Applications of Next-Generation Sequencing in Plants
Jingjing Jin, Limsoon Wong, Nam-Hai Chua
Plant metabolites are compounds synthesized by plants for essential functions,
such as growth and development (primary metabolites, such as lipid),
and specific functions, such as pollinator attraction and defense against
herbivores (secondary metabolites). Many of them are also used directly,
or as derivatives, to treat a wide range of diseases for humans.
There is thus much interest to study the biosynthesis of different
plant metabolites and improve their yield.
In this project, we apply next-generation sequencing techniques to
to investigate lipid and secondary metabolisms, as well as
to identify relevant DNA variations, in important crops.
- Reference-based genome assembly pipeline. The pipeline has good ability
to detect mis-assembled scaffolds, repeat scaffolds, etc. and properly
- Genome annotation pipeline. The pipeline has to annotate protein-coding
genes, small noncoding RNAs, long noncoding RNAs, etc.
- Comparative genome analysis pipeline. The pipeline has to identify
SNPs and other sites of variations in the input genomes.
- Gene expression analysis technique. The difficulties for this technique
include: 1/ It has to support wild-type vs mutant comparison. This extreme
small sample size renders most statistical approaches useless.
2/ It has to take into consideration tghe dependencies between
different metabolic pathways as metabolites are produced and
consumed in multiple pathways.
- Apply the above technologies to a few important crops.
NGS applications for plants
- Jingjing Jin, Jun Liu, Huan Wang, Limsoon Wong, Nam-Hai Chua.
PLncDB: Plant Long noncoding RNA Database.
Bioinformatics, 29(8):1068--1071, April 2013.
- Jingjing Jin, Deepa Panicker, Qian Wang, Mi Jung Kim, Jun Liu,
Jun-Lin Yin, Limsoon Wong, In-Cheol Jang, Nam-Hai Chua, Rajani Sarojam.
Next generation sequencing unravels the biosynthetic ability of
spearmint (Mentha spicata) peltate glandular trichomes
through comparative transcriptomics.
BMC Plant Biology, 14:292, November 2014.
- May Lee, Jun Hong Xia, Zhongwei Zou, Jian Ye, Rahmadsyah, Yuzer Alfiko,
Jingjing Jin, Jessica Virginia Lieando, Maria Indah Purnamasari,
Chin Huat Lim, Antonius Suwanto, Limsoon Wong, Nam-Hai Chua, Gen Hua Yue.
A consensus linkage map of oil palm and a major QTL for stem height.
Scientific Reports, 5:8232, February 2015.
- Jingjing Jin, Mi Jung Kim, Savitha Dhandapani, Jessica Gambino Tjhang,
Jun-Lin Yin, Limsoon Wong, Rajani Sarojam, Nam-Hai Chua, In-Cheol Jang.
The floral transcriptome of ylang ylang (Cananga odorata var. fruticosa)
uncovers biosynthetic pathways for volatile organic compounds and a
multifunctional and novel sesquiterpene synthase.
Journal of Experimental Botany,
66(13):3959--3975, July 2015.
- Mi Jung Kim, Jingjing Jin, Junshi Zheng, Limsoon Wong, Nam Hai Chua,
Comparative transcriptomics unravel biochemical specialization of leaf
tissues of Stevia for diterpenoid production.
Plant Physiology, 169(4):2462-2480, December 2015.
- Jingjing Jin, May Lee, Bin Bai, Yanwei Sun, Jing Qu, Rahmadsyah,
Yuzer Alfiko, Chin Huat Lim, Antonius Suwanto, Maria Sugiharti,
Limsoon Wong, Jian Ye, Nam-Hai Chua, Gen Hua Yue.
Draft genome sequence of an elite Dura palm and whole-genome
patterns of DNA variation in oil palm.
DNA Research, 23(6):527-533, December 2016.
- Jingjing Jin, Yanwei Sun, Jing Qu, Rahmadsyah, Chin-Huat Lim,
Yuzer Alfiko, Nur Estya Bte Rahman, Antonius Suwanto, Genhua Yue,
Limsoon Wong, Nam Hai Chua, Jian Ye.
Transcriptome and functional analysis reveals hybrid vigor for
oil biosynthesis in oil palm.
Scientific Reports, 7:439, March 2017.
NGS processing teachnologies
- Yuansheng Liu, Hui Peng, Limsoon Wong, Jinyan Li.
High-speed and high-ratio referential genome compression.
Bioinformatics, 33(21):3364--3372, November 2017.
- Liang Zhao, Qingfeng Chen, Wencui Li, Peng Jiang, Limsoon Wong, Jinyan Li.
MapReduce for accurate error correction of
next-generation sequencing data.
Bioinformatics, 33(23):3844--3851, December 2017.
This project is supported in part by
NRF CRP grant NRF-G-CRP-2997-04-082(d) and an
unrestricted gift of Temasek Lifesciences Laboratory.
Last updated: 28/11/17, Limsoon Wong.