Stem trichome small RNA-Seq from the 20 accessions

<p><strong>Total and Small RNA Isolation</strong></p> <p>Total RNA from stem trichomes (n = 1) were&nbsp;isolated using concentrated TRIzol reagent (Life Technologies). Total RNA was isolated using the E.Z.N.A.^&reg;&nbsp;MicroElute RNA Clean Up Kit (Omega Bio-Tek). Briefly, TRIzol Reagent (Life Technologies) and chloroform was added according to the manufacturer&#39;s instructions. After centrifugation, the RNA-containing aqueous phase was collected, mixed with 1.5 volume of 100% ethanol and applied to a MicroElute spin column (Omega Bio-Tek). The column was washed according to the manufacturers&#39;s instructions: once with RWT buffer (Qiagen), once with RPE washing buffer (Qiagen) and finally with 80% ethanol. The RNA concentration was measured on a NanoDrop ND-2000 (Thermo Scientific) and RNA integrity was examined using the 2200 TapeStation System with Agilent RNA ScreenTapes (Agilent Technologies).</p> <p>Total RNA was spiked with ERCCs spike-in mix 1 (Life Technologies) as well as a synthetic spike-in set for Size Range Quality Control (SRQC) together with an External Reference for Data Normalization (ERDN;&nbsp;<a href="https://www.frontiersin.org/articles/10.3389/fpls.2016.01759/full#B38">Locati et al., 2015</a>). &nbsp;The total RNA was divided in a large and a small fraction. The large RNA fraction was bound to a mirVana&trade; spin column (mirVana&trade; miRNA Isolation Kit, Life Technologies) according to the manufacturer&#39;s instructions. Small RNAs (&lt;200 nts) were purified from the flow-through by adding ethanol to a final concentration of 65% (v/v) and bound to an E.Z.N.A.^&reg;&nbsp;MicroElute spin column. The column was washed once with RWT buffer, once with RPE buffer and once with 80% ethanol (Qiagen). The concentration and integrity of small RNA was examined as described above.</p> <p><strong>Next-Generation Sequencing</strong></p> <p>Bar-coded small RNA libraries were generated according to the manufacturer&#39;s protocols using the Ion Total RNA-Seq Kit v2 and the Ion Xpress&trade; RNA-Seq bar-coding kit (Life Technologies). The size distribution and yield of the bar-coded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes (Agilent Technologies). Sequencing templates were prepared on the Ion Chef&trade; System using the Ion PI Hi-Q Chef Kit (Life Technologies). Sequencing was performed on an Ion Proton&trade; System using Ion PI v3 chips (Life Technologies) according to the manufacturer&#39;s instructions.</p> <p><strong>References</strong></p> <p>Locati et al. 2015.&nbsp;Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization.&nbsp;<a href="https://www.ncbi.nlm.nih.gov/pubmed/25870415#">Nucleic Acids Res.</a>&nbsp;(2015).&nbsp;43(14):e89. doi: 10.1093/nar/gkv303.&nbsp;</p> <p><strong>Table of genotypes used</strong></p> <pre><code class="language-markdown">| accession | species | accession nr | synonym | origin | |------------|--------------------------------|--------------|---------|-------------| | LA2172 | S. arcanum | TR0009 | - | Peru | | LA1401* | S. cheesmaniae f. minor | EA00652 | - | Ecuador | | LA1840 | S. chmielewskii | - | - | unknown | | LA2695 | S. chmielewskii | EA00759 | - | Peru | | LA0407 | S. habrochaites f. glabratum | EA00558 | - | Ecuador | | LA1777 | S. habrochaites f. hirsutum | EA00703 | - | Peru | | PI134418 | S. habrochaites f. glabratum | TR00015 | LYC38 | unknown | | LYC4 | S. habrochaites f. hirsutum | TR00017 | - | unknown | | LA1718 | S. habrochaites f. glabratum | EA00699 | LYC4934 | Peru | | PI127826 | S. habrochaites f. hirsutum | - | - | Peru | | LA1364 | S. huaylasense | TR00030 | - | Peru | | Moneymaker | S. lycopersicum | - | C32 | Netherlands | | LA4024 | S. lycopersicum | TA209 | - | unknown | | LA2386 | S. lycopersicoides | - | - | Peru | LA2133 | S. neorickii/L. parviflorum | EA00729 | - | Peru | | LA0735 | S. neorickii | TR00025 | LYC140 | unknown | | LA0716 | S. pennellii | EA00585 | - | Peru | | LA1278 | S. peruvianum/pimpinellifolium | TR00005 | - | unknown | | LA1954 | S. peruvianum | EA00713 | - | Peru | | LA1578 | S. pimpinellifolium | EA00674 | - | Peru |</code></pre>