High-precision genome unveils the relict species Ginkgo biloba

High-precision genome unveils the relict species Ginkgo biloba

High-precision genome unveils the relict species Ginkgo biloba High-precision genome unveils the relict species Ginkgo veil

Ginkgo Fruit Photo courtesy of Cao Fuliang

Ginkgo Fruit Photo courtesy of Cao Fuliang

As the only relict species of the gymnosperm Ginkgo, Ginkgo not only has special scientific research value, but also has important application value
.

Recently, Nanjing Forestry University and the Institute of Agricultural Genomics of the Chinese Academy of Agricultural Sciences published a chromosome-level ginkgo reference genome online in Nature-Plants, which is currently the highest-quality gymnosperm reference genome published
.

Cao Fuliang, the co-corresponding author of the paper and an academician of the Chinese Academy of Engineering, told the Chinese Journal of Science that this work provides a new perspective on the evolution of the gymnosperm genome
.

Relic plants that retain their original characteristics

Relic plants that retain their original characteristics

Gymnosperms, as a unique plant species, are mainly composed of four branches: Ginkgo, Cycas, Pine and Cedarwood
.

According to Yin Tongming, the co-corresponding author of the paper and a professor at the College of Forestry of Nanjing Forestry University, there are only 1 order, 4 families, 11 genera and about 124 species of Cycas
.

The Class Pines is the largest and most widely classified group of existing gymnosperms, with 4 orders, 7 families, 57 genera, and about 600 species

Ginkgo biloba Linn

In fact, the Ginkgo biloba was very prosperous in ancient times and was a species of the same age as the dinosaurs
.

Ginkgo plants appeared in the Late Carboniferous, reached their peak in the Jurassic and Early Cretaceous, and were widely distributed in the temperate regions of the Eurasian and North American continents

At present, there is only one species of Ginkgo in the class Ginkgo.

"All other species in this class are fossil plants

At the same time, ginkgo also has a variety of application values
.

Yin Tongming introduced that ginkgo is a fast-growing and precious timber species with excellent material.

At the same time, the ginkgo tree has a beautiful shape, the leaves are green in spring and summer, and turn yellow in autumn.
It is an important urban and garden greening tree
.

Huge and complex genome

Huge and complex genome

"The ginkgo genome is huge, heterozygous, and the content of repetitive sequences is extremely high, so it is difficult to obtain a high-quality ginkgo reference genome
.

" Cao Fuliang said

Yin Tongming told the Chinese Journal of Science that the human genome is relatively large, with more than 3 billion bases, while the ginkgo genome is three times more than the human genome, approaching 10 billion bases
.

Ginkgo has 12 pairs of chromosomes, while humans have 23 chromosomes.

"The whole genome sequencing of many gymnosperms has been completed internationally, including Norway spruce, loblolly pine, etc.

But mostly based on second-generation sequencing technology, the quality of genome assembly is not high
.

" Yin Tongming said

Hailin Liu, the first author of the paper, introduced that this work used the latest genome sequencing technology to obtain a 9.

87G reference genome map and assembled it on the 12 chromosomes of Ginkgo biloba
.
Accurately annotated 27832 ginkgo genome protein-coding genes, replacing the genes of the original draft genome, and it is the highest quality gymnosperm reference genome published so far
.

They found that the introns of the gene encoding Ginkgo biloba were significantly longer
.
"Other gymnosperms also have this phenomenon, and the introns of ginkgo coding genes are much longer than the introns of other gymnosperm coding genes that have been reported
.
" Liu Hailin said that there is no reasonable explanation for this phenomenon.
It is speculated that it may be related to the more active replication of repeated sequences
.

They further analyzed and discovered the mechanism of ginkgo genome expansion
.
"Whole-genome duplication events are the main reason for the expansion of plant genomes
.
" Yin Tongming said, but they confirmed that Ginkgo has only one whole-genome duplication event, which is different from previous research results
.

"Therefore, the expansion of the ginkgo genome is not mainly through genome-wide replication, but is mainly caused by the insertion and accumulation of long terminal repeats
.
" Cao Fuliang said, molecular evidence shows that the most recent outbreak of long terminal repeats was 8-12 Millions of years ago, it was issued after the Ginkgo genome replication event
.

Reveal the molecular mechanism of original features

Reveal the molecular mechanism of original features

After obtaining a high-quality genome map, they revealed the molecular mechanism of some of the original features of Ginkgo biloba
.

In 1896, Sakugoro Hiraze, a botanist at the University of Tokyo in Japan, discovered that ginkgo has multi-flagella motile sperm
.
Among seed plants, only Ginkgo biloba and Cycads retain the original feature of sperm flagella, showing the special status of Ginkgo biloba in evolution
.

"We analyzed more than 20 kinds of lower and higher plants and found that ginkgo, like lower plants, retains genes related to sperm flagella synthesis, and these genes are missing in other gymnosperms and angiosperms
.
" Yin Tongming said.

.

In addition, Ginkgo biloba is a crypto-flowered plant, and the flower organs such as petals, calyx, pistil, and stamen are not visible
.

By comparing the genome research, "We found that these led to the disappearance of floral organs or hidden because some key features missing genes"
.
Liu Hailin said
.

Ginkgo leaves have similar characteristics on both sides, without obvious polarity
.
Through further analysis, they found that the lack of multiple key genes related to leaf polarity in the ginkgo genome caused the key synthesis pathway to be blocked and the polarity characteristics could not be displayed
.

"This clarifies the genetic basis of the special floral organs and leaf polarity characteristics of Ginkgo biloba at the genomic level
.
" Cao Fuliang said
.

Related paper information: https://doi.
org/10.
1038/s41477-021-00933-x