De novo assembly of the desert tree Haloxylon ammodendron (C. A. Mey.) based on RNA-Seq data provides insight into drought response, gene discovery and marker identification

BMC Genomics

Xin Wu Pei¹  Zhanhai Dang²  Jianping Zhang²  Qiong Zhang²  Shanshan Wu¹  Xinjie Tian¹  Jingwen Zhang¹  Yan Long¹ 

[1] Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing 100081, China;Crop Institute, Gansu Agricultural Academy, Lanzhou 730070, China

关键词: EST-SSR;    Digital gene expression;    Transcriptome;    Drought;    Haloxylon ammodendron;   

Others  :  1127298
DOI  :  10.1186/1471-2164-15-1111

 received in 2014-08-11, accepted in 2014-12-11,  发布年份 2014

【 摘 要 】

Background

Haloxylon ammodendron (C. A. Mey.) is widely distributed across a range of habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in Asian and African deserts. To date, no genomic information or expressed sequence tag-simple sequence repeat (EST-SSR) marker has been reported for H. ammodendron plants.

Results

Using Illumina sequencing technology, we generated over two billion bases of high-quality sequence data on H. ammodendron and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 79,918 unigenes (mean length = 728 bp). Based on similarity searches comparing these unigenes with known proteins in the non-redundant (nr) protein database, 25,619 unigenes were functionally annotated with a cut-off E-value of 10^-5. In addition, DGE reads were mapped to the assembled transcriptome for gene expression analysis under drought stress. In total, 1,060 differentially expressed genes were identified. Among these genes, 356 genes were upregulated after drought treatment, and 704 genes were downregulated. We used the KEGG database to annotate these drought-induced genes; 207 unigenes were identified in the KEGG pathway annotation, and approximately 12.1% of the unigenes with known function fell into categories related to fatty acid metabolism, starch and sucrose metabolism, and nitrogen metabolism, suggesting that these pathways or processes may be involved in the drought response. Together, a total of 35 drought-inducible transcription factors were identified, including WRKY, MYB and bZIP family members.

Conclusions

Our study is the first to provide a transcriptome sequence resource for H. ammodendron plants and to determine its digital gene expression profile under drought conditions using the assembled transcriptome data for reference. These data provide a valuable resource for genetic and genomic studies of desert plants under abiotic conditions.

【 授权许可】

   
2014 Long et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

【 参考文献 】

• [1]Shanker AK, Maheswari M, Yadav SK, Desai S, Bhanu D, Attal NB, Venkateswarlu B: Drought stress responses in crops. Funct Int Genom 2014, 14(1):11-22.
• [2]Golldack D, Li C, Mohan H, Probst N: Tolerance to drought and salt stress in plants: unraveling the signaling networks. Front Plant Sci 2014, 5:151.
• [3]Matsui A, Ishida J, Morosawa T, Mochizuki Y, Kaminuma E, Endo TA, Okamoto M, Nambara E, Nakajima M, Kawashima M, Satou M, Kim JM, Kobayashi N, Toyoda T, Shinozaki K, Seki M: Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol 2008, 49(8):1135-1149.
• [4]Jeong JS, Kim YS, Baek KH, Jung H, Ha SH, Do Choi Y, Kim M, Reuzeau C, Kim JK: Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. Plant Physiol 2010, 153(1):185-197.
• [5]Ren X, Chen Z, Liu Y, Zhang H, Zhang M, Liu Q, Hong X, Zhu JK, Gong Z: ABO3, a WRKY transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis. Plant J 2010, 63(3):417-429.
• [6]Cominelli E, Sala T, Calvi D, Gusmaroli G, Tonelli C: Over-expression of the Arabidopsis AtMYB41 gene alters cell expansion and leaf surface permeability. Plant J 2008, 53(1):53-64.
• [7]Chen CD, Zhang LY, Hu WK: The basic characteristics of plant communities, flora and their distribution in the sandy district of Gurbantungut. Acta Phytoecol Geobot Sin 1983, 7:89-99.
• [8]Tobe K, Li XM, Omasa K: Effects of sodium chloride on seed germination and growth of two Chinese desert shrubs, Haloxylon ammodendron and H-persicum (Chenopodiaceae). Aust J Bot 2000, 48(4):455-460.
• [9]Ma HB, Bao GX, Ma WD, Rong ZJ, Wang XY, Li B: The resource,protection and utilization of Haloxylon ammodendron deserted grassland in Inner Mongolia. Pratacult Sci 2000, 17:1-5.
• [10]Gao S, Su P, Yan Q, Ding S: Canopy and leaf gas exchange of Haloxylon ammodendron under different soil moisture regimes. Sci China Life Sci 2010, 53(6):718-728.
• [11]Xie TT, Zhang XM, Liang SM, Shan LS, Yang XL, Hua YH: Effects of different irrigations on the water physiological characteristics of Haloxylon ammodendron in Taklimakan Desert hinterland. Ying Yong Sheng Tai Xue Bao 2008, 19(4):711-716.
• [12]Yang YF, Zhou HF, Xu LG: Dynamic variations of soil moisture in Haloxylon ammodendron root zone in Gurbantunggut Desert. Ying Yong Sheng Tai Xue Bao 2011, 22(7):1711-1716.
• [13]Shi L, Gan XY, Xia XL, Chen YC, Li M, Song YX: Cloning of choline monooxygenase gene from Haloxylon ammodendron and construction of its plant expression vector. Acta Bot Boreali Occidentalia Sin 2010, 30(8):1514-1519.
• [14]Zhou XY, Shi L, Gan XY, Chen YC, Song YX: Cloning and sequence analysis of ADP-ribosylation factors genes from Haloxylon ammodendron. Acta Agricult Boreali Occidentalis Sin 2012, 21(7):67-71.
• [15]Zhou XY, Gan XY, Shi L, Chen YC, Li M, Song YX: Cloning and sequence analysis of EF-hand CaBP gene from Haloxylon ammodendron. Acta Bot Boreali Occidentalia Sin 2012, 21(6):47-52.
• [16]Hegedus Z, Zakrzewska A, Agoston VC, Ordas A, Racz P, Mink M, Spaink HP, Meijer AH: Deep sequencing of the zebrafish transcriptome response to mycobacterium infection. Mol Immunol 2009, 46(15):2918-2930.
• [17]Tian DQ, Pan XY, Yu YM, Wang WY, Zhang F, Ge YY, Shen XL, Shen FQ, Liu XJ: De novo characterization of the Anthurium transcriptome and analysis of its digital gene expression under cold stress. BMC Genomics 2013, 14:827. BioMed Central Full Text
• [18]Yates SA, Swain MT, Hegarty MJ, Chernukin I, Lowe M, Allison GG, Ruttink T, Abberton MT, Jenkins G, Skot L: De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification. BMC Genomics 2014, 15:453. BioMed Central Full Text
• [19]Yu SC, Zhang FL, Yu YJ, Zhang DS, Zhao XY, Wang WH: Transcriptome profiling of dehydration stress in the Chinese Cabbage (Brassica rapa L. ssp pekinensis) by Tag sequencing. Plant Mol Biol Report 2012, 30(1):17-28.
• [20]Naegele R, Tomlinson AJ, Hausbeck MK: Evaluation of a diverse, worldwide collection of wild, cultivated and landrace peppers (Capsicum annuum) for resistance to Phytophthora fruit rot, genetic diversity and population structure. Phytopathology 2014, 105(1):110-118.
• [21]Ahmad Z, Mumtaz AS, Ghafoor A, Ali A, Nisar M: Marker Assisted Selection (MAS) for chickpea Fusarium oxysporum wilt resistant genotypes using PCR based molecular markers. Mol Biol Rep 2014, 41(10):6755-6762.
• [22]Talukder ZI, Gong L, Hulke BS, Pegadaraju V, Song Q, Schultz Q, Qi L: A high-density SNP map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12. PLoS One 2014, 9(7):e98628.
• [23]Li DJ, Deng Z, Qin B, Liu XH, Men ZH: De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics 2012, 13:192. BioMed Central Full Text
• [24]Zhao Y, Williams R, Prakash C, He G: Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.). BMC Plant Biol 2012, 12(1):237. BioMed Central Full Text
• [25]Shi Y, Yan X, Zhao P, Yin H, Zhao X, Xiao H, Li X, Chen G, Ma XF: Transcriptomic analysis of a tertiary relict plant, extreme xerophyte Reaumuria soongorica to identify genes related to drought adaptation. PLoS One 2013, 8(5):e63993.
• [26]Li C, Wang Y, Huang X, Li J, Wang H, Li J: De novo assembly and characterization of fruit transcriptome in Litchi chinensis Sonn and analysis of differentially regulated genes in fruit in response to shading. BMC Genomics 2013, 14:552. BioMed Central Full Text
• [27]Liu M, Qiao G, Jiang J, Yang H, Xie L, Xie J, Zhuo R: Transcriptome sequencing and de novo analysis for Ma bamboo (Dendrocalamus latiflorus Munro) using the Illumina platform. PLoS One 2012, 7(10):e46766.
• [28]Lulin H, Xiao Y, Pei S, Wen T, Shangqin H: The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers. PLoS One 2012, 7(6):e38653.
• [29]Xu DL, Long H, Liang JJ, Zhang J, Chen X, Li JL, Pan ZF, Deng GB, Yu MQ: De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode. BMC Genomics 2012, 13:133. BioMed Central Full Text
• [30]Novaes E, Drost DR, Farmerie WG, Pappas GJ Jr, Grattapaglia D, Sederoff RR, Kirst M: High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 2008, 9:312. BioMed Central Full Text
• [31]Zhao AF, Zhang LX, Du MW, Chen HS: Characteristic in photosynthesis, transpiration and water use effiency of Haloxylon ammodendron and Calligonum mongolicum of desert species. Acta Bot Boreali Occidentalis Sin 2003, 23(1):11-17.
• [32]Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, Harper JF: Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 2002, 130(4):2129-2141.
• [33]Chen Y, Liu Z-H, Feng L, Zheng Y, Li D-D, Li X-B: Genome-wide functional analysis of cotton (Gossypium hirsutum) in response to drought. PLoS ONE 2013, 8(11):e80879.
• [34]Du FK, Xu F, Qu H, Feng S, Tang J, Wu R: Exploiting the transcriptome of Euphrates Poplar, Populus euphratica (Salicaceae) to develop and characterize new EST-SSR markers and construct an EST-SSR Database. PLoS ONE 2013, 8(4):e61337.
• [35]Durand J, Bodenes C, Chancerel E, Frigerio JM, Vendramin G, Sebastiani F, Buonamici A, Gailing O, Koelewijn HP, Villani F, Mattioni C, Cherubini M, Goicoechea PG, Herran A, Ikaran Z, Cabane C, Ueno S, Alberto F, Dumoulin PY, Guichoux E, de Daruvar A, Kremer A, Plomion C: A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genomics 2010, 11(1):570. BioMed Central Full Text
• [36]Qiu L, Yang C, Tian B, Yang J-B, Liu A: Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.). BMC Plant Biol 2010, 10(1):278. BioMed Central Full Text
• [37]Triwitayakorn K, Chatkulkawin P, Kanjanawattanawong S, Sraphet S, Yoocha T, Sangsrakru D, Chanprasert J, Ngamphiw C, Jomchai N, Therawattanasuk K, Tangphatsornruang S: Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map. DNA Res 2011, 18(6):471-482.
• [38]Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng QD, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011, 29(7):644-U130.
• [39]Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21(18):3674-3676.
• [40]Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J: WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 2006, 34(Web Server issue):W293-W297.
• [41]Li B, Dewey CN: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinf 2011, 12:323. BioMed Central Full Text
• [42]Harwood S: Vector NTI. Biotechnol Softw I J 1996, 13(5):22-30.
• [43]Anders S, Huber W: Differential expression analysis for sequence count data. Genome Biol 2010, 11(10):R106. BioMed Central Full Text
• [44]Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ: A large genome center's improvements to the Illumina sequencing system. Nat Methods 2008, 5(12):1005-1010.
• [45]Del Sal G, Manfioletti G, Schneider C: The CTAB-DNA precipitation method: a common mini-scale preparation of template DNA from phagemids, phages or plasmids suitable for sequencing. BioTech 1989, 7(5):514-520.