Mining and characterizing EST-SSR markers from ESTs of Torreya grandis

Application of EST-SSR markers developed from the transcriptome of Torreya grandis (Taxaceae), a threatened nut-yielding conifer tree

“…In this study, 1,923 unigenes containing 2,065 EST-SSRs were detected from total 69,920 unigenes in the transcriptome of T. grandis. The distribution frequency (2.75% of the total unigenes) and average number (0.03 SSRs per unigene) of EST-SSRs were lower than those reported for T. grandis “Merrillii” (3.72% and 0.037 SSRs) ( Yi et al, 2016 ). The detection criteria of EST-SSRs may be generated by the difference between T. grandis and other conifer species.…”

“…In this study, a total of 38,626,498 clean reads (4.83 Gb) were generated from the transcriptome sequencing of T. grandis . The total number of assembled unigenes (69,920) was much larger than previously reported for T. grandis “Merrillii” (46,000) ( Yi et al, 2016 ). Similarly, the mean and N50 length of the unigenes in our study, 766 and 1,503 bp ( Table 1 ), respectively, were also longer than those reported for the cultivar (731 and 1,426 bp, respectively) ( Yi et al, 2016 ), indicating that the transcriptome sequencing data were well assembled for T. grandis in the present study.…”

“…The detection criteria of EST-SSRs may be generated by the difference between T. grandis and other conifer species. For example, in this study, a minimum of six, five, five, five, and five repeats were, respectively, used for di-, tri-, tetra-, penta-, and hexanucleotide motifs, whereas six, five, four, four, and four repeats were applied in T. grandis “Merrillii” ( Yi et al, 2016 ), and six, five, five, four, and four repeats employed in Pinus dabeshanensis ( Xiang et al, 2015 ). Therefore, the uniformly detected criteria of EST-SSRs are important and should be considered for the evaluation of distribution frequency and density of EST-SSRs.…”

“…Alternatively, transcriptome sequencing by next-generation sequencing technologies, like expressed sequence tag (EST), is a promising strategy to obtain genomic information. Although a transcriptome have been generated for the cultivar T. grandis “Merrillii” that was selected by conventional breeding ( Li et al, 2004 ; Yi et al, 2016 ), its limited genomic information might be insufficient for the investigation of wild genetic sources of T. grandis . Meanwhile, many studies on T. grandis have mainly focused on its medicinal component ( Saeed et al, 2007 ), physiological ecology ( Shen et al, 2014 ; Tang et al, 2015 ), nutrient content ( Li et al, 2005 ; Feng et al, 2011 ), and field investigation ( Li et al, 2005 ; Wu et al, 2006 ).…”

“…However, these markers were dominant and/or uniparental inheritance, and underestimated the genetic diversity of T. grandis . Despite a set of codominant EST-SSRs developed from T. grandis “Merrillii” ( Yi et al, 2016 ), these EST-SSRs were not employed to evaluate the genetic diversity and population structure of wild T. grandis .…”