Cheng Libao, Li Shuyan, Chen Sainan, Wang Yan, Yu Meizhen, Chen Xuehao, Li Liangjun, Yin Jingjing
School of Horticulture and Plant Protection of Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China.
Guangling College of Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China.
PLoS One. 2016 Oct 7;11(10):e0164223. doi: 10.1371/journal.pone.0164223. eCollection 2016.
The product organ (storage organ; corm) of the Chinese water chestnut has become a very popular food in Asian countries because of its unique nutritional value. Corm formation is a complex biological process, and extensive whole genome analysis of transcripts during corm development has not been carried out. In this study, four corm libraries at different developmental stages were constructed, and gene expression was identified using a high-throughput tag sequencing technique. Approximately 4.9 million tags were sequenced, and 4,371,386, 4,372,602, 4,782,494, and 5,276,540 clean tags, including 119,676, 110,701, 100,089, and 101,239 distinct tags, respectively, were obtained after removal of low-quality tags from each library. More than 39% of the distinct tags were unambiguous and could be mapped to reference genes, while 40% were unambiguous tag-mapped genes. After mapping their functions in existing databases, a total of 11,592, 10,949, 10,585, and 7,111 genes were annotated from the B1, B2, B3, and B4 libraries, respectively. Analysis of the differentially expressed genes (DEGs) in B1/B2, B2/B3, and B3/B4 libraries showed that most of the DEGs at the B1/B2 stages were involved in carbohydrate and hormone metabolism, while the majority of DEGs were involved in energy metabolism and carbohydrate metabolism at the B2/B3 and B3/B4 stages. All of the upregulated transcription factors and 9 important genes related to product organ formation in the above four stages were also identified. The expression changes of nine of the identified DEGs were validated using a quantitative PCR approach. This study provides a comprehensive understanding of gene expression during corm formation in the Chinese water chestnut.
荸荠的产品器官（贮藏器官；球茎）因其独特的营养价值，已成为亚洲国家非常受欢迎的食物。球茎形成是一个复杂的生物学过程，尚未对球茎发育过程中的转录本进行广泛的全基因组分析。在本研究中，构建了四个不同发育阶段的球茎文库，并使用高通量标签测序技术鉴定基因表达。测序了约490万个标签，从每个文库中去除低质量标签后，分别获得了4371386、4372602、4782494和5276540个干净标签，包括119676、110701、100089和101239个不同标签。超过39%的不同标签是明确的，可映射到参考基因，而40%是明确的标签映射基因。在现有数据库中对其功能进行映射后，分别从B1、B2、B3和B4文库中注释了总共11592、10949、10585和7111个基因。对B1/B2、B2/B3和B3/B4文库中差异表达基因（DEG）的分析表明，B1/B2阶段的大多数DEG参与碳水化合物和激素代谢，而B2/B3和B3/B4阶段的大多数DEG参与能量代谢和碳水化合物代谢。还鉴定了上述四个阶段中所有上调的转录因子和9个与产品器官形成相关的重要基因。使用定量PCR方法验证了9个已鉴定的DEG的表达变化。本研究全面了解了荸荠球茎形成过程中的基因表达。
