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opencc-by-4.0Feb 2023View details →

HypoRiPPAtlas - plant transcriptome datasets

Plant transcriptome datasets from Supplementary Table S2

Fig. 6 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge

Fig. 6. Characterization of Aa7DR1 as a 7-dehydrocholesterol reductase 1 from A. asphodeloides Bunge.

Fig. 4 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge

Fig. 4. Transcriptional levels of candidate 7-DR genes involved in timosaponin biosynthesis by RT-qPCR. The characters on the X-axis indicate the roots (R), shortening stem (S) and leaves (L). The Y-axis represents the fold change in gene expression. The ubiquitin gene was used as an internal reference.

Fig. 5. 7 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge

Fig. 5. 7-dehydrocholesterol reductase (7-DR) are involved in cholesterol and phytosterol biosynthesis. CAS: cycloartenol synthase; LAS: lansterol synthase; SMT: sterol C-24 methyltransferase; SSR: sterol side chain reductase; Erg1:squalene epoxidase; Erg5: sterol C-22 desaturase; Erg4: C-24 sterol reductase.

Fig. 3 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge

Fig. 3. Content analyses of steroidal saponins (A) and phytosterols in different organs of A. asphodeloides Bunge. Corresponding histograms indicate the difference in concentration among the different organs. Three biological replicates were performed for each sample.

Fig. 7 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge

Fig. 7. Phylogenetic tree of 7-dehydrocholesterol reductase. Sequences from the following species were represented: A. asphodeloides Bunge (Aa), Arabidopsis thaliana L. (Brassicaceae) (At), Brachypodium distachyon L. (Poaceae) (Bd), Capsicum annuum L. (Solanaceae) (Ca), Chlamydomonas reinhardtii (Cr), Homo sapiens (Hs), Medicago truncatula Gaetn (Leguminosae) (Mt), Nicotiana. Benthamiana Domin (Solanaceae) (Nb), Ostreococcus lucimarinus (Ol), Oryza sativa L. (Poaceae) (Os), Ostreococcus tauri (Ot), Physcomitrella patens (Pp), Sorghum bicolor L. (Poaceae) (Sb), Saccharomyces cerevisiae (Sc), Solanum lycopersicum L. (Solanaceae) (Sl), Solanum melongena L. (Solanaceae) (Sm), Solanum tuberosum L. (Solanaceae) (St), Volvax carteri (Vc), Vitis vinifera L. (Vitaceae) (Vv) and Zea mays L. (Poaceae) (Zm).

publicApr 2016View details →

Data from: Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing

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publicMar 2018View details →

Data from: Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae)

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publicJul 2019View details →

Data from: Transcriptomics of monarch butterflies (Danaus plexippus) reveals that toxic host plants alter expression of detoxification genes and down-regulate a small number of immune genes

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publicJun 2019View details →

Data from: Transcriptomics of host-specific interactions in natural populations of the parasitic plant purple witchweed (Striga hermonthica)

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opencc-by-4.0Mar 2020View details →

Progress Towards Plant Community Transcriptomics: Pilot RNA-Seq Data from 24 Species of Vascular Plants at Harvard Forest

Assembled transcriptomes of 24 vascular plant species from Harvard Forest. Transcriptomes for each species were sequenced and assembled as described below. Additional details available in the associated manuscript: https://doi.org/10.1101/2020.03.31.018945. Raw reads for each available at NCBI SRA SRP127805 and BioProject PRJNA422719. Taxon selection and sampling  The Harvard Forest Flora <a href="https://paperpile.com/c/nMUYEV/hd5w">(Jenkins et al., 2008)</a> was used to select taxa to represent each category (native/invasive, diploid/polyploid). Invasive species status was determined from the Harvard Forest Flora Database <a href="https://paperpile.com/c/nMUYEV/g5Tw">(Jenkins and Motzkin, 2009)</a>. Putative diploids and neo-polyploid species were identified from chromosome counts obtained from the Chromosome Counts Database <a href="https://paperpile.com/c/nMUYEV/6Vzo">(Rice et al., 2015)</a>. Congeneric species pairs were selected based on their phylogenetic relatedness. The Harvard Forest Flora Database was used to assesscalculate recent encounter rates of each target species, and locate sampling sites.  Tissue from mature leaves was collected from an individual representing each target species at two time points (July and August) during the 2016 growing season. The same individual was sampled at both time points for perennial individuals, and the same population was sampled for annuals. Field sampling for plant RNA-seq followed the protocol described in Yang et al. 2017 <a href="https://paperpile.com/c/nMUYEV/n5lK">(Yang et al., 2017)</a>. Leaf tissues were flash frozen in liquid nitrogen in the field, and shipped on dry ice to the University of Arizona for RNA extraction.   RNA extraction and RNA-seq Total RNA was extracted from leaf tissue collected at each time point for all species using the Spectrum Plant Total RNA Kit (Sigma-Aldrich Co., St. Louis, MO, USA) following Protocol A. RNA was used to prepare cDNA using Nugen’s Ovation RNA-Seq System via single primer isothermal amplification (Catalogue # 7102-A01) and automated on the Apollo 324 liquid handler (Wafergen). cDNA was quantified on the Nanodrop (Thermo Fisher Scientific) and was sheared to approximately 300 bp fragments using the Covaris M220 ultrasonicator. Libraries were generated using Kapa Biosystem’s library preparation kit (KK8201). Fragments were end repaired and A-tailed, and individual indexes and adapters (Bioo, catalogue #520999) were ligated on each separate sample. The adapter ligated molecules were cleaned using AMPure beads (Agencourt Bioscience/Beckman Coulter, A63883), and amplified with Kapa’s HIFI enzyme (KK2502). Each library was then analyzed for fragment size on an Agilent’s Tapestation, and quantified by qPCR (KAPA Library Quantification Kit, KK4835) on Thermo Fisher Scientific’s Quantstudio 5 before multiplex pooling (13-16 samples per lane) and paired-end sequencing at 2x150 bp on the Illumina NextSeq500 platform at Arizona State University’s CLAS Genomics Core facility. Raw read quality was assessed using fastQC <a href="https://paperpile.com/c/nMUYEV/mvKN">(Andrews, 2010)</a>.   De novo transcriptome assembly Raw sequence reads were processed using the SnoWhite pipeline <a href="https://paperpile.com/c/nMUYEV/4el87+4OvN">(Barker et al., 2010a; Dlugosch et al., 2013)</a>, which included trimming adapter sequences and bases with a quality score below 20 from the 3' ends of all reads, removing reads that are entirely primer and/or adapter fragments using TagDust <a href="https://paperpile.com/c/nMUYEV/4I38S">(Lassmann et al., 2009)</a>, and removing polyA/T tails with SeqClean (<a href="https://sourceforge.net/projects/seqclean/">https://sourceforge.net/projects/seqclean/</a>). The cleaned reads from each sample time point were merged together by pairs, and pooled to assemble a reference de novo transcriptome for each species. All transcriptomes were assembled with SOAPdenovo-Trans v1.03 <a href="https://paperpile.com/c/nMUYEV/3Szww">(Xie et al., 2014)</a> using a k-mer of 57.

opencc-by-4.0Apr 2020View details →

Transcriptome and Metabolome Reprogramming in Tomato Plants by Trichoderma Harzianum strain T22 Primes and Enhances Defense Responses Against Aphids

Figure 1 Effect of T. harzianum T22 on aphid survival over time. Survival curves (percentage) of M. euphorbiae reared on the untreated water control and the T. harzianum T22 treated tomato plants are significantly different, p < 0.05 (LogRank test). For the aphid longevity assay, 10 plants for each CTRL or T22 treatment were infested with 5 newly born first instar nymphs of M. euphorbiae. The presence of aphids and of shed exuviae, as an indicator of molting occurrence, was daily monitored. Survival curves were compared by LogRank analysis.

opencc-zeroDec 2013View details →

Data from: Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species

C4 photosynthesis outperforms the ancestral C3 state in a wide range of natural and agro-ecosystems by affording higher water-use and nitrogen-use efficiencies. It therefore represents a prime target for engineering novel, high-yielding crops by introducing the trait into C3 backgrounds. However, the genetic architecture of C4 photosynthesis remains largely unknown. To define the divergence in gene expression modules between C3 and C4 photosynthesis during leaf ontogeny, we generated comprehensive transcriptome atlases of two Cleomaceae species, Gynandropsis gynandra (C4) and Tarenaya hassleriana (C3), by RNA sequencing. Overall, the gene expression profiles appear remarkably similar between the C3 and C4 species. We found that known C4 genes were recruited to photosynthesis from different expression domains in C3, including typical housekeeping gene expression patterns in various tissues as well as individual heterotrophic tissues. Furthermore, we identified a structure-related module recruited from the C3 root. Comparison of gene expression patterns with anatomy during leaf ontogeny provided insight into genetic features of Kranz anatomy. Altered expression of developmental factors and cell cycle genes is associated with a higher degree of endoreduplication in enlarged C4 bundle sheath cells. A delay in mesophyll differentiation apparent both in the leaf anatomy and the transcriptome allows for extended vein formation in the C4 leaf.

opencc-zeroDec 2014View details →

Data from: Adaptation of a polyphagous herbivore to a novel host plant extensively shapes the transcriptome of herbivore and host

Generalist arthropod herbivores rapidly adapt to a broad range of host plants. However, the extent of transcriptional reprogramming in the herbivore and its hosts associated with adaptation remains poorly understood. Using the spider mite Tetranychus urticae and tomato as models with available genomic resources, we investigated the reciprocal genomewide transcriptional changes in both spider mite and tomato as a consequence of mite's adaptation to tomato. We transferred a genetically diverse mite population from bean to tomato where triplicated populations were allowed to propagate for 30 generations. Evolving populations greatly increased their reproductive performance on tomato relative to their progenitors when reared under identical conditions, indicative of genetic adaptation. Analysis of transcriptional changes associated with mite adaptation to tomato revealed two main components. First, adaptation resulted in a set of mite genes that were constitutively downregulated, independently of the host. These genes were mostly of an unknown function. Second, adapted mites mounted an altered transcriptional response that had greater amplitude of changes when re-exposed to tomato, relative to nonadapted mites. This gene set was enriched in genes encoding detoxifying enzymes and xenobiotic transporters. Besides the direct effects on mite gene expression, adaptation also indirectly affected the tomato transcriptional responses, which were attenuated upon feeding of adapted mites, relative to the induced responses by nonadapted mite feeding. Thus, constitutive downregulation and increased transcriptional plasticity of genes in a herbivore may play a central role in adaptation to host plants, leading to both a higher detoxification potential and reduced production of plant defence compounds.

opencc-zeroDec 2015View details →

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

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.

opencc-zeroDec 2013View details →

Data from: Comparative transcriptome resources of eleven Primulina species, a group of "stone plants" from a biodiversity hotspot

The genus Primulina is an emerging model system in studying the drivers and mechanisms of species diversification, for its high species richness and endemism, together with high degree of habitat specialization. In this study, we sequenced transcriptomes for eleven Primulina species across the phylogeny of the genus using the Illumina HiSeq 2000 platform. A total of 336 million clean reads were processed into 355 573 unigenes with a mean length of 1336 bp and an N50 value of 2191 bp after pooling and reassembling twelve individual pre-assembled unigene sets. Of these unigenes, 249 973 (70%) were successfully annotated and 256 601 (72%) were identified as coding sequences (CDSs). We identified a total of 38 279 simple sequence repeats (SSRs) and 367 123 single nucleotide polymorphisms (SNPs). Marker validation assay revealed that 354 (27.3%) of the 1296 SSR and 795 (39.6%) of the 2008 SNP loci showed successful genotyping performance and exhibited expected polymorphism profiles. We screened 834 putative single-copy nuclear genes and proved their high effectiveness in phylogeny construction and estimation of ancestral population parameters. We identified a total of 85 candidate orthologs under positive selection for 46 of the 66 species pairs. This study provided an efficient application of RNA-seq in development of genomic resources for a group of 'stone plants' from south China Karst regions, a biodiversity hot spot of the World. The assembled unigenes with annotations and the massive gene-associated molecular markers would help guide further molecular systematic, population genetic and ecological genomics studies in Primulina and its relatives.

opencc-zeroDec 2016View details →

Data from: De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens

Noccaea caerulescens of the Brassicaceae family has become the key model plant among the metal hyperaccumulator plants. Populations/accessions of N. caerulescens from geographic locations with different soil metal concentrations differ in their ability to hyperaccumulate and hypertolerate metals. Comparison of transcriptomes in several accessions provides candidates for detailed exploration of the mechanisms of metal accumulation and tolerance and local adaptation. This can have implications in the development of plants for phytoremediation and improved mineral nutrition. Transcriptomes from root and shoot tissues of four N. caerulescens accessions with contrasting Zn, Cd and Ni hyperaccumulation and tolerance traits were sequenced with Illumina Hiseq2000. Transcriptomes were assembled using the Trinity de novo assembler and were annotated and the protein sequences predicted. The comparison against the BUSCO plant early release dataset indicated high-quality assemblies.The predicted protein sequences have been clustered into ortholog groups with closely related species. The data serve as important reference sequences in whole transcriptome studies, in analyses of genetic differences between the accessions and other species, and for primer design.

Fig. 2 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge

Fig. 2. GO (A) and KEGG (B) analyses of unigenes.

Fig. 1 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge

Fig. 1. The proposed timosaponin biosynthetic pathway in A. asphodeloides Bunge.