The Scientist: Recent Top Genome Sequencing Results Top5
[Introduction] In view of the increasing attention paid to genomic research in recent years, The Scientist magazine has launched "Genome Digest" to share the latest popular genomic research results.
The Scientist magazine was founded in 1986 by Eugene Garfield, founder of the Institute of Scientific Information (ISI, now Thomson Reuters Technology Group), and later turned into a monthly magazine, accompanied by There are daily updated online news. It mainly publishes life science related information and helps scientists analyze research to help decision making affect their work life. In view of the increasing attention paid to genomic research in recent years, The Scientist magazine launched the "Genome Digest" to share the latest popular genomic research results.
Species: cultivated pineapple (Ananas comosus) and wild pineapple (A. bracteatus)
Genome: 526 million base pairs
Original title: The pineapple genome and the evolution of CAM photosynthesis
The results were completed by 17 research institutions including Fujian Agriculture and Forestry University, Chinese Academy of Sciences, and University of Illinois at Urbana-Champaign. The study demonstrated for the first time that the photosynthesis gene of sedum acid was developed by changing the regulatory sequences, which proved that the transposon is the main factor causing instability of the pineapple genome, and the pineapple genome can be used as a reference genome for all monocots. The research results have made a milestone contribution to the genetic improvement of global pineapple, and have important reference significance for the functional research and industrial development of a large number of monocots including grass crops.
Pineapple is the most important cash crop with photosynthesis metabolism (CAM) photosynthesis. The sedative acid metabolism pathway is a carbon-fixed pathway that is different from C3 plants and originated in arid regions with high water use efficiency. Compared with typical C3 plants, sedative acid metabolizing plants can save up to 80% of water, so they can grow in poor soil such as arid and poor. The other more than 10,000 species of CAM plants are distributed in 35 families, including agave, fairy palm, dragon fruit and most orchids. The pineapple genome was used to control the photosynthesis pathway of sedative acid metabolism, and all the genes involved in the sedative acid metabolism pathway were identified. This laid the foundation for subsequent genetic modification of photosynthesis of sedative acid in crops.
Beans with less "bean flavor"
Species: Vigna angularis
Genome: 542 billion base pairs
Original title: Genome sequencing of adzuki bean (Vigna angularis) provides insight into high starch and low fat accumulation and domestication
This achievement was also completed by Chinese scholars: researchers from the Beijing Agricultural College and the International Semi-Arid Tropical Crops Research Institute used the second-generation sequencing technology to complete the sequencing of the whole genome of the adzuki bean and assembled a high-quality genome map of the adzuki bean. The results showed that the adzuki bean had more than 34,000 genes. The researchers also analyzed the evolutionary relationship between adzuki bean and other known legume genomes, and the results showed that adzuki bean was most closely related to kidney bean.
The researchers sequenced and analyzed the genes of 49 wild adzuki beans, semi-wild adzuki beans and cultivated adzuki beans, and confirmed that the relationship between semi-wild adzuki beans and cultivated adzuki beans was close to that of wild adzuki beans, indicating that semi-wild adzuki beans were the initial farmer varieties during the domestication of adzuki bean.
Unlike other legumes such as soybeans, adzuki bean has a very low fat content of 0.59% on average, while the total starch content is high, averaging 57.06%. In contrast, the soybean starch content is 25.3% and the fat content is as high as 22.5%. New research suggests that differences in the transcriptional levels of related genes lead to these differences. At the same time, because the expression of lipoxygenase in the small bean is small, the bean flavor is less than other legumes, such as soybeans.
Species: Asian tiger mosquito (Aedes albopictus)
Genome: 1.97 million base pairs
Original title: Genome sequence of the Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution
After more than three years of unremitting efforts, the researchers of Southern Medical University and Huada Gene finally sequenced, assembled and annotated the Aedes albopictus genome, and combined with their transcriptome to analyze important gene families. The main findings were :
(1) Aedes albopictus has a huge genome, nearly 2Gb, which is the largest mosquito genome reported so far; the abundant gene reserve in the huge genome may be adapted to the environmental and climate changes of Aedes albopictus and spread to different parts of the world. And the spread of multiple pathogens provides a genetic basis.
(2) By comparing the genomes of different mosquitoes, it is found that the most important factor affecting the size of the mosquito genome is the proportion of the repeat sequences. The higher the ratio, the larger the genome.
(3) By comparing the composition of the repeat sequences (TE) in the Aedes albopictus and Aedes aegypti genomes, it was found that an important reason for the size differentiation of the two genomes was: the insertion rate of Aedes albopictus TE from 71 million years ago. Compared with Aedes aegypti, the rate of elimination is basically the same.
(4) For the first time, many arboviruses, including the insertion sequence of dengue virus, were found in the genome of Aedes albopictus. These may be the genetic basis of Aedes albopictus as a vector for many viruses, in order to further study the interaction between mosquito and pathogens. The mechanism provides clues.
(5) Through the re-sequencing of male and female mosquitoes of Aedes albopictus and comparative analysis of their transcriptomes at different developmental stages, the researchers have made breakthroughs in the male determinants of Aedes albopictus, and the relevant results have been published in Science, 2015; 348:1268 (The study was led by Zhijian Jake Tu of Virginia Tech, who is also the co-author of this PNAS article).
(6) Through the analysis of immune-related genes, insecticide-related genes, and diapause-related genes in the genome and transcriptome of Aedes albopictus, the researchers found that these important functional gene families have different degrees of expansion in Aedes albopictus. This may be related to the rapid spread of Aedes albopictus and as a vector for multiple infectious diseases, providing clues for further analysis. The results of this study provide a very useful platform for big data analysis for vector biology, genetic evolution and prevention of transmitted diseases in Aedes albopictus.
Wild ancestor of cattle
Species: European bison (Bos primigenius)
Original title: Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle
During the long evolutionary process, cattle evolved into approximately 260 different ethnic groups, types and varieties, all over the world. For example, North American wild cattle and Chinese yak. The wild ancestor of today's cattle is a carnivorous animal called Auroch. The early humans were afraid and worshipped the cows of the time, because the early cows had crescent-shaped horns, and the crescent-shaped horns were religious. Later, the cattle were domesticated to produce milk, which produced meat to meet human needs, and the application of castration and exfoliation greatly facilitated this domestication.
The last known Auroch died in Poland in 1627, but now researchers have extracted DNA from ancient bones of 6750 years old and reconstructed an aurochs genome for analyzing the evolutionary history of European cattle.
The researchers compared the genome of aurochs with the genome of modern cattle and found some evolutionary selection pressures for genes involved in neurobiology and muscle development, suggesting that early farmers domesticated the animals causing changes in cattle, and researchers also Aurochs and domestic cattle were found to have crossed in the UK and Ireland.
Species: Date palm tree (Phoenix dactylifera)
Genome: 690 million base pairs
Original title: Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop
Date palm is an important crop in the Middle East and North Africa. Researchers from New York University's Abu Dhabi campus have sequenced 62 different date palms. The plant was found to have been domesticated in the Middle East and its west, then spread to North Africa, or brought to North Africa.
The researchers found that 56 genomic regions in date palm were associated with selective stress, and one of the genetic mutations caused a change in fruit color (date palms produced red or yellow fruits), and this mutation and oil palm (Elaeis guineensis) Consistently, the two were divided about 60 million years ago.
(Jilin Qijian Biotechnology Co., Ltd. www.qjbio.com.cn)