A new resource for the development of SSR markers: Millions of loci from a thousand plant transcriptomes

Abstract

Premise of the study:The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility.Methods and Results:Using software packages and custom scripts, we identified microsatellite loci in 1KP transcriptomes. We assessed the potential for cross-amplification and whether loci were biased toward exons, as compared to markers derived from genomic DNA. We characterized over 5.7 million simple sequence repeat (SSR) loci from 1334 plant transcriptomes. Eighteen percent of loci substantially overlapped with open reading frames (ORFs), and electronic PCR revealed that over half the loci would amplify successfully in conspecific taxa. Transcriptomic SSRs were approximately three times more likely to map to translated regions than genomic SSRs.Conclusions:We believe microsatellites still have a place in the genomic age—they remain effective and cost-efficient markers. The loci presented here are a valuable resource for researchers.

Optimizing depth and type of high‐throughput sequencing data for microsatellite discovery

“…In general, there were more di-than tri-or tetranucleotide repeat SSR loci in the genome assemblies (with the exception of tomato), and trinucleotide repeat SSR loci were more prevalent in the transcriptome assemblies (with the exception of lablab). This pattern follows previous studies wherein dinucleotide repeats prevail in genomes and trinucleotide repeats are more common in transcriptomes (e.g., in Glycine; Hodel et al, 2016b); the latter is presumably because a portion of each transcript is coding, and therefore triplet insertions or deletions will not interrupt the reading frame (Morgante et al, 2002).…”

“…Transcriptome‐derived markers tend to be more conserved at the sequence level, which means the markers usually show less polymorphism than random genome‐wide SSR markers (Chabane et al., ; Pashley et al., ) but are more transferable between species (Liewlaksaneeyanawin et al., ; Varshney et al., ; reviewed in Ellis and Burke, ). The ease of identification and ubiquity of SSRs in plant transcriptomes are highlighted by a recent in silico analysis of transcriptomes from more than 1000 plant species, which revealed over 5.7 million putative SSR markers (Hodel et al., 2016b).…”

The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century

“…However, RAD/GBS will generate many more loci, but it would be much more economical to add additional individuals if using SSRs. If microsatellites can be developed for free using existing public NGS data, it is worth investigating this option—it can considerably reduce the cost (see companion paper [Hodel et al, 2016], which presents over five million SSR loci that can be used in thousands of plant species). As shown in Table 3, publicly available data sets not designed for microsatellite development can be mined to yield many SSR loci to test.…”

“…Another resource for researchers is the One Thousand Plant Transcriptomes Project (1KP; www.onekp.com; Matasci et al, 2014), which has transcriptome assemblies for over 1000 plant species. The companion paper to our review presents over five million SSR loci that can be used in thousands of plant species (Hodel et al, 2016). It is important to note that once potential loci are identified from NGS data, this is just the starting point for developing a functional microsatellite genotyping system and extensive and costly screening of loci will be required, as outlined in the budget in Appendix 2.…”

“…Its results are in tabular form, giving a summary of different statistics, such as the frequency of a specific microsatellite type. However, some studies indicate that MISA may have mined redundantly in overlapped microsatellites (e.g., Wang et al, 2013; Hodel et al, 2016). …”