BMC Genomics. 2015 Sep 30;16:738. doi: 10.1186/s12864-015-1887-4.
Transcriptome sequencing and analysis of major genes involved in calcium signaling pathways in pear plants (Pyrus calleryana Decne.).
BMC genomics
Yuanyuan Xu, Xiaogang Li, Jing Lin, Zhonghua Wang, Qingsong Yang, Youhong Chang
Affiliations
Affiliations
- Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China.
- Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China. [email protected].
- Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China. [email protected].
PMID: 26424153
PMCID: PMC4590731 DOI: 10.1186/s12864-015-1887-4
Abstract
BACKGROUND: Pears (Pyrus spp. L.) are an important genus of trees that produce one of the world's oldest fruit crops. Salinity stress is a common limiting factor for plant productivity that significantly affects the flavor and nutritional quality of pear fruits. Much research has shown that calcium signaling pathways, mediated by Calcineurin B-like proteins (CBLs) and their interacting kinases (CIPKs), are closely associated with responses to stresses, including salt. However, little is known about the molecular mechanisms that govern the relationship between salt stress and calcium signaling pathways in pear plants. The available genomic information for pears has promoted much functional genomic analysis and molecular breeding of the genus. This provided an ample foundation for characterizing the transcriptome of pear under salt stress.
RESULTS: A high-throughput Illumina RNA-seq technology was used to identify a total of 78,695 unigenes that were successfully annotated by BLASTX analysis, using the publicly available protein database. Additionally, 2,855 novel transcripts, 218,167 SNPs, 23,248 indels and 18,322 alternative splicing events occurred. Assembled unique sequences were annotated and classified with Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, which revealed that the main activated genes in pear are predominately involved in functions such as basic physiological processes, metabolic pathways, operation of cellular components, signal transduction mechanisms, and other molecular activities. Through targeted searches of the annotations, the majority of the genes involved in calcium signaling pathways were identified, among which, four genes were validated by molecular cloning, while 11 were validated by RT-qPCR expression profiles under salt stress treatment.
CONCLUSIONS: These results facilitate a better understanding of the molecular genetics and functional genomic mechanisms of salt stress in pear plants. Furthermore, they provide a valuable foundation for additional research on the molecular biology and functional genomics of pear and related species.
References
- Genome Res. 2013 Feb;23(2):396-408 - PubMed
- Annu Rev Plant Biol. 2008;59:651-81 - PubMed
- PLoS One. 2013;8(8):e71763 - PubMed
- Nucleic Acids Res. 2000 Jan 1;28(1):27-30 - PubMed
- J Exp Bot. 2009;60(12):3545-57 - PubMed
- PLoS Genet. 2013 Aug;9(8):e1003755 - PubMed
- Plant Physiol. 2004 Jan;134(1):43-58 - PubMed
- BMC Plant Biol. 2013;13:70 - PubMed
- BMC Genomics. 2012;13:648 - PubMed
- BMC Genomics. 2012;13:700 - PubMed
- Planta. 2012 Jul;236(1):101-13 - PubMed
- Genome Res. 2010 Jan;20(1):45-58 - PubMed
- Front Genet. 2012 Mar 15;3:35 - PubMed
- Mol Gen Genet. 1994 Aug 15;244(4):331-40 - PubMed
- Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61 - PubMed
- BMC Genomics. 2011;12:131 - PubMed
- Nat Rev Mol Cell Biol. 2005 May;6(5):386-98 - PubMed
- Trends Plant Sci. 2005 Aug;10(8):383-9 - PubMed
- J Biol Chem. 2006 Sep 15;281(37):27405-15 - PubMed
- BMC Genomics. 2013;14:789 - PubMed
- Cell Res. 2008 Oct;18(10):1047-60 - PubMed
- Plant Mol Biol. 1999 Nov;41(5):577-85 - PubMed
- Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W293-7 - PubMed
- Plant Physiol. 2002 Jun;129(2):469-85 - PubMed
- Nucleic Acids Res. 2007 Jul;35(Web Server issue):W345-9 - PubMed
- BMC Genomics. 2013;14:823 - PubMed
- PLoS One. 2012;7(2):e30630 - PubMed
- Plant Cell. 2004 Jul;16(7):1912-24 - PubMed
- Plant Cell Physiol. 2013 Jul;54(7):1132-51 - PubMed
- Plant Cell. 1999 Dec;11(12):2393-405 - PubMed
- Trends Plant Sci. 2010 Oct;15(10):573-81 - PubMed
- PLoS One. 2012;7(6):e38653 - PubMed
- Plant Mol Biol. 2008 Mar;66(4):429-43 - PubMed
- New Phytol. 2009 Nov;184(3):517-28 - PubMed
- Genome Res. 2010 May;20(5):646-54 - PubMed
- Genome Res. 2012 Sep;22(9):1760-74 - PubMed
- Bioinformatics. 2005 Sep 15;21(18):3674-6 - PubMed
- Mamm Genome. 2010 Dec;21(11-12):592-8 - PubMed
- J Exp Bot. 2006;57(5):1097-107 - PubMed
- BMC Genomics. 2013;14:29 - PubMed
- Plant J. 2000 Aug;23(3):319-27 - PubMed
- Bioinformatics. 2007 Jul 1;23(13):i149-58 - PubMed
- Ecotoxicol Environ Saf. 2005 Mar;60(3):324-49 - PubMed
- Nat Methods. 2013 Dec;10(12):1185-91 - PubMed
- Annu Rev Biochem. 2003;72:291-336 - PubMed
- Genome Res. 2009 Jun;19(6):1124-32 - PubMed
- Nature. 2008 Nov 27;456(7221):470-6 - PubMed
- Plant Cell Rep. 2014 Feb;33(2):203-14 - PubMed
- Plant J. 2004 Jan;37(1):115-27 - PubMed
- Nat Rev Genet. 2010 May;11(5):345-55 - PubMed
- Biochim Biophys Acta. 2005 Jul 10;1729(3):174-85 - PubMed
- Nat Protoc. 2012 Mar;7(3):562-78 - PubMed
- Annu Rev Plant Biol. 2010;61:593-620 - PubMed
- Mol Biol Rep. 2012 Jul;39(7):7327-38 - PubMed
- Biochem Biophys Res Commun. 2012 Aug 3;424(3):398-403 - PubMed
- PLoS One. 2013;8(6):e66539 - PubMed
- Biochim Biophys Acta. 2012 Aug;1820(8):1283-93 - PubMed
- PLoS One. 2014;9(1):e85282 - PubMed
- Trends Plant Sci. 2009 Jan;14(1):37-42 - PubMed
- Mol Biotechnol. 2012 Jun;51(2):160-73 - PubMed
- Bioinformatics. 2008 Mar 1;24(5):713-4 - PubMed
- Proc Int Conf Intell Syst Mol Biol. 1999;:138-48 - PubMed
- J Biol Chem. 2012 Mar 9;287(11):7956-68 - PubMed
- Methods Enzymol. 2007;428:419-38 - PubMed
- BMC Genomics. 2013;14:836 - PubMed
- Mol Biol Rep. 2012 Feb;39(2):969-87 - PubMed
- BMC Genomics. 2012;13:123 - PubMed
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