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Publication Type J
Authors Xie, Q; Niu, J; Xu, XL; Xu, LX; Zhang, YB; Fan, B; Liang, XH; Zhang, LJ; Yin, SX; Han, LB
Author Full Name Xie, Qi; Niu, Jun; Xu, Xilin; Xu, Lixin; Zhang, Yinbing; Fan, Bo; Liang, Xiaohong; Zhang, Lijuan; Yin, Shuxia; Han, Liebao
Title De novo assembly of the Japanese lawngrass (Zoysia japonica Steud.) root transcriptome and identification of candidate unigenes related to early responses under salt stress
Source FRONTIERS IN PLANT SCIENCE
Language English
Document Type Article
Author Keywords Zoysia japonica Steud.; RNA sequencing (RNA-Seq); salt-stress; transcription factor; simple sequence repeats (SSRs)
Keywords Plus GENOME-WIDE ANALYSIS; SALINITY STRESS; ARABIDOPSIS-THALIANA; GENE-EXPRESSION; OSMOTIC-STRESS; TOLERANCE; PLANTS; DROUGHT; WHEAT; RICE
Abstract Japanese lawngrass (Zoysia japonica Steud.) is an important warm-season turfgrass that is able to survive in a range of soils, from infertile sands to clays, and to grow well under saline conditions. However, little is known about the molecular mechanisms involved in its resistance to salt stress. Here, we used high-throughput RNA sequencing (RNA-seq) to investigate the changes in gene expression of Zoysia grass at high NaCI concentrations. We first constructed two sequencing libraries, including control and NaCI-treated samples, and sequenced them using the Illumina HiSeq (TM) 2000 platform. Approximately 157.20 million paired-end reads with a total length of 68.68 Mb were obtained. Subsequently, 100,800 unigenes with an N50 length of 1104 bp were assembled using Trinity, among which 70,127 unigenes were functionally annotated (E <= 10(-5)) in the non-redundant protein (NR) database. Furthermore, three public databases, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Swiss-prot, and Clusters of Orthologous Groups (COGs), were used for gene function analysis and enrichment. The annotated genes included 46 Gene Ontology (GO) terms, 120 KEGG pathways, and 25 COGs. Compared with the control, 6035 genes were significantly different (false discovery rate <= 0.01, vertical bar log(2)Ratio vertical bar >= 1) in the NaCI-treated samples. These genes were enriched in 10 KEGG pathways and 58 GO terms, and subjected to 25 COG categories. Using high-throughput next-generation sequencing, we built a database as a global transcript resource for Z. japonica Steud. roots. The results of this study will advance our understanding of the early salt response in Japanese lawngrass roots.
Author Address [Xie, Qi; Xu, Lixin; Zhang, Yinbing; Fan, Bo; Liang, Xiaohong; Yin, Shuxia; Han, Liebao] Beijing Forestry Univ, Coll Forestry, Inst Turfgrass Sci, Beijing 100083, Peoples R China; [Niu, Jun] Beijing Forestry Univ, Coll Nat Conservat, Lab Systemat Evolut & Biogeog Woody Plants, Beijing 100083, Peoples R China; [Xu, Xilin] Hunan Agr Univ, Coll Plant Protect, Bioinformat, Changsha, Hunan, Peoples R China; [Zhang, Lijuan] Jinan Univ, Shenzhen Tourism Coll, Shenzhen, Peoples R China
Reprint Address Yin, SX (reprint author), Beijing Forestry Univ, 35 East Qinghua Rd, Beijing 100083, Peoples R China.
E-mail Address yinsx369@163.com; hanliebao@163.com
Funding Agency and Grant Number National High Technology Research and Development Program of China (863 Program) [2013AA102607]
Funding Text We are grateful to Biomarker Technologies for providing assistance with the Illumina sequencing. We wish to thank Luo Yingfeng (Beijing Institute of Genomics, Chinese Academy of Sciences) for GO analysis and removal of redundant sequences. We also thank Drs. Lihuang Zhu and Li, and the members of Dr. Zhu's lab at the State Key Laboratory of Plant Genomics and National Plant Gene Research Center (Beijing, China), for their technical assistance and suggestions. This study was supported by the National High Technology Research and Development Program of China (863 Program) (No. 2013AA102607).
Cited References Agarwal PK, 2006, PLANT CELL REP, V25, P1263, DOI 10.1007/s00299-006-0204-8; Ahn JH, 2015, PLOS ONE, V10, DOI 10.1371/journal.pone.0124497; Aida M, 1997, PLANT CELL, V9, P841, DOI 10.1105/tpc.9.6.841; ASANO Y, 1989, PLANT CELL REP, V8, P141, DOI 10.1007/BF00716826; Bartels D, 2005, CRIT REV PLANT SCI, V24, P23, DOI 10.1080/07352680590910410; Bian SM, 2009, SCI HORTIC-AMSTERDAM, V120, P264, DOI 10.1016/j.scienta.2008.10.014; Cao ZH, 2013, PLOS ONE, V8, DOI 10.1371/journal.pone.0069955; Chen JW, 2014, BMC GENOMICS, V15, DOI 10.1186/1471-2164-15-571; Chen SS, 2013, PLOS ONE, V8, DOI [10.1371/journal.pone.0053662, 10.1371/journal.pone.0084575]; Cominelli E, 2008, PLANT J, V53, P53, DOI 10.1111/j.1365-313X.2007.03310.x; Cordeiro GM, 2001, PLANT SCI, V160, P1115, DOI 10.1016/S0168-9452(01)00365-X; Dai HY, 2013, PLOS ONE, V8, DOI 10.1371/journal.pone.0072910; Dang ZH, 2013, BMC GENOMICS, V14, DOI 10.1186/1471-2164-14-29; Marinho LED, 2013, WATER AIR SOIL POLL, V224, DOI 10.1007/s11270-013-1669-z; Du HM, 2009, J AM SOC HORTIC SCI, V134, P417; Dyachenko OV, 2006, BIOCHEMISTRY-MOSCOW+, V71, P461, DOI 10.1134/S000629790604016X; Fukao T, 2011, PLANT CELL, V23, P412, DOI 10.1105/tpc.110.080325; Ge YX, 2006, PLANT CELL REP, V25, P792, DOI 10.1007/s00299-006-0123-8; Gilmour SJ, 2000, PLANT PHYSIOL, V124, P1854, DOI 10.1104/pp.124.4.1854; Grabherr MG, 2011, NAT BIOTECHNOL, V29, P644, DOI 10.1038/nbt.1883; Guan QM, 2013, PLOS GENET, V9, DOI 10.1371/journal.pgen.1003755; Gupta PK, 2003, MOL GENET GENOMICS, V270, P315, DOI 10.1007/s00438-003-0921-4; Haas BJ, 2013, NAT PROTOC, V8, P1494, DOI 10.1038/nprot.2013.084; Hao YJ, 2011, PLANT J, V68, P302, DOI 10.1111/j.1365-313X.2011.04687.x; Harris MA, 2004, NUCLEIC ACIDS RES, V32, pD258, DOI 10.1093/nar/gkh036; He YA, 2012, J EXP BOT, V63, P1511, DOI 10.1093/jxb/err389; Hong CY, 2009, PLANT SOIL, V320, P103, DOI 10.1007/s11104-008-9874-z; Hu LX, 2012, J PLANT PHYSIOL, V169, P146, DOI 10.1016/j.jplph.2011.08.020; Huda KMK, 2013, J EXP BOT, V64, P3099, DOI 10.1093/jxb/ert182; Inokuma C, 1998, PLANT CELL REP, V17, P334; Jiang YQ, 2009, PLANT MOL BIOL, V69, P91, DOI 10.1007/s11103-008-9408-3; Jung J, 2007, PLANTA, V225, P575, DOI 10.1007/s00425-006-0373-2; Kim S, 2004, PLANT J, V40, P75, DOI 10.1111/j.1365-313X.2004.02192.x; Knight H, 1997, PLANT J, V12, P1067, DOI 10.1046/j.1365-313X.1997.12051067.x; Li M-Y, 2014, HORTIC RES, V1, P1, DOI DOI 10.1038/H0RTRES.2014.10; Li SJ, 2011, PLANTA, V233, P1237, DOI 10.1007/s00425-011-1375-2; Liang C, 2013, BMC GENOMICS, V14, DOI 10.1186/1471-2164-14-146; Liu SZ, 2012, PLOS ONE, V7, DOI 10.1371/journal.pone.0036406; Looso M, 2013, GENOME BIOL, V14, DOI 10.1186/gb-2013-14-2-r16; Lu PL, 2007, PLANT MOL BIOL, V63, P289, DOI 10.1007/s11103-006-9089-8; Miao Y, 2007, PLANT CELL, V19, P819, DOI 10.1105/tpc.106.042705; Mittler R, 2004, TRENDS PLANT SCI, V9, P490, DOI 10.1016/j.tplants.2004.08.009; Munns R, 2005, NEW PHYTOL, V167, P645, DOI 10.1111/j.1469-8137.2005.01487.x; Nakano T, 2006, PLANT PHYSIOL, V140, P411, DOI 10.1104/pp.105.073783; Nakashima K, 2012, BBA-GENE REGUL MECH, V1819, P97, DOI 10.1016/j.bbagrm.2011.10.005; Olsen AN, 2005, TRENDS PLANT SCI, V10, P79, DOI 10.1016/j.tplants.2004.12.010; Park JM, 2001, PLANT CELL, V13, P1035, DOI 10.1105/tpc.13.5.1035; Petricka JJ, 2012, ANNU REV PLANT BIOL, V63, P563, DOI 10.1146/annurev-arplant-042811-105501; Puranik S, 2011, J PLANT PHYSIOL, V168, P280, DOI 10.1016/j.jplph.2010.07.005; Qing DJ, 2009, PLANT CELL PHYSIOL, V50, P889, DOI 10.1093/pcp/pcp038; Riechmann JL, 2000, SCIENCE, V290, P2105, DOI 10.1126/science.290.5499.2105; Schippers JHM, 2012, CELL MOL LIFE SCI, V69, P3245, DOI 10.1007/s00018-012-1092-4; Schmidt R, 2013, PLANT CELL, V25, P2115, DOI 10.1105/tpc.113.113068; Sun Li-Jun, 2012, Yichuan, V34, P993, DOI 10.3724/SP.J.1005.2012.00993; Sun QH, 2010, BMC PLANT BIOL, V10, DOI 10.1186/1471-2229-10-90; Tracy FE, 2008, PLANT CELL ENVIRON, V31, P1063, DOI 10.1111/j.1365-3040.2008.01817.x; Tsuruta S, 2011, WILD CROP RELATIVES: GENOMIC AND BREEDING RESOURCES: MILLETS AND GRASSES, P297, DOI 10.1007/978-3-642-14255-0_16; Uddin K., 2012, THESCIENTIFICWORLDJO, V2012, DOI [10.1100/2012/905468, DOI 10.1100/2012/905468]; Ueda A, 2006, THEOR APPL GENET, V112, P1286, DOI 10.1007/s00122-006-0231-4; Ueda A, 2004, J EXP BOT, V55, P2213, DOI 10.1093/jxb/erh242; Vanderauwera S, 2005, PLANT PHYSIOL, V139, P806, DOI 10.1104/pp.105.065896; Wang KH, 2007, CROP SCI, V47, P232, DOI 10.2135/cropsci2006.07.0498; Wang Y, 2013, BMC GENOMICS, V14, DOI 10.1186/1471-2164-14-836; Wang YY, 2001, J CHEM ECOL, V27, P327, DOI 10.1023/A:1005632506230; Wei SW, 2013, MOL BIOL REP, V40, P2915, DOI 10.1007/s11033-012-2307-3; Wu HL, 2008, PROG NAT SCI, V18, P697, DOI 10.1016/j.pnsc.2007.12.006; Xu CB, 2013, PLOS ONE, V8, DOI 10.1371/journal.pone.0068214; Xu JJ, 2013, PLANT MOL BIOL, V83, P77, DOI 10.1007/s11103-013-0025-4; Xuan JP, 2013, PLOS ONE, V8, DOI 10.1371/journal.pone.0075705; Yang YL, 2007, J PLANT PHYSIOL, V164, P1429, DOI 10.1016/j.jplph.2006.08.009; Cho Yg I. T., 2000, THEOR APPL GENET, V100, P713, DOI [10.1007/s001220051343, DOI 10.1007/S001220051343]; Yoon SK, 2014, PLANT PHYSIOL BIOCH, V84, P158, DOI 10.1016/j.plaphy.2014.09.008; Yun KY, 2010, BMC PLANT BIOL, V10, DOI 10.1186/1471-2229-10-16; Zhang LX, 2011, PLANT PHYSIOL, V157, P854, DOI 10.1104/pp.111.179028; Zhou X, 2011, MOL CELLS, V31, P303, DOI 10.1007/s10059-011-0047-1; Zhu JK, 2002, ANNU REV PLANT BIOL, V53, P247, DOI 10.1146/annurev.arplant.53.091401.143329
Cited Reference Count 76
Times Cited 7
Total Times Cited Count (WoS, BCI, and CSCD) 7
Publisher FRONTIERS MEDIA SA
Publisher City LAUSANNE
Publisher Address PO BOX 110, EPFL INNOVATION PARK, BUILDING I, LAUSANNE, 1015, SWITZERLAND
ISSN 1664-462X
29-Character Source Abbreviation FRONT PLANT SCI
ISO Source Abbreviation Front. Plant Sci.
Publication Date AUG 20
Year Published 2015
Volume 6
Article Number 610
Digital Object Identifier (DOI) 10.3389/fpls.2015.00610
Page Count 14
Web of Science Category Plant Sciences
Subject Category Plant Sciences
Document Delivery Number CQ2OF
Unique Article Identifier WOS:000360440000001
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