Identification of Genic SSRs Provide a Perspective for Studying Environmental Adaptation in the Endemic Shrub Tetraena mongolica

Microsatellite Content in 397 Nuclear Exons and Their Flanking Regions in the Fern Family Ophioglossaceae

Microsatellites or SSRs are small tandem repeats that are 1-6 bp long. They are usually highly polymorphic and form important portions of genomes. They have been extensively analyzed in humans, animals and model plants; however, information from non-flowering plants is generally lacking. Here, we examined 29 samples of Ophioglossaceae ferns, mainly from the genera Botrychium and Sceptridium. We analyzed the SSR distribution, density and composition in almost 400 nuclear exons and their flanking regions. We detected 45 SSRs in exons and 1475 SSRs in the flanking regions. In the exons, only di-, tri- and tetranucleotides were found, and all of them were 12 bp long. The annotation of the exons containing SSRs showed that they were related to various processes, such as metabolism, catalysis, transportation or plant growth. The flanking regions contained SSRs from all categories, with the most numerous being dinucleotides, followed by tetranucleotides. More than one-third of all the SSRs in the flanking regions were 12 bp long. The SSR densities in the exons were very low, ranging from 0 to 0.07 SSRs/kb, while those in the flanking regions ranged from 0.24 to 0.81 SSRs/kb; and those in the combined dataset ranged from 0.2 to 0.81 SSRs/kb. The majority of the detected SSRs in the flanking regions were polymorphic and present at the same loci across two or more samples but differing in the number of repeats. The SSRs detected here may serve as a basis for further population genetic, phylogenetic or evolutionary genetic studies, as well as for further studies focusing on SSRs in the genomes and their roles in adaptation, evolution and diseases.

Transcriptome Analysis to Identify Genes Related to Flowering Reversion in Tomato

Flowering reversion is a common phenomenon in plant development in which differentiated floral organs switch from reproductive growth to vegetative growth and ultimately form abnormal floral organs or vegetative organs. This greatly reduces tomato yield and quality. Research on this phenomenon has recently increased, but there is a lack of research at the molecular and gene expression levels. Here, transcriptomic analyses of the inflorescence meristem were performed in two kinds of materials at different developmental stages, and a total of 3223 differentially expressed genes (DEGs) were screened according to the different developmental stages and trajectories of the two materials. The analysis of database annotations showed that these DEGs were closely related to starch and sucrose metabolism, DNA replication and modification, plant hormone synthesis and signal transduction. It was further speculated that tomato flowering reversion may be related to various biological processes, such as cell signal transduction, energy metabolism and protein post-transcriptional regulation. Combined with the results of previous studies, our work showed that the gene expression levels of CLE9, FA, PUCHI, UF, CLV3, LOB30, SFT, S-WOX9 and SVP were significantly different in the two materials. Endogenous hormone analysis and exogenous hormone treatment revealed a variety of plant hormones involved in flowering reversion in tomato. Thus, tomato flowering reversion was studied comprehensively by transcriptome analysis for the first time, providing new insights for the study of flower development regulation in tomato and other plants.

Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing

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.