Xu Yuanyuan, Li Xiaogang, Lin Jing, Wang Zhonghua, Yang Qingsong, Chang Youhong
Jiangsu Academy of Agricultural Sciences; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Nanjing, 210014, People's Republic of China.
BMC Genomics. 2015 Sep 30;16:738. doi: 10.1186/s12864-015-1887-4.
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.
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.
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.
梨（Pyrus spp. L.）是一类重要的树木，其果实是世界上最古老的水果作物之一。盐胁迫是影响植物生产力的常见限制因素，会显著影响梨果实的风味和营养品质。许多研究表明，由类钙调神经磷酸酶B蛋白（CBLs）及其相互作用激酶（CIPKs）介导的钙信号通路与包括盐胁迫在内的多种胁迫反应密切相关。然而，关于梨植株中盐胁迫与钙信号通路之间关系的分子机制，我们所知甚少。梨的现有基因组信息推动了该属植物的大量功能基因组分析和分子育种研究。这为表征盐胁迫下梨的转录组提供了充分的基础。
利用高通量Illumina RNA测序技术共鉴定出78,695个单基因，通过BLASTX分析利用公开的蛋白质数据库成功对其进行了注释。此外，还出现了2,855个新转录本、218,167个单核苷酸多态性（SNP）、23,248个插入缺失（indel）和18,322个可变剪接事件。通过基因本体论（GO）、直系同源簇（COG）和京都基因与基因组百科全书（KEGG）分析对组装得到的独特序列进行注释和分类，结果显示梨中主要被激活的基因主要参与基本生理过程、代谢途径、细胞组分运作、信号转导机制及其他分子活动等功能。通过对注释进行靶向搜索，鉴定出了大多数参与钙信号通路的基因，其中4个基因通过分子克隆得到验证，11个基因通过盐胁迫处理下的RT-qPCR表达谱得到验证。
这些结果有助于更好地理解梨植株中盐胁迫的分子遗传学和功能基因组机制。此外，它们为进一步研究梨及相关物种的分子生物学和功能基因组学提供了有价值的基础。
