Why does bamboo grow fast?

Rapid growth is a key innovative trait of woody bamboo, enabling it to compete with other trees and adapt to the forest environment
.

- China Ke Xueyuan Kunming Institute of Botany plant diversity and genomics team leader, Germplasm Bank of Wild Species in Southwest China, director Li baht researcher

In the subtropical areas of southern China, the widely cultivated bamboo can reach up to 20 meters, while other species, such as the dragon bamboo in tropical Yunnan, are more than 30 meters high.

The young stalks of Phyllostachys pubescens, also known as "bamboo shoots", can grow up to 1 meter a day, which can be said to be the fastest growing plant, hundreds of times faster than other woody trees
.
Because of this, "spring shoots after the rain" is often used to describe the massive and rapid emergence of new things

Recently, China Ke Xueyuan researcher Kunming Institute of Botany Li baht team, Zhang Cheng Jun teamwork with the University of Chicago Professor Long Manyuan, carried out research of new gene functions of bamboo evolution

Bamboo is a good "model" for researching new genes and evolutionary innovation

The rice, wheat, corn, sorghum and a variety of pastures that humans depend on for survival, as well as important species such as reeds, awns, sugar cane and bamboo, all come from the grass family
.

"Grass is also the fifth major family of angiosperms, with about 770 genera and 12,000 species.
It is the most closely related to human production and life and the most economically valuable major family
.
" According to researcher Li Dezhu, the gramineous family is also important Its ecological value shows a wide range of ecological adaptability, from forests to grasslands, swamps to deserts, mountains to the Arctic

Bamboo is the general term for the bamboo subfamily of grasses in the forest ecosystem
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There are more than 1,600 species in the world .

The team led by researcher Li Dezhu has been devoted to the taxonomy, phylogeny and genomics research of bamboo for many years
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With the continuous deepening of research, research work has gradually expanded from woody bamboos in the bamboo subfamily to herbaceous bamboos and grass roots

Dr.
Ma Pengfei, associate researcher of the Kunming Institute of Botany, one of the first authors of the paper, introduced to reporters that as the bamboo subfamily, it is the only grass plant that diversifies into forest habits.
Bamboo includes four different ploidy plants with a chromosome base of 12 Branches, herbaceous bamboos are diploid, while woody bamboos such as giant dragon bamboo are allotetraploid or hexaploid.
These "excess" chromosomes are the material basis for genetic variation, which may promote woody The formation of unique characteristics of bamboo
.

Ma Pengfei said that compared with its related species in the Gramineae, woody bamboo has more evolutionary and innovative characteristics, such as fast-growing and lignified stalks, and underground stems with strong meristematic expansion ability
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Combining the previous research of the team showed that woody bamboo has generally experienced genome duplication events, and gene duplication is one of the most important ways for the origin of new genes, making bamboo an important model system for the study of new genes and evolutionary innovation

Fast-growing bamboo shoots, or "incubators" of new genes

Evolutionary innovation runs through the entire tree of life
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The flowers of angiosperms, the lungs of mammals, and the feathers of birds provide important prerequisites for them to develop and adapt to new niches

This is a basic question and an important challenge in evolutionary and developmental biology research
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"How to originate new traits has become a basic issue in evolutionary biology
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However, most studies have focused on the external environmental induction of innovation
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In recent years, more and more studies have shown that new genes are the main source of evolutionary innovation.
One of the driving forces
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" Researcher Li Dezhu said that almost all species contain a certain number of unique new genes, that is, orphan genes
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There are many ways to originate orphan genes, the most striking of which is the de novo origin, because de novo genes are a key role in driving evolutionary innovation
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Recent studies have also confirmed the real existence of de novo genes from rice plants of the same genus.
However, is this type of gene widespread in other plants? Does its evolution promote phenotypic innovation? How do orphan genes quickly affect the diversity of protein levels and their biological functions? These questions need to be answered by further research
.

The collaborative research team further discovered that of the 1,622 bamboo-specific orphan genes they identified over the past 46 million years, 19 evolved from non-coding ancestral sequences and reconstructed the entire process from scratch
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Four of these genes are also supported by protein evidence
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"These new genes, whether they originated from the beginning or not, are mainly expressed in fast-growing bamboo shoots, making the transcriptome of bamboo shoots appear the youngest in various bamboo tissues, rather than the youngest transcriptome of reproductive tissues as in other plants
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"Li Dezhu said
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Previous studies have shown that new genes are mainly expressed in reproductive organs, such as the pollen of angiosperms
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Interestingly, in bamboo, both orphan genes and de novo genes are highly expressed in fast-growing bamboo shoots, especially at the turning point of its rapid growth.
The fast-growing bamboo shoots may be the result of new bamboo genes.
” Incubator"
.

What are the main ways of origin of orphan genes? What is the biggest difference between it and non-orphan genes? Dr.
Jin Guihua, one of the first authors, introduced that orphan genes have many ways of origin, including gene "repeat-differentiation", transposon expansion, and de novo origin
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Compared with non-orphan genes, the biggest difference is that the gene coding sequence is short, the number of introns is small, the evolution rate is fast, the function is unknown, and the tissue-specific expression is more inclined
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"But it needs to be pointed out that not all orphan genes can promote evolutionary innovation
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" Jin Guihua said that after most orphan genes originate, they may not have functions, or even the ability to transcribe and translate into proteins.
Many orphan genes Even after the origin, it faces the fate of loss
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In a paper published in the journal Nature in 2012, a hypothesis called "protogenes" was proposed: these genes may be part of DNA at first, and their corresponding RNA and protein products did not have any function at first.

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However, under appropriate environmental conditions, these original genes can bring some advantages to organisms, and since then began to evolve under the action of natural selection, thus forming a new gene that promotes evolution and innovation
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A new cell type called long parenchyma has even evolved in woody bamboo with a clear phenotypic innovation, and the recent genome-wide duplication event provides the main source of new genes
.

New genes interact with repetitive sequence genes, allowing bamboo to grow quickly

"Previously, we knew very little about the genetic basis for the emergence of phenotypic novelty, although the connection between innovation and genome novelty and new genes has long been hypothesized
.
Recent studies have attributed phenotypic innovation to the evolution of new genes, thus Provides direct evidence for this hypothesis
.
"

In order to trace the phylogenetic origin of woody bamboo genes, the research team selected one herbaceous bamboo and three woody bamboos with sequenced genomes, as well as other 65 representative genomes on the tree of life, for systematic stratigraphic analysis
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The three woody species represent all three main lineages of the bamboo subfamily woody bamboo
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According to the trapezoidal phylogenetic tree, 12 phylogenetic levels are defined.
From the oldest cell organism to the youngest species specificity, a total of 50936 genes are assigned to the above 12 levels, and the number of genes at each level is positively correlated with gene age
.

The study also found that it is precisely because of genome-wide repetition events that repetitive genes are specifically and highly expressed in bamboo shoots "preferentially", and the formation time of most repetitive genes coincides with the repetition time of the woody bamboo genome
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"The new study found that the unique orphan genes of woody bamboo are highly expressed in the fast-growing stalks
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A copy of the gene produced by the genomic repetition event has expression-specific differentiation, and it is also highly expressed in the fast-growing stalks
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" Ma Pengfei said, These orphan genes and the repetitive genes expressing differentiation may work together to reshape the expression network of stem growth, thereby driving the formation of the innovative trait of rapid growth of bamboo stems
.

"This research provides a new perspective for the analysis of the genetic basis of the evolution of the unique characteristics of bamboo rapid growth, and also provides a brand-new example of how new genes act on the origin of new characteristics
.
" Li Dezhu said
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