College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.
Sci Rep. 2020 Oct 1;10(1):16249. doi: 10.1038/s41598-020-73289-5.
Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.
乌兰胡杨是中国山东省特有的濒危物种。尽管该物种具有经济和观赏价值，但很少有基因组学和遗传学研究。在这项研究中，我们对乌兰胡杨的全长转录组测序数据进行了相关分析，获得了具有多态性的表达序列标签（EST）-简单序列重复（SSR）标记，可用于进一步的遗传研究。总共获得了 8.18GB（3521665 条）清洁读数，平均 GC 含量为 42.12%。经过 CD-HIT 校正后，从 64737 个高质量的同工型中获得了 42323 个转录序列。在这些转录序列中，有 41876 个序列成功被注释。从 16057 个序列中总共鉴定出 23539 个潜在的 EST-SSR。除单核苷酸外，最丰富的基序是三核苷酸 SSR（47.80%），其次是二核苷酸 SSR（46.80%）、四核苷酸 SSR（2.98%）、六核苷酸 SSR（1.58%）和五核苷酸 SSR（0.84%）。在设计的 100 个 EST-SSR 中，有 18 个具有高 PIC 值（0.721 和 0.683）的多态性，可用于分析乌兰胡杨的遗传多样性和种群结构。这些全长转录组测序数据将促进乌兰胡杨的基因发现和功能基因组学研究，而我们研究中开发的新型 EST-SSR 将促进该物种的分子辅助育种、遗传多样性和保护生物学研究。
