community site people could
contribute to each others' online plant collections, including update
the data. These "citizen scientists" can help to observe and collect
plants in their vicinity, as has been done by amateur birdwatchers,
who have contributed very important data on the distribution of birds
in the United States and Europe.  South Africa also held an ant
research project last year, which involved 3,000 students from 13 high
schools.

One important aspect of the project is that they start from field
collections at Gunung Palung. And this January turns out to be the
most important month for collecting. "Right now there is a rare
fruiting season (a mast) for dipterocarps, which happens only every
five years or longer in these forests of Kalimantan.  Over a duration
of four months, we can see complete reproductive cycle of plants, from
flowers to fruit," said Webb, who worked on the current project there
since November 2008.

The plant family of meranti or dipterocarpa (Dipterocarpaceae) is a
tropical plant group whose members are commonly used for timber, and
includes meranti, keruing, mersawa, kapur, and tengkawang.  Members
of the family are usually large trees with heights up to 70-85 meters.
Because many are exploited, some tree species of this family are
listed in the "red list" of the International Union for Conservation
of Nature (IUCN) as endangered species, such as some types of kruing,
kapur, yellow meranti, red meranti, and meranti batu.

Gunung Palung is an area of about 90,000. There are various forest
types, from swamps and lowland forest to montane forest at the peak of
Gunung Palung (ca. 1,116 meters ASL). This park is home to orangutans
and many species of hornbills. For most of the time since the park was
gazetted in 1937 the majority of the area has not been disturbed by
man, except by those collecting of firewood or gaharu
(eaglewood). However, since 1995 the park has been threatened by
illegal loggers seeking dipterocarps along major rivers that lead into
the park.

Webb and Teguh share the work. Webb, assisted by parataxonomists
(trained technicians), National Park forest rangers, and local
community members, seeks out and collects specimens of plants, which
are photographed and sent to Bogor.  Important for this project is
that collections of plants must be complete with leaves, and flowers
or fruits.

"These specimens are like identity cards," said Teguh. They have
names, photographs, and other information. "If the the specimen has
fruit, flowers, and leaves, we can usually identify it to species, and
then use that as a starting point for making DNA barcoding library."

LIPI wants Indonesia to conduct this kind of project. But Teguh
admitted that for cost efficiency some samples were sent to Macrogen
in South Korea (for sequencing only). "We've got the tools, but our
speed is limited to only 4 samples per 2 hours. And we need to go
faster," he said.

Up to now more than 500 samples have been collected at Gunung
Palung. Of these collections, 228 plants have been DNA sequenced. The
mixing of taxonomy with DNA sequencing (DNA barcoding) is still a new
step in the world of taxonomy.

DNA barcoding for taxonomy was first promoted in 2003 by Paul
D.N. Hebert, a professor at the University of Guelph in Ontario,
Canada. He proposed the creation of a public library of DNA barcodes
linked with the specimens. This library is hoped to be a vital part of
the process of identifying species.  Later, scientists established
Barcode of Life Initiative (IBoL), which encourages scientists use DNA
barcoding as a standard part of their research. So far the consortium
for this initiative (CBoL) consists of 170 institutions in more than
50 countries, including universities, herbaria, zoos, botanical
gardens, government agencies, and conservation organizations.

This particular barcode contains 640 base pairs of DNA (represented by
the letters A, C, G, and T). This is just a small part of the billions
of base pairs that make up the entire genome of the organism. But this
small piece is considered enough to give the identity of a plant or
animal. DNA barcodes can only be used to identify the specimen, and
not for medical purposes such as developing pharmaceuticals. So far in
the database at Barcode of Life Data Systems there are 65,578 species
with official barcodes, from a total of 768,707 records.

The benefits of plant databases, said Teguh, are many, for example, to
determine the type of timber after logging activities. "If we want to
know what kind of the wood it is, we can extract the DNA from the
timber.  DNA sequences can then be matched with our database. The
process takes only two weeks, including the travel of specimens from
the site to our lab," said Teguh.

Before now, we needed complete, physical plant collections, which we
used to observe the plant's structure. With only fragments of a plant,
"sometimes we could just get to the determination of the genus, or
even family or tribe. More specific than that was hard, "he said.

Webb and his team also take 10-20 high-resoultion pictures of each
plant they collect.  Photographs of plants in their fresh state are
valuable for taxonomists because the original colors are clear, and
certain plant parts, such as hairs on the stem or other features are
still recognizable. Color is lost when specimens are dried and put
into a herbarium.

All the plants' information, including photographs and DNA barcodes,
are then uploaded to the Xmalesia website
(http://phylodiversity.net/flora-tngp/).  Malesia is the biological
region containing Indonesia, Malaysia, Singapore, Brunei, Philippines,
and Papua New Guinea.  The website data can also be used to analyze
phylogenetic community structure, and the relationship between groups
of organisms based on the underlying evolutionary processes.

One advantage of sharing data and image information on the Internet is
that it can speed up the finding of new plant species. After the data
was uploaded to the web, experts who saw the data told the team that
three species were probably new to science. One species was kind of
pandan, and another was a Hoya, a vine with flowers as big as a thumb
that they found by the river near where they bathe. "We knew it was a
Hoya, but do not know the type. When we put it on the site, there was
a Hoya expert from Italy who said that this is a new Hoya species,"
said Teguh.

According to the Teguh, this database is also important to know how
much of Indonesia's biodiversity is being lost to extinction. "Two
species of seaweed in Java, for example, have already been lost. I did
a survey with the Indonesian Institute of Oceanography; in our
herbarium is a note that a certain two types of plants had been found
on the north coast of West Java and East Java. Now they are gone," he
said.

[Originally posted at: http://majalah.tempointeraktif.com/id/arsip/
2010/01/18/ILT/mbm.20100118.ILT132491.id.html]