Table_2_Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing.DOCX

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.

Pseudotaxus chienii（中国红豆杉，Taxaceae科）是一种原产于中国的濒危针叶树种。然而，由于缺乏合适的分子标记，对该物种的基因组学和遗传学研究受到了阻碍。本研究从新测序的P. chienii转录组中，对微卫星标记进行了特征描述和开发。在161,131条非冗余单基因序列中，共检测到21,835个微卫星位点，SSR（简单序列重复）的频率为13.55%，平均每9.18 kb存在一个SSR位点。单核苷酸、二核苷酸和三核苷酸是主要的重复类型，分别占所有SSR的50.06%、13.49%和29.39%。在分布位置上，编码区（CDS）中微卫星较少，主要由三核苷酸构成。微卫星的长度在基因区域和基序类型之间存在显著差异。功能注释显示，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相关，少数可能涉及基因表达调控和对环境压力的反应。此外，随机选取并合成了375对引物，用于微卫星标记的扩增和验证。成功扩增了77对引物，其中40对引物表现出多态性。最终，选取了20对多态性较高的引物，以评估四个P. chienii种群中的遗传多样性。此外，新开发的微卫星标记在Amentotaxus argotaenia中表现出高转移性（70%）。本研究能够促进对红豆杉科进行进一步的遗传多样性分析和功能基因挖掘。