De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments

被引:109
|
作者
Gahlan, Parul [2 ]
Singh, Heikham Russiachand [1 ]
Shankar, Ravi [1 ]
Sharma, Niharika [2 ]
Kumari, Anita [2 ]
Chawla, Vandna [1 ]
Ahuja, Paramvir Singh [2 ]
Kumar, Sanjay [2 ]
机构
[1] CSIR, Inst Himalayan Bioresource Technol, Council Sci & Ind Res, Studio Computat Biol & Bioinformat, Palampur 176061, Himachal Prades, India
[2] CSIR, Inst Himalayan Bioresource Technol, Div Biotechnol, Council Sci & Ind Res, Palampur 176061, Himachal Prades, India
来源
BMC GENOMICS | 2012年 / 13卷
关键词
Mevalonate; Gene expression; 2-C-methyl-D-erythritol; 4-phosphate; Next generation sequencing; Phenylpropanoid; Picrorhiza kurrooa; Picrosides; Transcriptome; ISOPRENOID BIOSYNTHESIS; GENE-EXPRESSION; MONOTERPENE BIOSYNTHESIS; ACID BIOSYNTHESIS; PLANT-METABOLISM; FACTOR FAMILY; HEAT-STRESS; GENOME-WIDE; ARABIDOPSIS; PATHWAY;
D O I
10.1186/1471-2164-13-126
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: Picrorhiza kurrooa Royle ex Benth. is an endangered plant species of medicinal importance. The medicinal property is attributed to monoterpenoids picroside I and II, which are modulated by temperature. The transcriptome information of this species is limited with the availability of few hundreds of expressed sequence tags (ESTs) in the public databases. In order to gain insight into temperature mediated molecular changes, high throughput de novo transcriptome sequencing and analyses were carried out at 15 degrees C and 25 degrees C, the temperatures known to modulate picrosides content. Results: Using paired-end (PE) Illumina sequencing technology, a total of 20,593,412 and 44,229,272 PE reads were obtained after quality filtering for 15 degrees C and 25 degrees C, respectively. Available (e. g., De-Bruijn/Eulerian graph) and in-house developed bioinformatics tools were used for assembly and annotation of transcriptome. A total of 74,336 assembled transcript sequences were obtained, with an average coverage of 76.6 and average length of 439.5. Guanine-cytosine (GC) content was observed to be 44.6%, while the transcriptome exhibited abundance of trinucleotide simple sequence repeat (SSR; 45.63%) markers. Large scale expression profiling through "read per exon kilobase per million (RPKM)", showed changes in several biological processes and metabolic pathways including cytochrome P450s (CYPs), UDP-glycosyltransferases (UGTs) and those associated with picrosides biosynthesis. RPKM data were validated by reverse transcriptase-polymerase chain reaction using a set of 19 genes, wherein 11 genes behaved in accordance with the two expression methods. Conclusions: Study generated transcriptome of P. kurrooa at two different temperatures. Large scale expression profiling through RPKM showed major transcriptome changes in response to temperature reflecting alterations in major biological processes and metabolic pathways, and provided insight of GC content and SSR markers. Analysis also identified putative CYPs and UGTs that could help in discovering the hitherto unknown genes associated with picrosides biosynthesis.
引用
收藏
页数:21
相关论文
共 50 条
  • [21] De Novo Sequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicum L.)
    Wang, Yi
    Wang, Chao
    Wang, Xiaolu
    Peng, Fan
    Wang, Ruijiao
    Jiang, Yulin
    Zeng, Jian
    Fan, Xing
    Kang, Houyang
    Sha, Lina
    Zhang, Haiqin
    Xiao, Xue
    Zhou, Yonghong
    INTERNATIONAL JOURNAL OF GENOMICS, 2016, 2016
  • [22] De Novo Assembly and Transcriptome Characterization of Canine Retina Using High-Throughput Sequencing
    Reddy, Bhaskar
    Patel, Amrutlal K.
    Singh, Krishna M.
    Patil, Deepak B.
    Parikh, Pinesh V.
    Kelawala, Divyesh N.
    Koringa, Prakash G.
    Bhatt, Vaibhav D.
    Rao, Mandava V.
    Joshi, Chaitanya G.
    GENETICS RESEARCH INTERNATIONAL, 2015, 2015
  • [23] De novo Sequencing, Assembly and Characterization of Antennal Transcriptome of Anomala corpulenta Motschulsky (Coleoptera: Rutelidae)
    Chen, Haoliang
    Lin, Lulu
    Xie, Minghui
    Zhang, Guangling
    Su, Weihua
    PLOS ONE, 2014, 9 (12):
  • [24] De Novo Transcriptome Sequencing of Serangium japonicum (Coleoptera: Coccinellidae) and Application of Two Assembled Unigenes
    Hu, Ya Hui
    Liu, Yong
    Wei, Lin
    Chen, Hao Tao
    G3-GENES GENOMES GENETICS, 2020, 10 (01): : 247 - 254
  • [25] De novo transcriptome sequencing of Camellia sasanqua and the analysis of major candidate genes related to floral traits
    Huang, Hui
    Xia, En-Hua
    Zhang, Hai-Bin
    Yao, Qiu-Yang
    Gao, Li-Zhi
    PLANT PHYSIOLOGY AND BIOCHEMISTRY, 2017, 120 : 103 - 111
  • [26] Transcriptome sequencing and de novo analysis of the northern snakehead, Ophiocephalus argus
    Mingsong Xiao
    Fangyin Bao
    Yan Zhao
    Qingsen Hu
    Journal of Genetics, 2019, 98
  • [27] De novo transcriptome sequencing of the thecate colonial hydrozoan, Dynamena pumila
    Kupaeva, Daria
    Konorov, Evgenii
    Kremnyov, Stanislav
    MARINE GENOMICS, 2020, 51
  • [28] Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon
    Michele Vidotto
    Alessandro Grapputo
    Elisa Boscari
    Federica Barbisan
    Alessandro Coppe
    Gilberto Grandi
    Abhishek Kumar
    Leonardo Congiu
    BMC Genomics, 14
  • [29] Sequencing, de novo assembly and comparative analysis of Raphanus sativus transcriptome
    Wu, Gang
    Zhang, Libin
    Yin, Yongtai
    Wu, Jiangsheng
    Yu, Longjiang
    Zhou, Yanhong
    Li, Maoteng
    FRONTIERS IN PLANT SCIENCE, 2015, 6
  • [30] De novo transcriptome sequencing of a non-model polychaete species
    Cannarsa, E.
    Zampicinini, G.
    Friard, O.
    Santovito, A.
    Cervella, P.
    MARINE GENOMICS, 2016, 29 : 31 - 34