De Novo Transcriptomic Analysis and Development of EST–SSRs for Styrax japonicus

Abstract

Styrax japonicus sieb. et Zucc. is widely distributed in China with ornamental and medicinal values. However, the transcriptome of S. japonicus has not yet been reported. In this study, we carried out the first transcriptome analysis of S. japonicus and developed a set of expressed sequence tag-simple sequence repeats (EST-SSRs). We obtained 338,570,222 clean reads in total, of which the mean GC content was 41.58%. In total, 136,071 unigenes were obtained having an average length of 611 bp and 71,226 unigenes were favorably annotated in the database. In total, we identified 55,977 potential EST-SSRs from 38,611 unigenes, of which there was 1 SSR per 6.73 kb. The di-nucleotide repeats (40.40%) were the most identified SSRs. One set of 60 primer pairs was randomly selected, and the amplified products in S. japonicus were validated; 28 primer pairs successfully produced clear amplicons. A total of 21 (35%) polymorphic genic SSR markers were identified between two populations. In total, 15 alleles were detected and the average number was 6. The average of observed heterozygosity and expected heterozygosity was 0.614 and 0.552, respectively. The polymorphism information content (PIC) value fluctuated between 0.074 and 0.855, with a mean value of 0.504, which was also the middle level. This study provides useful information for diversity studies and resource assessments of S. japonicus.

Transcriptome Sequencing of Different Avocado Ecotypes: de novo Transcriptome Assembly, Annotation, Identification and Validation of EST-SSR Markers

“…Because it is inexpensive and rapid, transcriptome sequencing is useful for obtaining a large number of unigene sequences from organisms lacking a reference sequence [46][47][48]. The N50 and mean lengths of avocado unigenes in our study were 1283 bp and 922 bp, respectively, which implies that our sequence assembly was accurate and effective.…”

Single-Molecule Long-Read Sequencing of Avocado Generates Microsatellite Markers for Analyzing the Genetic Diversity in Avocado Germplasm

“…Transcriptome sequencing is a useful technique for obtaining a large number of transcripts for organisms lacking a reference sequence, at least partly because it is inexpensive and can be completed rapidly [51][52][53]. To date, several short-read next-generation sequencing (NGS) transcriptome databases have been developed for avocado mesocarp samples [54,55] and avocado mixed tissue samples [18,56].…”

Transcriptomic Identification of Floral Transition and Development-Associated Genes in Styrax japonicus

“…The basic transcriptome information of S. japonicus have been reported in a previous study [2]. By comparing unigene transcript levels in samples from these three stages of floral development, we were able to explore the transcriptomic dynamics of this flowering process.…”

“…Owing to its ornamental value and practical characteristics, S. japonicus is widely used in city greening efforts. However, there have been relatively few studies conducted to date regarding the basic biology and genetics of this species, with previous molecular biology studies on this plant only focused on the development of simple sequence repeat markers [2].…”