High-quality genomic study of a rubber plant

High-quality genomic study of a rubber plant COMMENTARIES Commentaries on research article by Lin et al. This study indeed demonstrates an attractive system for the The article “Genome analysis of Taraxacum kok-saghyz Rodin NR biosynthetic pathway. It also provides valuable resources provides new insights into rubber biosynthesis” by Lin et al.isa and new insights into the mechanism of NR biosynthesis. high-quality genomic study of a rubber plant [1]. This study therefore facilitates the development of a new NR- Natural rubber (NR) is a very important industrial material. producing crop. Characterization of the NR biosynthetic pathway is always of great interest. This study focuses on a perennial plant, Tarax- Bin Han acum kok-saghyz Rodin (TKS), which could be widely planted National Center for Gene Research, in high- and low-latitude climates. It is important that the roots Shanghai Institute of Plant Physiology and Ecology, of TKS produce a large amount of NR (up to ∼20% dry weight) Chinese Academy of Sciences, China in order that TKS can be used as a model plant for NR biosyn- Recommender of NSR thetic pathway studies. E-mail: bhan@ncgr.ac.cn The manuscript reports a high-quality draft genome of TKS with a total length of 1.29 Gb, containing 46 731 predicted REFERENCE protein-coding genes. In-depth analysis of the genome explores evolutionary tracks for two important families of CPT/CPTL 1. Lin T, Xu X and Ruan J et al. Natl Sci Rev, 2018; 5: 78–87. and REF/SRPP in rubber biosynthesis, and several key iso- National Science Review forms. The authors also do gene expression profiling in the latex, 5: 88, 2018 and predict crucial functions of the CPT/CPTL and REF/SRPP doi: 10.1093/nsr/nwx101a gene families in rubber biosynthesis. Advance access publication 27 November 2017 Natural rubber and the Russian dandelion genome The world needs rubber. Rubber is crucial for the tires on the In this issue, Lin et al. present the de novo assembly of the TKS cars, trucks and airplanes that propel modern transportation. genome [2]. The genome is not particularly large; at ∼1.2 Gb, It is equally important for daily tasks: latex gloves in the lab, it is one-half to one-third the size of the maize [3] and barley balloons in angioplasty and wetsuits that warm a cold dip in genomes [4]. It is, however, challenging to assemble, because the ocean. Rubber can be made synthetically from petroleum the genome is both highly repetitive and highly heterozygous. derivatives, but synthetic rubber is not as strong as rubber iso- To assemble the genome sequence, Lin et al. generated 48-fold lated from plants. The principal plant source for natural rubber coverage with PacBio long reads, 58-fold coverage with Illu- (NR) is the sap of the Parat ´ ree(Hevea brasiliensis), which is mina short reads and additional mate-pair data with varied inser- grown throughout Southeast Asia. Unfortunately, the produc- tion sizes. The resulting assembly yielded N50 contigs of 47 kb tion capacity of the Para´ tree is limited by the availability of and scaffolds of 100 kb, which are smaller than some equally suitable land and by labor-intensive harvesting methods. The challenging, highly heterozygous genomes [5]. Nonetheless, the sustainability of the Para´ crop is also constrained by its narrow genome contains a fairly complete representation of coding re- genetic base, which may make the crop susceptible to disease. gions, based on the presence of 92% out of 956 universal single- There is great interest in developing additional plant models copy orthologs in the final assembly [ 6]. for NR production. Thousands of plant species produce compo- The hope is that the TKS genome assembly will accelerate nents of NR in their sap, but only a few produce high-molecular- breeding and provide additional insights into the genetics of weight rubber suitable for production. One such plant is the rubber biosynthesis. Toward the latter, Lin et al. analyzed the Russian dandelion, Taraxacum kok-saghyz (or TKS). Like other copy number and expression of a set of 102 candidate rubber dandelions, TKS plants grow quickly, can be cultivated across biosynthetic genes. They found that TKS and another rubber- a wide range of environments and are potentially easy to har- producing plant (Hevea sp.) had higher copy numbers for some vest. Research on TKS has already yielded important discover- genic types than a related, non-rubber-producing species (globe ies, such as the cloning and characterization of rubber biosyn- artichoke). The genes with higher copy number were either thesis genes [1]. in the mevalonate (MVA) pathway, which produces a critical The Author(s) 2017. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd. All rights reserved. For permissions, plea se e-mail: Downloaded from https://academic.oup.com/nsr/article-abstract/5/1/88/4668756 by Ed 'DeepDyve' Gillespie user journals.permissions@oup.com on 16 March 2018 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png National Science Review Oxford University Press

High-quality genomic study of a rubber plant

Free
1 page

Loading next page...
1 Page
 
/lp/ou_press/high-quality-genomic-study-of-a-rubber-plant-I0fvw0WsSR
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/nwx101a
Publisher site
See Article on Publisher Site

Abstract

COMMENTARIES Commentaries on research article by Lin et al. This study indeed demonstrates an attractive system for the The article “Genome analysis of Taraxacum kok-saghyz Rodin NR biosynthetic pathway. It also provides valuable resources provides new insights into rubber biosynthesis” by Lin et al.isa and new insights into the mechanism of NR biosynthesis. high-quality genomic study of a rubber plant [1]. This study therefore facilitates the development of a new NR- Natural rubber (NR) is a very important industrial material. producing crop. Characterization of the NR biosynthetic pathway is always of great interest. This study focuses on a perennial plant, Tarax- Bin Han acum kok-saghyz Rodin (TKS), which could be widely planted National Center for Gene Research, in high- and low-latitude climates. It is important that the roots Shanghai Institute of Plant Physiology and Ecology, of TKS produce a large amount of NR (up to ∼20% dry weight) Chinese Academy of Sciences, China in order that TKS can be used as a model plant for NR biosyn- Recommender of NSR thetic pathway studies. E-mail: bhan@ncgr.ac.cn The manuscript reports a high-quality draft genome of TKS with a total length of 1.29 Gb, containing 46 731 predicted REFERENCE protein-coding genes. In-depth analysis of the genome explores evolutionary tracks for two important families of CPT/CPTL 1. Lin T, Xu X and Ruan J et al. Natl Sci Rev, 2018; 5: 78–87. and REF/SRPP in rubber biosynthesis, and several key iso- National Science Review forms. The authors also do gene expression profiling in the latex, 5: 88, 2018 and predict crucial functions of the CPT/CPTL and REF/SRPP doi: 10.1093/nsr/nwx101a gene families in rubber biosynthesis. Advance access publication 27 November 2017 Natural rubber and the Russian dandelion genome The world needs rubber. Rubber is crucial for the tires on the In this issue, Lin et al. present the de novo assembly of the TKS cars, trucks and airplanes that propel modern transportation. genome [2]. The genome is not particularly large; at ∼1.2 Gb, It is equally important for daily tasks: latex gloves in the lab, it is one-half to one-third the size of the maize [3] and barley balloons in angioplasty and wetsuits that warm a cold dip in genomes [4]. It is, however, challenging to assemble, because the ocean. Rubber can be made synthetically from petroleum the genome is both highly repetitive and highly heterozygous. derivatives, but synthetic rubber is not as strong as rubber iso- To assemble the genome sequence, Lin et al. generated 48-fold lated from plants. The principal plant source for natural rubber coverage with PacBio long reads, 58-fold coverage with Illu- (NR) is the sap of the Parat ´ ree(Hevea brasiliensis), which is mina short reads and additional mate-pair data with varied inser- grown throughout Southeast Asia. Unfortunately, the produc- tion sizes. The resulting assembly yielded N50 contigs of 47 kb tion capacity of the Para´ tree is limited by the availability of and scaffolds of 100 kb, which are smaller than some equally suitable land and by labor-intensive harvesting methods. The challenging, highly heterozygous genomes [5]. Nonetheless, the sustainability of the Para´ crop is also constrained by its narrow genome contains a fairly complete representation of coding re- genetic base, which may make the crop susceptible to disease. gions, based on the presence of 92% out of 956 universal single- There is great interest in developing additional plant models copy orthologs in the final assembly [ 6]. for NR production. Thousands of plant species produce compo- The hope is that the TKS genome assembly will accelerate nents of NR in their sap, but only a few produce high-molecular- breeding and provide additional insights into the genetics of weight rubber suitable for production. One such plant is the rubber biosynthesis. Toward the latter, Lin et al. analyzed the Russian dandelion, Taraxacum kok-saghyz (or TKS). Like other copy number and expression of a set of 102 candidate rubber dandelions, TKS plants grow quickly, can be cultivated across biosynthetic genes. They found that TKS and another rubber- a wide range of environments and are potentially easy to har- producing plant (Hevea sp.) had higher copy numbers for some vest. Research on TKS has already yielded important discover- genic types than a related, non-rubber-producing species (globe ies, such as the cloning and characterization of rubber biosyn- artichoke). The genes with higher copy number were either thesis genes [1]. in the mevalonate (MVA) pathway, which produces a critical The Author(s) 2017. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd. All rights reserved. For permissions, plea se e-mail: Downloaded from https://academic.oup.com/nsr/article-abstract/5/1/88/4668756 by Ed 'DeepDyve' Gillespie user journals.permissions@oup.com on 16 March 2018

Journal

National Science ReviewOxford University Press

Published: Jan 1, 2018

There are no references for this article.

You’re reading a free preview. Subscribe to read the entire article.


DeepDyve is your
personal research library

It’s your single place to instantly
discover and read the research
that matters to you.

Enjoy affordable access to
over 18 million articles from more than
15,000 peer-reviewed journals.

All for just $49/month

Explore the DeepDyve Library

Search

Query the DeepDyve database, plus search all of PubMed and Google Scholar seamlessly

Organize

Save any article or search result from DeepDyve, PubMed, and Google Scholar... all in one place.

Access

Get unlimited, online access to over 18 million full-text articles from more than 15,000 scientific journals.

Your journals are on DeepDyve

Read from thousands of the leading scholarly journals from SpringerNature, Elsevier, Wiley-Blackwell, Oxford University Press and more.

All the latest content is available, no embargo periods.

See the journals in your area

DeepDyve

Freelancer

DeepDyve

Pro

Price

FREE

$49/month
$360/year

Save searches from
Google Scholar,
PubMed

Create lists to
organize your research

Export lists, citations

Read DeepDyve articles

Abstract access only

Unlimited access to over
18 million full-text articles

Print

20 pages / month

PDF Discount

20% off