China obtained the first chromosomal-level rubber tree reference genome map

Xin'an Kunming, December 16th, reporters from China
Kunming Plant Research Institute was informed that by the Institute and Yunnan Province Institute of Tropical Crop Science, South China Agricultural University Genomics and Bioinsynatics Research Center composed of a joint research team, after 6 years, the use of single molecule real-time Sequencing (SMRT) and Hi-C technology, for the first time in the world to achieve chromosomal level of high-quality Brazilian rubber tree excellent varieties GT1 reference genome sequence, and reveal the chromosomal evolution of the geese plant genome, latex biosynthetic and rubber tree domestication.
rubber tree is a geese plant native to the Amazon basin of Brazil, South America, whose domestication began in 1896 and spread to countries such as Malaysia, Indonesia and Thailand. Of the approximately 2,500 rubber-producing plants in the plant community, rubber trees produce more than 98% of the world's natural rubber, with poly isoprene as the main functional component. China has 1.14 million hectares of rubber cultivation, the third largest in Asia (after Indonesia and Malaysia), but annual production of natural rubber is less than 20% of annual consumption, well below the internationally recognized safety line (30%). Since the beginning of the 21st century, Yunnan has ranked first in China in terms of total rubber tree planting area, total output and output per unit area.
, brazilian rubber tree species resources and genomics research is a hot area of international competition. Between 2013 and 2016, research teams in Malaysia, Thailand and China published four genome sketches of rubber trees using second- or second-generation and third-generation sequencing hybrid assembly techniques. However, the evolution of chromosomes in the genome of geese plants, why rubber trees can produce high latex and how rubber trees have been domesticated in the last century are still major scientific issues that have been outstanding for a long time in the study of rubber-producing plants;
Tropical Crop Species Resources and Genomics Yunnan Innovation Team Lead Scientist,
Kunming Plant Research Institute Researcher Gao Lizhi led the Yunnan Province Institute of Tropical Crop Science, China
Kunming Plant Research Institute and South China Agricultural University Genomics and Bioinnomics Research Center joint research team, after 6 years, with Huada Gene, the University of Washington, Harvard University On the basis of completing the second generation genome sequencing and assembly, the paper further overcomes the difficulties of large rubber tree genome, high hybridization and high repetition, and obtains the reference genome sequence of GT1, a high-quality Brazilian rubber tree variety with chromosome level for the first time in the world by using single-molecule real-time sequencing (SMRT) and Hi-C technology.
Compared with previously published genome sketches, genomics analysis showed that the genome map obtained by the study had been greatly improved in assembly accuracy and completeness, and that about 1.47Gb of genome sequences assembled had been mounted on 18 false chromosomes. At the same time, the study further confirmed that ancient multiply events occurred in the common ancestors of cassava genus and rubber genus, that chromosomal evolution models of geyser plants were first constructed through comparative genomic analysis at chromosomal levels, and that analysis of the reference genome sequence of the high-quality rubber tree revealed that, after differentiation with cassava genus, the rubber tree genome had three LTR reverse transcription transsortors in the last 10 million years. Rapid family eruptions increased the rubber tree genome by 890Mbp (about 60.44%), and the study identified gene families associated with the entire latex biosynthetic family, analyzed expression samples of latex biosynthetic pathways and important genes, and found significant expansion of genes associated with basic metabolic processes, ethylene biosynthetics, and polysaccharide and glycorotein coagulation activities associated with latex de-discharge.
addition, the study built the first accurate map of genomic variation representing wild and cultivated rubber trees, resulting in approximately 15.7 million high-quality SNPs. Although rubber trees have a history of domestication for more than a century, the study identified hundreds of domesticated-related candidate genes that have very low genomic diversity in cultivated rubber trees compared to wild rubber trees, some of which are closely related to the biosynthetic of latex.
The obtainion of the brazilian rubber tree as an important reference genome, the analysis of the latex biosynthic path, the construction of precise map of the genome variation of the wild rubber tree, and the understanding of the domestication of the cultivated rubber tree are of great significance to the protection, exploration and breeding of excellent rubber quality resources in China in the future.
the results were published in The Chromosome-base Rubber Tree Gene Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis, a leading international botany publication.