Additional file 1: Figure S1. of Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data

Chart flow for the Organelle_PBA software. Reads are mapped to an organelle reference using BlasR (1). The BlasR output is parsed and the sequence IDs are used to retrieve the reads from the input file (2). Organelle identified reads are assembled using Sprai (3). The program checks if the assembly is complete comparing its length with the reference (4). If it is not complete, it performs a scaffolding using SSPACE-Long and the whole PacBio dataset (5). It is complete it moves to the new checking point where it check for circularity (6). If it detects circularity by a self-BlastN, it trims the sequence corresponding to the circular overlap (6). Finally it check for the repeat assembly (7) and if it finds it, it breaks in four parts, identify the complete inverted repeat (IR), duplicate it (IRa and IRb) and re-assemble it will the long and short single copy (LSC, SSC) (9). (TIFF 5352 kb

Supplemental Material and Data for Blankers et al., 2018

<div>Genotype data (.raw files) and final linkage maps (.txt files) for the three mapping crosses as well as the slightly modified agp file for the anchored assembly.</div><div><br></div><div>Supplementary tables S1-S4 and supplementary figures S1-S3.</div

Code for Blankers et al., 2018

R scripts for the statistical analyses for collinearity of the linkage maps, segregation distortion, and the estimation of recombination rates along the genome

Transcriptomic Analysis of <i>Petunia hybrida</i> in Response to Salt Stress Using High Throughput RNA Sequencing

<div><p>Salinity and drought stress are the primary cause of crop losses worldwide. In sodic saline soils sodium chloride (NaCl) disrupts normal plant growth and development. The complex interactions of plant systems with abiotic stress have made RNA sequencing a more holistic and appealing approach to study transcriptome level responses in a single cell and/or tissue. In this work, we determined the <i>Petunia</i> transcriptome response to NaCl stress by sequencing leaf samples and assembling 196 million Illumina reads with Trinity software. Using our reference transcriptome we identified more than 7,000 genes that were differentially expressed within 24 h of acute NaCl stress. The proposed transcriptome can also be used as an excellent tool for biological and bioinformatics in the absence of an available <i>Petunia</i> genome and it is available at the SOL Genomics Network (SGN) <a href="http://solgenomics.net" target="_blank">http://solgenomics.net</a>. Genes related to regulation of reactive oxygen species, transport, and signal transductions as well as novel and undescribed transcripts were among those differentially expressed in response to salt stress. The candidate genes identified in this study can be applied as markers for breeding or to genetically engineer plants to enhance salt tolerance. Gene Ontology analyses indicated that most of the NaCl damage happened at 24 h inducing genotoxicity, affecting transport and organelles due to the high concentration of Na⁺ ions. Finally, we report a modification to the library preparation protocol whereby cDNA samples were bar-coded with non-HPLC purified primers, without affecting the quality and quantity of the RNA-seq data. The methodological improvement presented here could substantially reduce the cost of sample preparation for future high-throughput RNA sequencing experiments.</p></div

Additional file 2: of Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica

Figure S1. Members of the xyloglucan transglycosylase/hydrolase (XTH) family are significantly differentially upregulated in Sue 16 relative to Sue 1. Shown are FPKM expression values with confidence intervals from Cuffdiff analysis for both homoeologs of XTH4 and XTH22. (PDF 471 kb

Comparison and functional annotation of transcript abundance in ‘Reads per Kilobase of Exon per Million Reads Mapped’ (RPKM) and functional annotation of the 5 most expressed transcripts.

<p>The first two columns transcript abundance measured in RPKM (Avg ± S.E) for the top five most expressed genes across the 29 libraries. Third column is sequence (Seq.) description obtained through functional annotation used in Blast2GO software. Sequence length of <i>de novo</i> assembled transcripts varied for all the transcripts shown.</p

Boxplot comparisons of <i>de novo</i> assembled transcripts length distribution using Trinity, SOAPdenovo-trans and TransABySS software.

<p>First column (ITAG2.3 CDS) indicates tomato full CDS transcriptome, 2^nd column represents Trinity assembly using default k-mer set at 25. Third and 4^th columns represent assembly generated with SOAPdenovo-trans (SOAP) with k-mers (K) set at 25 and 47, respectively. Last column represents assembly generated with Trans-ABySS (T.ABySS) using trans k-mer. Transcripts longer than 5,000 bp were not plotted.</p

Unique Gene Ontology (GO) terms associated with samples at 24 h after salt stress.

<p>False Discovery Rate (FDR) cut-off was set at 0.05, and all biological GO terms were significantly overrepresented.</p

Additional file 4: of Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica

Table S7. Complete RNA seq data. (TXT 9489 kb

Candidate genes selected based on their high induction levels (RPKM).

<p>Candidate gens induced at 24; (A) Expansin-like B1-like, (B) Bidirectional sugar transporter SWEET11-like, (C) Phosphoenolpyruvate carboxylase kinase and (D) Low-temperature-induced 65 kDa protein-like.</p