AsianScientist (Sep. 17, 2018) – The Genome Atlas of Bamboo and Rattan (GABR) project has yielded a new chromosome-level genome assembly of moso bamboo (Phyllostachys edulis) and two representative rattan genomes—Calamus simplicifolius and Daemonorops jenkinsiana. The results are published in GigaScience.
The GABR Consortium was established in 2016 by the International Center for Bamboo and Rattan in Beijing. It was initiated as an international, collaborative, non-profit initiative to generate genomics resources to help improve the conservation and utilization of the world’s bamboo and rattan resources. Covering nearly 2,000 species, the global bamboo and rattan trade is worth ∼US$60 billion and involves approximately 1.5 billion people worldwide in its use or production.
Using Illumina, PacBio and Hi-C sequencing data, the researchers were able to generate a chromosome-level genome assembly of moso bamboo. The same technology was applied to obtain the first two representative rattan genomes for C. simplicifolius and D. jenkinsiana, which together represent more than 95 percent of the canes produced by the rattan industry.
In addition, researchers constructed a comprehensive alternative splicing atlas for bamboo species. Combing large-scale transcriptomic sequencing of 26 representative bamboo tissues, they identified 266,711 unique alternative splicing events in 25,225 genes. These genes were found to be conserved in related plant species, were more highly expressed and less tissue specific in their pattern of expression.
Based on sequencing data and the alternative splicing atlas, the researchers also reported that genes involved in the lignin biosynthetic pathway in C. simplicifolius and D. jenkinsiana underwent gene family expansion as well as alternative and positive selection. They noted that the identification of genes associated with lignin synthesis could be useful in breeding desirable bamboo strains, primarily because lignin is critical for the growth and development of bamboo.
The data for all these genomes are provided in the GigaDB repository, alongside the sequencing and assembly protocols.
The article can be found at: Zhao et al. (2017) Announcing the Genome Atlas of Bamboo and Rattan (GABR) Project: Promoting Research in Evolution and in Economically and Ecologically Beneficial Plants.
Source: GigaScience; Photo: Pixabay.
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