| 其他摘要 | The great diversity of life forms has been continually stimulating the research
passion of biologists including Darwin. How the various form of life evolved from
the common ancestor is one of the basic questions of biology since the establishment
of evolution theory. With the discovery of central dogma and the development in
whole genome sequencing, evolutionary genomics, comparing the genome sequences
of different organisms to find the genetic changes along the evolution, became one of
the fundamental methodologies to find the answer of this question.
Comparing the genomes of different species, we can see that new gene
origination is a fundamental process during organism evolution. The new genes
constitute an important part of genetic novelties during the evolution of genome. A
lot of studies establish the duplication of old genes as the major way of new gene
origination. De novo origination, origin from non-coding sequence, was thought to
seldom happen. Jacob even stated that there is no de novo evolution in an influential
essay. Only recently, scientists found de novo gene in fruit fly. However, there is no
protein or functional evidence to support their predicted de novo genes. Here we find
a newly evolved de novo gene in baker’s yeast by comparing the genomes sequences
of its sibling species. And the functionality and coding capability of our de novo gene
is supported with population genetics, expression, proteomics and synthetic lethal
data. Based on the observation of expression of its ortholog sequences in sibling
species, we proposed a two step evolution model of de novo evolution: first a piece
of DNA sequence get transcribed via recruiting the transcription elements and
machine, followed by the transcribed sequence giving birth to a novel protein-coding
gene. Further analysis suggest that this de novo gene may be involved in DNA repair
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pathway during the stationary phase of baker’s yeast, and contribute to the robustness
of baker’s yeast, when shifted to nutrient-poor environment. The stationary phase is
also a process that happens during fermentation industry. The evolution of this de
novo gene may indicate important adaptation to the industry application of baker’s
yeast.
Giant panda is a unique kind of bear. It belongs to the clade of carnivores but its
major diet is bamboo. To adapt its diet, the sesame bone developed into a ―false
thumb‖ to help it manipulate the bamboo. How these traits evolved is still unknown.
Evolutionary genomics provide a method to find the answer to this question.
However, there is no whole genome sequence for giant panda. Using next-generation
sequencing technology alone, we have successfully generated and assembled a draft
sequence of the giant panda genome. Comparisons with the dog and human showed
that the panda genome has a lower divergence rate. The assessment of panda genes
potentially underlying some of its unique traits indicated that its bamboo diet might
be more dependent on its gut microbiome than its own genetic composition.
Oryza longistaminata, a wild rice is close relative of cultivated rice, both
belonging to the AA genome group. This wild rice has many important features for
rice improvement, such as pereniality, self-incompatbility, diseases resistance,
allelopathy, etc. Decoding the genetic mechanisms underlying there features is very
important for us to establish similar features in cultivated rice. We sequenced and
assembled the draft genome sequence of Oryza longistaminata. By comparing with
the rice reference genome and the previous mapping result, we found several
genomic regions for the two important traits, rhizome and self-incompatibility. Our
results provide candidate genes for further confirmation experiment. And the draft
genome generated is useful for further study on the mapping and clone of other
important traits. |
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