Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing.
Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing.
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基于转录组测序的紫杉科微卫星标记的表征和开发
DOI：
10.3389/fgene.2020.574304
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发表时间：
2020
影响因子：
3.7
通讯作者：
Wang T
中科院分区：
文献类型：
--
作者：
Xu R;Wang Z;Su Y;Wang T
白（Pseudotaxus chienii）是中国特有的濒危针叶树种。然而，由于缺乏合适的分子标记，阻碍了该物种的基因组和遗传研究。在这里，我们的特点和开发的微卫星标记，从一个新测序的P. chienii转录组。从161,131条非冗余单基因序列中检测到21,835个微卫星位点，SSR频率为13.55%，平均每9.18kb有1个SSR位点。单核苷酸、双核苷酸和三核苷酸重复类型占SSR总数的50.06%、13.49%和29.39%。从分布位置来看，编码区（CDS）微卫星较少，主要由三核苷酸组成。微卫星长度在不同基因区和不同基序类型间存在显著差异。功能注释表明，含有微卫星的单基因具有广泛的生物学功能，其中大部分与基础代谢有关，少数可能参与基因的表达调控和对环境胁迫的响应。另外，随机选取375对引物进行合成，用于微卫星标记的扩增和验证。共扩增出77对引物，其中40对引物表现出多态性。最后，筛选出20对多态性较高的引物，对4个千参居群的遗传多样性进行了分析。此外，新开发的微卫星标记在穗花杉中表现出较高的可转移性（70%）。本研究为红豆杉科植物的遗传多样性分析和功能基因挖掘奠定了基础。
Pseudotaxus chienii (Taxaceae) is an endangered conifer species endemic to China. However, a lack of suitable molecular markers hinders the genomic and genetic studies on this species. Here, we characterized and developed the microsatellite markers from a newly sequenced P. chienii transcriptome. A total of 21,835 microsatellite loci were detected from 161,131 non-redundant unigene sequences, and the frequency of SSRs was 13.55%, with an average of one SSR loci per 9.18 kb. Mono-nucleotide, di-nucleotide, and tri-nucleotide were the dominant repeat types, accounting for 50.06, 13.49, and 29.39% of the total SSRs, respectively. In terms of distribution location, the coding regions (CDS) with few microsatellites and mainly consisted of tri-nucleotides. There were significant differences in the length of microsatellite among genic regions and motif types. Functional annotation showed that the unigenes containing microsatellites had a wide range of biological functions, most of which were related to basic metabolism, and a few might be involved in expression regulation of gene and response to environmental stress. In addition, 375 primer pairs were randomly selected and synthesized for the amplification and validation of microsatellite markers. Seventy-seven primer pairs were successfully amplified and 40 primer pairs were found to be polymorphic. Finally, 20 pairs of primers with high polymorphism were selected to assess the genetic diversity in four P. chienii populations. In addition, the newly developed microsatellite markers exhibited high transferability (70%) in Amentotaxus argotaenia. Our study could enable further genetic diversity analysis and functional gene mining on Taxaceae.