title: Analysis of the global transcriptome of longan (Dimocarpus longan Lour.) embryogenic callus using Illumina paired-end sequencing.
abstract: BACKGROUND
  Longan is a tropical/subtropical fruit tree of great economic importance in Southeast Asia. Progress in understanding molecular mechanisms of longan embryogenesis, which is the primary influence on fruit quality and yield, is slowed by lack of transcriptomic and genomic information. Illumina second generation sequencing, which is suitable for generating enormous numbers of transcript sequences that can be used for functional genomic analysis of longan.
  
  
  RESULTS
  In this study, a longan embryogenic callus (EC) cDNA library was sequenced using an Illumina HiSeq 2000 system. A total of 64,876,258 clean reads comprising 5.84 Gb of nucleotides were assembled into 68,925 unigenes of 448-bp mean length, with unigenes ≥1000 bp accounting for 8.26% of the total. Using BLASTx, 40,634 unigenes were found to have significant similarity with accessions in Nr and Swiss- Prot databases. Of these, 38,845 unigenes were assigned to 43 GO sub-categories and 17,118 unigenes were classified into 25 COG sub-groups. In addition, 17,306 unigenes mapped to 199 KEGG pathways, with the categories of Metabolic pathways, Plant-pathogen interaction, Biosynthesis of secondary metabolites, and Genetic information processing being well represented. Analyses of unigenes ≥1000 bp revealed 328 embryogenesis-related unigenes as well as numerous unigenes expressed in EC associated with functions of reproductive growth, such as flowering, gametophytogenesis, and fertility, and vegetative growth, such as root and shoot growth. Furthermore, 23 unigenes related to embryogenesis and reproductive and vegetative growth were validated by quantitative real time PCR (qPCR) in samples from different stages of longan somatic embryogenesis (SE); their differentially expressions in the various embryogenic cultures indicated their possible roles in longan SE.
  
  
  CONCLUSIONS
  The quantity and variety of expressed EC genes identified in this study is sufficient to serve as a global transcriptome dataset for longan EC and to provide more molecular resources for longan functional genomics.
authors: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China. laizx01@163.com
authors: Zhongxiong
authors: Z
authors: Lai
authors: Yuling
authors: Y
authors: Lin
mesh_terms: D060406:Brassinosteroids / Q000096:biosynthesis; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions / Q000235:genetics; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D010788:Photosynthesis / Q000235:genetics; D015203:Reproducibility of Results; D017381:Spliceosomes / Q000235:genetics / Q000378:metabolism; D064028:Tracheophyta / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D060406:Brassinosteroids
references: Genomics. 2007 Nov;90(5):620-8
references: 17884330
references: BMC Genomics. 2010 Feb 08;11:94
references: 20141623
references: Genes Dev. 2003 Apr 15;17(8):977-90
references: 12672694
references: BMC Genomics. 2011 Jan 13;12:30
references: 21232141
references: PLoS One. 2011;6(6):e21220
references: 21731678
references: Nat Biotechnol. 2004 Aug;22(8):1006-11
references: 15247925
references: Plant Cell. 1993 Oct;5(10):1411-1423
references: 12271037
references: FEBS Lett. 2003 May 8;542(1-3):37-41
references: 12729894
references: Genome Res. 2006 Oct;16(10):1276-88
references: 16954541
references: Plant Physiol. 2003 May;132(1):118-36
references: 12746518
references: Planta. 2005 Jun;221(3):424-36
references: 15647901
references: Plant Physiol. 2004 Jul;135(3):1206-20
references: 15266054
references: PLoS One. 2011;6(11):e26980
references: 22087239
references: Plant Physiol. 2006 Jun;141(2):620-37
references: 16648215
references: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W293-7
references: 16845012
references: BMC Genomics. 2010 Dec 24;11:726
references: 21182800
references: Genome Res. 2010 May;20(5):646-54
references: 20305017
references: Tree Physiol. 2011 Apr;31(4):452-61
references: 21427158
references: Plant Mol Biol. 2009 May;70(1-2):173-92
references: 19199047
references: BMC Genomics. 2011 Apr 15;12:191
references: 21492485
references: Plant J. 1994 Oct;6(4):615-24
references: 7987417
references: Bioinformatics. 2005 Sep 15;21(18):3674-6
references: 16081474
references: Genomics. 2010 Dec;96(6):369-76
references: 20828606
references: BMC Genomics. 2011 Sep 19;12:451
references: 21929789
references: PLoS One. 2011;6(10):e26801
references: 22046362
references: PLoS One. 2007 Oct 24;2(10):e1074
references: 17957256
references: Nat Methods. 2008 Jul;5(7):621-8
references: 18516045
references: BMC Genomics. 2010 May 28;11:338
references: 20507633
references: Plant Mol Biol. 2006 Sep;62(1-2):1-14
references: 16845483
references: Plant Cell. 2002 Jan;14(1):101-18
references: 11826302
references: Plant Physiol. 2009 Nov;151(3):1486-97
references: 19734265
references: Plant Cell. 2004 Oct;16(10):2601-13
references: 15377760
references: EMBO J. 2002 Nov 15;21(22):6036-49
references: 12426376
references: Plant Cell. 2012 Jul;24(7):2886-97
references: 22786869
references: Genome Res. 2008 Oct;18(10):1602-9
references: 18653800
references: Plant Cell. 2005 Aug;17(8):2340-54
references: 15980260
references: Proc Int Conf Intell Syst Mol Biol. 1999;:138-48
references: 10786296
references: BMC Genomics. 2008 Dec 09;9:593
references: 19068109
references: Plant Physiol. 2007 May;144(1):155-72
references: 17384159
references: BMC Genomics. 2011 Feb 28;12:131
references: 21356090