This article presents the genome sequence of
Ginkgo biloba,
the oldest extant tree species. The research was carried out by a team
of scientists at BGI, Zheijiang University and the Chinese Academy of
Sciences, who tackled and analyzed an exceptionally large genome,
totalling more than 10 billion DNA "letters." Ginkgo is considered a
"living fossil," meaning its form and structure have changed very little
in the 270 million years since it first came into existence. Given its
longevity as a species and unique position in the evolutionary tree of
life, the ginkgo genome will provide an extensive resource for studies
concerning plant defenses against insects and pathogens, and research
investigating early events in tree evolution and in evolution overall.
To study the ginkgo's extraordinary biology at a genetic and
molecular level, sequencing its genome was high up on the wish list of
plant biologists. However, because of its size as well as the presence
of an enormous number of repeat sequences, assembling the whole genome
sequence would be a difficult task. The ginkgo genome stretches over
more than 10 Gb, which is 80 times larger than the "model plant" Arabidopsis thaliana
genome. The tree's genome is also larger than other plant species known
for extremely big genomes, such as maize or orchids. The great interest
in the history and biology of gingko, however, made the work of
sequencing and assembling the genome a challenge the researchers from
China felt worth taking, and one they succeeded in accomplishing.
Wenbin Chen from BGI explains some of the difficulties that they had
to overcome: "A huge amount of raw data (~2 TB) was generated, and the
computing capability for genome assembly was challenged by both the huge
data and the remarkably high proportion of repetitive sequences. So an
incredible amount of memory was required." He went on to highlight
several genome features: "The large genome of ginkgo may have resulted
from whole genome duplication and insertion of a remarkably high
proportion of repetitive sequences, at least 76.58%, and the longest
introns among all sequenced species due to insertions of transposable
elements."
Meeting the sequencing challenge was worth it for a variety of
reasons. One certainly relates to its status as a "living fossil," at
title shared by few other species, including the horseshoe crab and the
nautilus. As the only surviving representative of a highly unusual group
of non-flowering plants that appeared at least 270 million years ago,
the ginkgo has retained traits over millions of years, such as the
emblematic fan-shaped leaves, that are not seen in any other surviving
plant species surviving. It further holds a very unique position in the
plant evolutionary tree.
Professor Yunpeng Zhao, one of the authors from Zhejiang University,
explains how this evolutionary placement is of great interest to
researchers: "Ginkgo represents one of the five living groups of seed
plants, and has no living relatives. Such a genome fills a major
phylogenetic gap of land plants, and provides key genetic resources to
address evolutionary questions like phylogenetic relationships of
gymnosperm lineages, evolution of genome and genes in land plants,
innovation of developmental traits, evolution of sex as well as history
of demography and distribution, resistance and conservation of ginkgo."
Researchers are also fascinated by the ginkgo's resilience under
adverse conditions -- it is worth noting that ginkgo trees were one of
the few living things to survive the blast of the atomic bombing of
Hiroshima. This hardiness likely helped the ginkgo survive periods of
glaciation in China that killed many other species, and may also promote
the longevity of individual trees, some living up to several thousand
years, according to reports. The ginkgo is also able to defend itself
against a wide range of attackers, employing an arsenal of chemical
weapons against insects, bacteria and fungi.
To better understand the ginkgo's defensive systems, the authors
analysed the repertoire of genes present in the genome that are known to
play a role in fending off attackers. An initial analysis of the tree's
more than 40,000 predicted genes showed extensive expansion of gene
families that provide for a variety of defensive mechanisms.
Genes that
enable resistance against pathogens are often duplicated. Additionally,
ginkgo has a double-knockout punch in its fight against insects by
synthesizing chemicals that directly fight insects and by releasing
volatile organic compounds that specifically attract enemies of
plant-eating insects. These findings indicated that having multiple
mechanisms -- the expansion of gene families, higher doses of specific
genes, and versatility in its defence genes -- might be linked to the
ginkgo's extraordinary resilience. This information may then be useful
to aid in understanding plant defence system with an eye to improving
food security.
