Abstract
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.
Highlights
Pseudotaxus chienii, belonging to monotypic genus Pseudotaxus W
The Illumina HiSeq 2500 platform was used to sequence the transcriptome of P. chienii
We found that the microsatellites located in coding regions (CDS) regions were dominated by tri-nucleotides, while other SSR motifs accounted for a small proportion
Summary
Pseudotaxus chienii, belonging to monotypic genus Pseudotaxus W. The species is an evergreen shrub or small tree plants, up to 4 meters, characterized by seeds of a white fleshy aril (Fu et al, 1999). Most of its habitats are in the subtropical evergreen broad-leaved forest or deciduous broad-leaved forest at an Characterization and Development of Microsatellite Markers elevation of about 800–1500 m (Fu et al, 1999). The distribution range and population size of P. chienii have been continuously declining due to the low seed-setting rate, the difficult natural reproduction, the strict habitat requirements, and the impact of human activities (Fu and Jin, 1992; Yang et al, 2005). Due to the lack of genomic resources, the knowledge about functional gene analysis and molecular marker development of this species is limited
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
