Transcriptome sequencing discovers genes related to fatty acid biosynthesis in the seeds of Eucommia ulmoides

다국어 초록 (Multilingual Abstract)

Eucommia ulmoides is a focus of considerable attention because it is used to produce gutta-percha latex and raw materials for traditional Chinese medicine. The species has also been widely planted for vegetable oil production due to the high content of alpha-linolenic acid (ALA) in the seeds. However, little was known about fatty acid biosynthesis in the seeds. Here, we present transcriptome analyses that identified genes related to the fatty acid biosynthesis pathways in the seeds collected 70 and 160 days after flowering (DAF) from two varieties: ‘Huazhong No. 6’ (ALA content of 38.7 %) and ‘Huazhong No. 10’ (ALA content of 67.6 %). De novo assembly generated 96,469 unigenes with an average length of 690 bp. Among them, 11,260 unigenes identified by functional annotation against the Kyoto Encyclopedia of Genes and Genomes database were mapped to 117 metabolic pathways. 65 unigenes involved in fatty acid biosynthesis include 5 coding for 3-oxoacyl-ACP reductase, 2 coding for b-hydroxyacyl-ACP dehydratase, 10 coding for b-ketoacyl-ACP synthase II, and 2 coding for enoyl-ACP reductase I. Expression of the nine differentially expressed unigenes coding for major enzymes in fatty acid biosynthesis was validated by real-time fluorescent quantitative PCR (qPCR) using RNA from six seed stages (70, 88, 106, 124, 142, and 160 DAF) in ‘Huazhong No.
10’. The qPCR analysis showed that expression of these 9 unigenes all changed significantly at 88 DAF. This study provides a large-scale transcriptome annotation of E.
ulmoides, which is fundamental information for further characterizing gene functionals involved in the process of seed development.

참고문헌 (Reference)

1 Zhang L, "Transcriptomic identification and expression of starch and sucrose metabolism genes in the seeds of Chinese chestnut (Castanea mollissima)" 63 : 929-942, 2015

2 O’Loughlin A, "Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-Seq technology" 13 : 250-, 2012

3 Torales SL, "Transcriptome survey of Patagonian southern beech Nothofagus nervosa (=N. alpina): assembly, annotation and molecular marker discovery" 13 : 291-, 2012

4 Kimber MS, "The structure of (3R)- hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Pseudomonas aeruginosa" 279 : 52593-52602, 2004

5 White SW, "The structural biology of type II fatty acid biosynthesis" 74 : 791-831, 2005

6 Audic S, "The significance of digital gene expression profiles" 7 : 986-995, 1997

7 Call VB, "The fossil record of Eucommia (Eucommiaceae) in North America" 84 : 798-814, 1997

8 Sasaki Y, "The compartmentation of acetyl-coenzyme A carboxylase in plants" 108 : 445-449, 1995

9 Roesler K, "Targeting of the Arabidopsis homomeric acetyl-coenzyme A carboxylase to plastids of rapeseeds" 113 : 75-81, 1997

10 Chen R, "Selection of housekeeping genes for transgene expression analysis in Eucommia ulmoides Oliver using real-time RT-PCR" 2010

11 Iyer MK, "RNA-Seq unleashed" 29 : 599-600, 2011

12 Yang DH, "RNA-Seq liver transcriptome analysis reveals an activated MHC-I pathway and an inhibited MHC-II pathway at the early stage of vaccine immunization in zebrafish" 13 : 319-, 2012

13 Nakazawa Y, "Production of Eucommiarubber from Eucommia ulmoides Oliv. (Hardy Rubber Tree)" 26 : 71-79, 2009

14 Nikolau BJ, "Plant biotin-containing carboxylases" 414 : 211-222, 2003

15 Voelker T, "Plant acyl-ACP thioesterases:chain-length determining enzymes in plant fatty acid biosynthesis" 18 : 111-133, 1996

16 Sasaki Y, "Plant acety-CoA carboxylase: structure, biosynthesis, regulation, and gene manipulation for plant breeding" 68 : 1175-1184, 2004

17 Jones A, "Palmitoyl-acyl carrier protein (ACP) thioesterase and the evolutionary origin of plant Acyl-ACP thioesterases" 7 : 359-371, 1995

18 Mortazavi A, "Mapping and quantifying mammalian transcriptomes by RNASeq" 5 : 621-628, 2008

19 Wang Q, "Lower levels of expression of FATA2 gene promote longer siliques with modified seed oil content in Arabidopsis Thaliana" 31 : 1368-1375, 2013

20 Kanehisa M, "KEGG for integration and interpretation of large-scale molecular data sets" 40 : D109-D114, 2012

21 Nakazawa Y, "Histochemical study of trans–polyisoprene accumulation by spectral confocal laser scanningmicroscopy and a specific dye showing fluorescence solvatochromism in the rubber– producing plant, Eucommia ulmoides Oliver" 238 : 549-560, 2013

22 Zhou YH, "Genetic manipulation and gene engineering of fatty acid metabolism in plant seeds" 15 : 16-23, 1998

23 Altschul SF, "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs" 25 : 3389-3402, 1997

24 Grabherr MG, "Full-length transcriptome assembly from RNA-Seq data without a reference genome" 29 : 644-652, 2011

25 Duan XH, "Fatty acid and amino acid composition of Eucommia ulmoides oliver seeds" 31 : 214-217, 2010

26 Cao HP, "Developmental regulation of diacylglycerol acyltransferase family gene expression in tung tree tissues" 8 : e76946-, 2013

27 Shanklin J, "Desaturation and related modifications of fatty acids" 49 : 611-641, 1998

28 Dong SB, "Cloning, characterization, and expression analysis of acyl–acyl carrier protein (ACP)-thioesterase B from seeds of Chinese Spicehush (Lindera communis)" 542 : 16-22, 2014

29 Dormann P, "Cloning and Expression in Escherichia coli of a novel thioesterase from Arabidopsis thaliana Specific for long-chain acyl-acyl carrier proteins" 316 : 612-618, 1995

30 Salas JJ, "Characterization of substrate specificity of plant FatA and FatB acyl-ACP thioesterases" 403 : 25-34, 2002

31 Ohlrogge J, "Browse J(1995)Lipid biosynthesis" 7 : 957-970, 1995

32 Chen H, "Analysis of oil synthesis metabolism pathwanys based on transcriptome changes in tung oil tree’s seeds during three different development stages" 35 : 1403-1414, 2013

33 Shao W, "Alternative splicing and trans-splicing events revealed by analysis of the Bombyxmori transcriptome" 18 : 1395-1407, 2012

34 Konishi T, "Acetyl- CoA carboxylase in higher plants: most plants other than gramineae have both the prokaryotic and the eukaryotic forms of this enzyme" 37 : 117-122, 1996

35 Sun ZQ, "A novel silvicultural model for increasing biopolymer production from Eucommia ulmoides Oliver trees" 42 : 216-222, 2013

36 Reverdatto S, "A multisubunit acetyl coenzyme A carboxylase from soybean" 119 : 961-978, 1999