High-throughput analysis of small RNAs and characterization of novel microRNAs affected by abiotic stress in a local celery cultivar
High-throughput analysis of small RNAs and characterization of novel microRNAs affected by abiotic stress in a local celery cultivar
复制标题
本地芹菜品种中小 RNA 的高通量分析以及受非生物胁迫影响的新型 microRNA 的表征
DOI：
10.1016/j.scienta.2014.02.007
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发表时间：
2014-04-16
影响因子：
4.3
通讯作者：
Xiong, Ai-Sheng
中科院分区：
文献类型：
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作者：
Jiang, Qian;Wang, Feng;Xiong, Ai-Sheng
“六合黄心芹”是一种中国芹菜品种，它的叶子呈黄色或淡绿色，这是它与其他芹菜品种的区别。本研究表征了通过深度测序鉴定的各种sRNAs，并阐明了新型microRNAs （miRNAs）如何响应非生物胁迫（热、冷、盐和干旱）。总共获得了3,243,608个干净reads和1,028,137个独特reads，范围从16到30个核苷酸。通过与多个数据库比对，将rRNA、tRNA、snRNA、snoRNA和重复序列标注为小rna （sRNAs）。鉴定出457个独特的reads，属于35个已知的miRNA家族，以及12个新的miRNA。新mirna的平均最小自由能指数值为0.89，范围为0.50-1.39。5个新的mirna在非生物胁迫下被上调；6个新的mirna在非生物胁迫下下调。Targetfinder共预测了12个新mirna中的3个的8个潜在靶基因。对推测靶点和mirna的分析表明，这些新mirna在芹菜非生物相关基因调控过程中发挥了多重作用。(C) 2014 Elsevier B.V.版权所有
'Liuhe Huangxinqin', a Chinese celery cultivar, has yellow or pale green leaves, which distinguishes it from other celery cultivars. This study characterized the various sRNAs identified by deep sequencing and clarified how the novel microRNAs (miRNAs) responded to abiotic stresses (heat, cold, salinity and drought). A total of 3,243,608 clean reads and 1,028,137 unique reads ranging from 16 to 30 nucleotides were obtained. By aligning them to multiple databases, the rRNA, tRNA, snRNA, snoRNA and repeat sequences were annotated to the small RNAs (sRNAs). Four hundred fifty-seven unique reads, belonging to 35 known miRNA families, and 12 novel miRNAs were identified. The average minimum free energy index value of the novel miRNAs was 0.89, with a range of 0.50-1.39. Five novel miRNAs were showed to be up-regulated by abiotic stress; six novel miRNAs were down-regulated by abiotic stress. A total of 8 potential target genes were predicted for 3 out of 12 novel miRNAs by Targetfinder. The analysis of putative targets and miRNAs indicated that the novel miRNAs played multiple roles in abiotic related gene regulation process in celery. (C) 2014 Elsevier B.V. All rights reserved.