De novo assembly of Zea nicaraguensis root transcriptome identified 5 261 full-length transcripts

doi:10.1016/S2095-3119(15)61153-4

Journal of Integrative Agriculture ›› 2016, Vol. 15 ›› Issue (06): 1207-1217.DOI: 10.1016/S2095-3119(15)61153-4

De novo assembly of Zea nicaraguensis root transcriptome identified 5 261 full-length transcripts

JIANG Wei^{1, 2}, LIU Hai-lan¹, WU Yuan-qi¹, ZHANG Su-zhi¹, LIU Jian¹, LU Yan-li¹, TANG Qi-lin¹, RONG Ting-zhao¹

¹ Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
² Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R.China

收稿日期:2015-04-07 出版日期:2016-06-01 发布日期:2016-06-06
通讯作者: TANG Qi-lin, Tel: +86-28-86290916, Fax: +86-28-86290912, E-mail: tangqilin71@163.com
基金资助:
This work was supported by the Basic Research Program of China (973 Program, 2014CB138705), the National Natural Science Foundation of China (31371639) and the Sichuan Youth Science and Technology Foundation of China (12ZB091).

De novo assembly of Zea nicaraguensis root transcriptome identified 5 261 full-length transcripts

JIANG Wei^{1, 2}, LIU Hai-lan¹, WU Yuan-qi¹, ZHANG Su-zhi¹, LIU Jian¹, LU Yan-li¹, TANG Qi-lin¹, RONG Ting-zhao¹

¹ Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
² Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R.China

Received:2015-04-07 Online:2016-06-01 Published:2016-06-06
Contact: TANG Qi-lin, Tel: +86-28-86290916, Fax: +86-28-86290912, E-mail: tangqilin71@163.com
Supported by:
This work was supported by the Basic Research Program of China (973 Program, 2014CB138705), the National Natural Science Foundation of China (31371639) and the Sichuan Youth Science and Technology Foundation of China (12ZB091).

摘要/Abstract

Abstract: Zea nicaraguensis, a wild relative of cultivated maize (Zea mays subsp. mays), is considered to be a valuable germplasm to improve the waterlogging tolerance of cultivated maize. Use of reverse genetic-based gene cloning and function verification to discover waterlogging tolerance genes in Z. nicaraguensis is currently impractical, because little gene sequence information for Z. nicaraguensis is available in public databases. In this study, Z. nicaraguensis seedlings were subjected to simulated waterlogging stress and total RNAs were isolated from roots stressed and non-stressed controls. In total, 80 mol L^–1 Illumina 100-bp paired-end reads were generated. De novo assembly of the reads generated 81 002 final non-redundant contigs, from which 5 261 full-length transcripts were identified. Among these full-length transcripts, 3 169 had at least one Gene Ontology (GO) annotation, 2 354 received cluster of orthologous groups (COG) terms, and 1 992 were assigned a Kyoto encyclopedia of genes and genomes (KEGG) Orthology number. These sequence data represent a valuable resource for identification of Z. nicaraguensis genes involved in waterlogging response.

Key words: Zea nicaraguensis , teosinte , RNA-Seq , full-length transcript

JIANG Wei, LIU Hai-lan, WU Yuan-qi, ZHANG Su-zhi, LIU Jian, LU Yan-li, TANG Qi-lin, RONG Ting-zhao. De novo assembly of Zea nicaraguensis root transcriptome identified 5 261 full-length transcripts[J]. Journal of Integrative Agriculture, 2016, 15(06): 1207-1217.

参考文献

Abiko T, Kotula L, Shiono K, Malik A I, Colmer T D, Nakazono M. 2012. Enhanced formation of aerenchyma and induction of a barrier to radial oxygen loss in adventitious roots of Zea nicaraguensis contribute to its waterlogging tolerance as compared with maize (Zea mays ssp. mays). Plant Cell and Environment, 35, 1618–1630.

Atwell B J, Drew M C, Jackson M B. 1988. The influence of oxygen deficiency on ethylene synthesis, l-aminocyclopropane-1- carboxylic acid levels and aerenchyma formation in roots of Zea mays L. Physiologia Plantarum, 72, 15–22.

Bailey-Serres J, Lee S C, Brinton E. 2012. Waterproofing crops: Effective flooding survival strategies. Plant Physiology, 160, 1698–1709.

Bird R M. 2000. A remarkable new teosinte from Nicaragua: Growth and treatment of progeny. Maize Genetics Cooperation Newsletter, 74, 58–59.

Chen X, Zhu W, Azam S, Li H, Zhu F, Li H, Hong Y, Liu H, Zhang E, Wu H, Yu S, Zhou G, Li S, Zhong N, Wen S, Li X, Knapp S J, Ozias-Akins P, Varshney R K, Liang X. 2013. Deep sequencing analysis of the transcriptomes of peanut aerial and subterranean young pods identifies candidate genes related to early embryo abortion. Plant Biotechnology Journal, 11, 115–127.

Chu H T, Hsiao W W, Chen J C, Yeh T J, Tsai M H, Lin H, Liu Y W, Lee S A, Chen C C, Tsao T T, Kao C Y. 2013. EBARDenovo: Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection. Bioinformatics, 29, 1004–1010.

Conesa A, Götz S. 2008. Blast2GO: A comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics, 2008, 619832.

Conesa A, Götz S, García-Gómez J M, Terol J, Talón M, Robles M. 2005. Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674–3676.

Drew M C, He C J, Morgan P W. 2000. Programmed cell death and aerenchyma formation in roots.Trends in Plant Science, 5, 123–127.

Drew M C, Jackson M B, Giffard S C, Campbell R. 1981. Inhibition by silver ions of gas space (aerenchyma) formation in adventitious roots of Zea mays L. subjected to exogenous ethylene or to oxygen deficiency. Planta, 153, 217–224.

Evans D E. 2003. Aerenchyma formation. New Phytologist, 161, 35–49.

Grabherr M G, Haas B J, Yassour M, Levin J Z, Thompson D A, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren B W, Nusbaum C, Lindblad-Toh K, Friedman N. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29, 644–652.

Hattori Y, Nagai K, Furukawa S, Song X J, Kawano R, Sakakibara H, Wu J, Matsumoto T, Yoshimura A, Kitano H, Matsuoka M, Mori H, Ashikari M. 2009. The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature, 460, 1026–1030.

He C J, Drew M C, Morgan P W. 1994. Induction of enzymes associated with lysigenous aerenchyma formation in roots of Zea mays during hypoxia or nitrogen starvation. Plant Physiology, 105, 861–865.

He C J, Morgan P W, Drew M C. 1996. Transduction of an ethylene signal is required for cell death and lysis in the root cortex of maize during aerenchyma formation induced by hypoxia. Plant Physiology, 112, 463–472.

Huang X, Madan A. 1999. CAP3: A DNA sequence assembly program. Genome Research, 9, 868–877.

Iltis H H, Benz B F. 2000. Zea nicaraguensis (Poaceae), a new teosinte from Pacific coastal Nicaragua. Novon, 10, 382–390.

Jackson M B, Ishizawa K, Ito O. 2009. Evolution and mechanisms of plant tolerance to flooding stress. Annals of Botany, 103, 137–142.

Konings H. 1982. Ethylene-promoted formation of aerenchyma in seedling roots of Zea mays L. under aerated and non-aerated conditions. Physiologia Plantar, 54, 119–124.

Lai J, Dey N, Kim C S, Bharti A K, Rudd S, Mayer K F, Larkins B A, Becraft P, Messing J. 2004. Characterization of the maize endosperm transcriptome and its comparison to the rice genome. Genome Research, 14, 1932–1937.

Lee Y H, Kim K S, Jang Y S, Hwang J H, Lee D H, Choi I H. 2014. Global gene expression responses to waterlogging in leaves of rape seedlings. Plant Cell Reports, 33, 289–299.

Liu F, Vantoai T, Moy L P, Bock G, Linford L D, Quackenbush J. 2005. Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis. Plant Physiology, 137, 1115–1129.

Liu S, Zhang Y, Zhou Z, Waldbieser G, Sun F, Lu J, Zhang J, Jiang Y, Zhang H, Wang X, Rajendran K V, Khoo L, Kucuktas H, Peatman E, Liu Z. 2012. Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote. BMC Genomics, 13, 595.

Mano Y, Omori F. 2007. Breeding for flooding tolerant maize using ‘teosinte’ as a germplasm resource. Plant Root, 1, 17–21.

Mano Y, Omori F. 2008. Verification of QTL controlling root aerenchyma formation in a maize×teosinte “Zea nicaraguensis” advanced backcross population. Breeding Science, 58, 217–223.

Mano Y, Omori F. 2009. High-density linkage map around the root aerenchyma locus Qaer1.06 in the backcross populations of maize Mi29×teosinte ‘Zea nicaraguensis’. Breeding Science, 59, 427–433.

Mano Y, Omori F, Loaisiga C H, Bird R M. 2009. QTL mapping of above-ground adventitious roots during flooding inmaize×teosinte ‘Zea nicaraguensis’ backcross population. Plant Root, 3, 3–9.

Mano Y, Omori F, Takeda K. 2012. Construction of intraspecific linkage maps, detection of a chromosome inversion, and mapping of QTL for constitutive root aerenchyma formation in the teosinte Zea nicaraguensis. Molecular Breeding, 29, 137–146.

Mano Y, Omori F, Takamizo T, Kindiger B, Bird R M, Loaisiga CH, Takahashi H. 2007. QTL mapping of root aerenchyma formation in seedlings of a maize×rare teosinte ‘Zea nicaraguensis’ cross. Plant and Soil, 295, 103–113.

Mardis E R. 2008. The impact of next-generation sequencing technology on genetics. Trends in Genetics, 24, 133–141.

Özçubukçu S, Ergün N, Ilhan E. 2014. Waterlogging and nitric oxide induce gene expression and increase antioxidant enzyme activity in wheat (Triticum aestivum L.). Acta Biologica Hungarica, 65, 47–60.

Rajhi I, Yamauchi T, Takahashi H, Nishiuchi S, Shiono K, Watanabe R, Mliki A, Nagamura Y, Tsutsumi N, Nishizawa N K, Nakazono M. 2011. Identification of genes expressed in maize root cortical cells during lysigenous aerenchyma formation using laser microdissection and microarray analyses. New Phytologist, 190, 351–368.

Schnable P S, Ware D, Fulton R S, Stein J C, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves T A, Minx P, Reily A D, Courtney L, Kruchowski S S, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock S M. 2009. The B73 maize genome: Complexity, diversity, and dynamics. Science, 326, 1112–1125.

De Simone O, Haase K, Müller E, Junk W J, Hartmann K, Schreiber L, Schmidt W. 2003. Apoplasmic barriers and oxygen transport properties of hypodermal cell walls in roots from four amazonian tree species. Plant Physiology, 132, 206–217.

Soderlund C, Descour A, Kudrna D, Bomhoff M, Boyd L, Currie J, Angelova A, Collura K, Wissotski M, Ashley E, Morrow D, Fernandes J, Walbot V, Yu Y. 2009. Sequencing, mapping, and analysis of 27455 maize full-length cDNAs. PLoS Genetics, 5, e1000740.

Varshney R K, Nayak S N, May G D, Jackson S A. 2009. Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends in Biotechnology, 27, 522–530.

Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J. 2006. WEGO: A web tool for plotting GO annotations. Nucleic Acids Research, 34, W293–W297.

Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail A M, Bailey-Serres J, Ronald P C, Mackill D J. 2006. Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature, 442, 705–708.

Zou X, Jiang Y, Liu L, Zhang Z, Zheng Y. 2010. Identification of transcriptome induced in roots of maize seedlings at the late stage of waterlogging. BMC Plant Biology, 10, 189.

De novo assembly of Zea nicaraguensis root transcriptome identified 5 261 full-length transcripts

De novo assembly of Zea nicaraguensis root transcriptome identified 5 261 full-length transcripts

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