Natural rubber and the Russian dandelion genome

Natural rubber and the Russian dandelion genome The world needs rubber. Rubber is crucial for the tires on the cars, trucks and airplanes that propel modern transportation. It is equally important for daily tasks: latex gloves in the lab, balloons in angioplasty and wetsuits that warm a cold dip in the ocean. Rubber can be made synthetically from petroleum derivatives, but synthetic rubber is not as strong as rubber isolated from plants. The principal plant source for natural rubber (NR) is the sap of the Pará tree (Heveabrasiliensis), which is grown throughout Southeast Asia. Unfortunately, the production capacity of the Pará tree is limited by the availability of suitable land and by labor-intensive harvesting methods. The sustainability of the Pará crop is also constrained by its narrow genetic base, which may make the crop susceptible to disease. There is great interest in developing additional plant models for NR production. Thousands of plant species produce components of NR in their sap, but only a few produce high-molecular-weight rubber suitable for production. One such plant is the Russian dandelion, Taraxacum kok-saghyz (or TKS). Like other dandelions, TKS plants grow quickly, can be cultivated across a wide range of environments and are potentially easy to harvest. Research on TKS has already yielded important discoveries, such as the cloning and characterization of rubber biosynthesis genes [1]. In this issue, Lin et al. present the de novo assembly of the TKS genome [2]. The genome is not particularly large; at ∼1.2 Gb, it is one-half to one-third the size of the maize [3] and barley genomes [4]. It is, however, challenging to assemble, because the genome is both highly repetitive and highly heterozygous. To assemble the genome sequence, Lin et al. generated 48-fold coverage with PacBio long reads, 58-fold coverage with Illumina short reads and additional mate-pair data with varied insertion sizes. The resulting assembly yielded N50 contigs of 47 kb and scaffolds of 100 kb, which are smaller than some equally challenging, highly heterozygous genomes [5]. Nonetheless, the genome contains a fairly complete representation of coding regions, based on the presence of 92% out of 956 universal single-copy orthologs in the final assembly [6]. The hope is that the TKS genome assembly will accelerate breeding and provide additional insights into the genetics of rubber biosynthesis. Toward the latter, Lin et al. analyzed the copy number and expression of a set of 102 candidate rubber biosynthetic genes. They found that TKS and another rubber-producing plant (Hevea sp.) had higher copy numbers for some genic types than a related, non-rubber-producing species (globe artichoke). The genes with higher copy number were either in the mevalonate (MVA) pathway, which produces a critical rubber precursor, or involved in rubber elongation. By generating genome-wide expression data from 11 TKS tissues, Lin et al. were able to identify five of these genes that are predominantly expressed in roots and latex. Altogether, these observations identify a strong set of candidate genes that may form the basis both for further enhancement of TKS rubber production and also for establishing a viable NR alternative to the Pará tree. REFERENCES 1. Schmidt T, Hillebrand A, Wurbs D et al.   Plant Mol Biol Rep  2010; 28: 277– 84. CrossRef Search ADS   2. Lin T, Xu X, Ruan J et al.   Natl Sci Rev  2018; 5: 78– 87. 3. Jiao Y, Peluso P, Shi J et al.   Nature  2017; 546: 524– 7. PubMed  4. Mascher M, Gundlach H, Himmelbach A et al.   Nature  2017; 544: 427– 33. CrossRef Search ADS PubMed  5. Chin C, Peluso P, Sedlazeck FJ et al.   Nat Methods  2016; 13: 1050– 4. CrossRef Search ADS PubMed  6. Simão FA, Waterhouse RM, Ioannidis P et al.   Bioinformatics  2015; 31: 3210– 2. CrossRef Search ADS PubMed  © The Author(s) 2017. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png National Science Review Oxford University Press

Natural rubber and the Russian dandelion genome

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Publisher
Oxford University Press
Copyright
© The Author(s) 2017. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd.
ISSN
2095-5138
eISSN
2053-714X
D.O.I.
10.1093/nsr/nwx101b
Publisher site
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Abstract

The world needs rubber. Rubber is crucial for the tires on the cars, trucks and airplanes that propel modern transportation. It is equally important for daily tasks: latex gloves in the lab, balloons in angioplasty and wetsuits that warm a cold dip in the ocean. Rubber can be made synthetically from petroleum derivatives, but synthetic rubber is not as strong as rubber isolated from plants. The principal plant source for natural rubber (NR) is the sap of the Pará tree (Heveabrasiliensis), which is grown throughout Southeast Asia. Unfortunately, the production capacity of the Pará tree is limited by the availability of suitable land and by labor-intensive harvesting methods. The sustainability of the Pará crop is also constrained by its narrow genetic base, which may make the crop susceptible to disease. There is great interest in developing additional plant models for NR production. Thousands of plant species produce components of NR in their sap, but only a few produce high-molecular-weight rubber suitable for production. One such plant is the Russian dandelion, Taraxacum kok-saghyz (or TKS). Like other dandelions, TKS plants grow quickly, can be cultivated across a wide range of environments and are potentially easy to harvest. Research on TKS has already yielded important discoveries, such as the cloning and characterization of rubber biosynthesis genes [1]. In this issue, Lin et al. present the de novo assembly of the TKS genome [2]. The genome is not particularly large; at ∼1.2 Gb, it is one-half to one-third the size of the maize [3] and barley genomes [4]. It is, however, challenging to assemble, because the genome is both highly repetitive and highly heterozygous. To assemble the genome sequence, Lin et al. generated 48-fold coverage with PacBio long reads, 58-fold coverage with Illumina short reads and additional mate-pair data with varied insertion sizes. The resulting assembly yielded N50 contigs of 47 kb and scaffolds of 100 kb, which are smaller than some equally challenging, highly heterozygous genomes [5]. Nonetheless, the genome contains a fairly complete representation of coding regions, based on the presence of 92% out of 956 universal single-copy orthologs in the final assembly [6]. The hope is that the TKS genome assembly will accelerate breeding and provide additional insights into the genetics of rubber biosynthesis. Toward the latter, Lin et al. analyzed the copy number and expression of a set of 102 candidate rubber biosynthetic genes. They found that TKS and another rubber-producing plant (Hevea sp.) had higher copy numbers for some genic types than a related, non-rubber-producing species (globe artichoke). The genes with higher copy number were either in the mevalonate (MVA) pathway, which produces a critical rubber precursor, or involved in rubber elongation. By generating genome-wide expression data from 11 TKS tissues, Lin et al. were able to identify five of these genes that are predominantly expressed in roots and latex. Altogether, these observations identify a strong set of candidate genes that may form the basis both for further enhancement of TKS rubber production and also for establishing a viable NR alternative to the Pará tree. REFERENCES 1. Schmidt T, Hillebrand A, Wurbs D et al.   Plant Mol Biol Rep  2010; 28: 277– 84. CrossRef Search ADS   2. Lin T, Xu X, Ruan J et al.   Natl Sci Rev  2018; 5: 78– 87. 3. Jiao Y, Peluso P, Shi J et al.   Nature  2017; 546: 524– 7. PubMed  4. Mascher M, Gundlach H, Himmelbach A et al.   Nature  2017; 544: 427– 33. CrossRef Search ADS PubMed  5. Chin C, Peluso P, Sedlazeck FJ et al.   Nat Methods  2016; 13: 1050– 4. CrossRef Search ADS PubMed  6. Simão FA, Waterhouse RM, Ioannidis P et al.   Bioinformatics  2015; 31: 3210– 2. CrossRef Search ADS PubMed  © The Author(s) 2017. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Journal

National Science ReviewOxford University Press

Published: Jan 1, 2018

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