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

Transcriptome Analysis Reveals the Stress Tolerance Mechanisms of Cadmium in Zoysia japonica

Cadmium (Cd) is a severe heavy metal pollutant globally. Zoysia japonica is an important perennial warm-season turf grass that potentially plays a role in phytoremediation in Cd-polluted soil areas; however, the molecular mechanisms underlying its Cd stress response are unknown. To further investigate the early gene response pattern in Z. japonica under Cd stress, plant leaves were harvested 0, 6, 12, and 24 h after Cd stress (400 μM CdCl2) treatment and used for a time-course RNA-sequencing analysis. Twelve cDNA libraries were constructed and sequenced, and high-quality data were obtained, whose mapped rates were all higher than 94%, and more than 601 million bp of sequence were generated. A total of 5321, 6526, and 4016 differentially expressed genes were identified 6, 12, and 24 h after Cd stress treatment, respectively. A total of 1660 genes were differentially expressed at the three time points, and their gene expression profiles over time were elucidated. Based on the analysis of these genes, the important mechanisms for the Cd stress response in Z. japonica were identified. Specific genes participating in glutathione metabolism, plant hormone signal and transduction, members of protein processing in the endoplasmic reticulum, transporter proteins, transcription factors, and carbohydrate metabolism pathways were further analyzed in detail. These genes may contribute to the improvement of Cd tolerance in Z. japonica. In addition, some candidate genes were highlighted for future studies on Cd stress resistance in Z. japonica and other plants. Our results illustrate the early gene expression response of Z. japonica leaves to Cd and provide some new understanding of the molecular mechanisms of Cd stress in Zosia and Gramineae species.

Multispecies comparison of host responses to Fusarium circinatum challenge in tropical pines show consistency in resistance mechanisms

Fusarium circinatum poses a threat to both commercial and natural pine forests. Large variation in host resistance exists between species, with many economically important species being susceptible. Development of resistant genotypes could be expedited and optimised by investigating the molecular mechanisms underlying host resistance and susceptibility as well as increasing the available genetic resources. RNA-seq data, from F. circinatum inoculated and mock-inoculated ca. 6-month-old shoot tissue at 3- and 7-days postinoculation, was generated for three commercially important tropical pines, Pinus oocarpa, Pinus maximinoi and Pinus greggii. De novo transcriptomes were assembled and used to investigate the NLR and PR gene content within available pine references. Host responses to F. circinatum challenge were investigated in P. oocarpa (resistant) and P. greggii (susceptible), in comparison to previously generated expression profiles from Pinus tecunumanii (resistant) and Pinus patula (susceptible). Expression results indicated crosstalk between induced salicylate, jasmonate and ethylene signalling is involved in host resistance and compromised in susceptible hosts. Additionally, higher constitutive expression of sulfur metabolism and flavonoid biosynthesis in resistant hosts suggest involvement of these metabolites in resistance.

Transcriptome analysis of gall oak (Quercus infectoria): De novo assembly, functional annotation and metabolic pathways analysis

Gall oak (Quercus infectoria) is a native tree of Iran, whose gall extract is used to treat many diseases. The presence of abundant secondary metabolites with various bioactivities in this plant has made it medically important. Despite its medicinal value, due to the lack of genomic information, the biosynthetic pathways of these compounds in this species are still unknown. The current research was aimed at observing, characterizing, and investigating the biosynthetic pathways of these compounds in Q.infectoria. De novo transcriptome assembly was conducted using the RNA sequencing technique. A total of 89,335 unigenes were generated, of which 6928 unigenes showed differential expression in leaves compared to root tissue. Gene ontology examination of DEGs revealed GO-term enrichment was related to cellular processes and enzyme activity. KEGG enrichment analysis for DEGs showed that most unigenes were related to metabolic pathways and biosynthesis of secondary metabolites. Moreover, 39 families of transcription factors were identified, of which the C2H2, bZIP, bHLH, and ERF TFs had the highest frequency. In the absence of a reference genome, the overall study of transcriptome will provide a reference for future functional and comparative studies. Moreover, the data obtained from sequencing and de novo assembly can be a valuable scientific resource for Q.infectoria.

Multimodal synchrotron X-ray fluorescence imaging reveals elemental distribution in seeds and seedlings of the Zn-Cd-Ni hyperaccumulator Noccaea caerulescens

The molecular biology and genetics of the Ni-Cd-Zn hyperaccumulator Noccaea caerulescens has been extensively studied, but no information is yet available on Ni and Zn redistribution and mobilization during seed germination. Due to the different physiological functions of these elements, and their associated transporter pathways, we expected differential tissue distribution and different modes of translocation of Ni and Zn during germination. This study used synchrotron X-ray fluorescence tomography techniques as well as planar elemental X-ray imaging to elucidate elemental (re)distribution at various stages of the germination process in contrasting accessions of N. caerulescens. The results show that Ni and Zn are both located primarily in the cotyledons of the emerging seedlings and Ni is highest in the ultramafic accessions (up to 0.15 wt%), whereas Zn is highest in the calamine accession (up to 600 μg g-1). The distribution of Ni and Zn in seeds was very similar, and neither element was translocated during germination. The Fe maps were especially useful to obtain spatial reference within the seeds, as it clearly marked the vasculature. This study shows how a multimodal combination of synchrotron techniques can be used to obtain powerful insights about the metal distribution in physically intact seeds and seedlings.

Defining key metabolic roles in osmotic adjustment and ROS homeostasis in the recretohalophyte Karelinia caspia under salt stress

The recretohalophyte Karelinia caspia is of forage and medical value and can remediate saline soils. We here assess the contribution of primary/secondary metabolism to osmotic adjustment and ROS homeostasis in Karelinia caspia under salt stress using multi-omic approaches. Computerized phenomic assessments, tests for cellular osmotic changes and lipid peroxidation indicated that salt treatment had no detectable physical effect on K. caspia. Metabolomic analysis indicated that amino acids, saccharides, organic acids, polyamine, phenolic acids, and vitamins accumulated significantly with salt treatment. Transcriptomic assessment identified differentially expressed genes closely linked to the changes in above primary/secondary metabolites under salt stress. In particular, shifts in carbohydrate metabolism (TCA cycle, starch and sucrose metabolism, glycolysis) as well as arginine and proline metabolism were observed to maintain a low osmotic potential. Chlorogenic acid/vitamin E biosynthesis was also enhanced, which would aid in ROS scavenging in the response of K. caspia to salt. Overall, our findings define key changes in primary/secondary metabolism that are coordinated to modulate the osmotic balance and ROS homeostasis to contribute to the salt tolerance of K. caspia.

Pilot RNA-seq data from 24 species of vascular plants at Harvard Forest

PREMISE

Large-scale projects such as the National Ecological Observatory Network (NEON) collect ecological data on entire biomes to track climate change. NEON provides an opportunity to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA-seq data from diverse plant communities.

METHODS

We generated >650 Gbp of RNA-seq for 24 vascular plant species representing 12 genera and nine families at the Harvard Forest NEON site. Each species was sampled twice in 2016 (July and August). We assessed transcriptome quality and content with TransRate, BUSCO, and Gene Ontology annotations.

RESULTS

Only modest differences in assembly quality were observed across multiple k-mers. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated transcripts between diploid and polyploid transcriptomes.

DISCUSSION

We provide new RNA-seq data sets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high-quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers opportunities for large-scale studies at the intersection of ecology and genomics.

Elucidating the Genetic Architecture of Fiber Quality in Hemp (Cannabis sativa L.) Using a Genome-Wide Association Study

Hemp (Cannabis sativa L.) is a bast-fiber crop with a great potential in the emerging bio-based economy. Yet, hemp breeding for fiber quality is restricted and that is mainly due to the limited knowledge of the genetic architecture of its fiber quality. A panel of 123 hemp accessions, with large phenotypic variability, was used to study the genetic basis of seven cell wall and bast fiber traits relevant to fiber quality. These traits showed large genetic variance components and high values of broad sense heritability in this hemp panel, as concluded from the phenotypic evaluation across three test locations with contrasting environments. The hemp panel was genotyped using restriction site associated DNA sequencing (RAD-seq). Subsequently, a large set (> 600,000) of selected genome-wide single nucleotide polymorphism (SNP) markers was used for a genome-wide association study (GWAS) approach to get insights into quantitative trait loci (QTLs) controlling fiber quality traits. In absence of a complete hemp genome sequence, identification of QTLs was based on the following characteristics: (i) association level to traits, (ii) fraction of explained trait variance, (iii) collinearity between QTLs, and (iv) detection across different environments. Using this approach, 16 QTLs were identified across locations for different fiber quality traits, including contents of glucose, glucuronic acid, mannose, xylose, lignin, and bast fiber content. Among them, six were found across the three environments. The genetic markers composing the QTLs that are common across locations are valuable tools to develop novel genotypes of hemp with improved fiber quality. Underneath the QTLs, 12 candidate genes were identified which are likely to be involved in the biosynthesis and modification of monosaccharides, polysaccharides, and lignin. These candidate genes were suggested to play an important role in determining fiber quality in hemp. This study provides new insights into the genetic architecture of fiber traits, identifies QTLs and candidate genes that form the basis for molecular breeding for high fiber quality hemp cultivars.

Spatially-resolved localization and chemical speciation of nickel and zinc in Noccaea tymphaea and Bornmuellera emarginata

Hyperaccumulator plants present the ideal model system for studying the physiological regulation of the essential (and potentially toxic) transition elements nickel and zinc. This study used synchrotron X-ray Fluorescence Microscopy (XFM) elemental imaging and spatially resolved X-ray Absorption Spectroscopy (XAS) to elucidate elemental localization and chemical speciation of nickel and zinc in the hyperaccumulators Noccaea tymphaea and Bornmuellera emarginata (synonym Leptoplax emarginata). The results show that in the leaves of N. tymphaea nickel and zinc have contrasting localization, and whereas nickel is present in vacuoles of epidermal cells, zinc occurs mainly in the mesophyll cells. In the seeds Ni and Zn are similarly localized and strongly enriched in the cotyledons in N. tymphaea. Nickel is strongly enriched in the tip of the radicle of B. emarginata. Noccaea tymphaea has an Fe-rich provascular strand network in the cotyledons of the seed. The chemical speciation of Ni in the seeds of N. tymphaea is unequivocally associated with carboxylic acids, whereas Zn is present as the phytate complex. The spatially resolved spectroscopy did not reveal any spatial variation in chemical speciation of Ni and Zn within the N. tymphaea seed. The dissimilar ecophysiological behaviour of Ni and Zn in N. tymphaea and B. emarginata raises questions about the evolution of hyperaccumulation in these species.

Biomolecular approaches to understanding metal tolerance and hyperaccumulation in plants

Trace metal elements are essential for plant growth but become toxic at high concentrations, while some non-essential elements, such as Cd and As, show toxicity even in traces.

Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts

BACKGROUND

Poinsettia is a popular and important ornamental crop, mostly during the Christmas season. Its bract coloration ranges from pink/red to creamy/white shades. Despite its ornamental value, there is a lack of knowledge about the genetics and molecular biology of poinsettia, especially on the mechanisms of color formation. We performed an RNA-Seq analysis in order to shed light on the transcriptome of poinsettia bracts. Moreover, we analyzed the transcriptome differences of red- and white-bracted poinsettia varieties during bract development and coloration. For the assembly of a bract transcriptome, two paired-end cDNA libraries from a red and white poinsettia pair were sequenced with the Illumina technology, and one library from a red-bracted variety was used for PacBio sequencing. Both short and long reads were assembled using a hybrid de novo strategy. Samples of red- and white-bracted poinsettias were sequenced and comparatively analyzed in three color developmental stages in order to understand the mechanisms of color formation and accumulation in the species.

RESULTS

The final transcriptome contains 288,524 contigs, with 33% showing confident protein annotation against the TAIR10 database. The BUSCO pipeline, which is based on near-universal orthologous gene groups, was applied to assess the transcriptome completeness. From a total of 1440 BUSCO groups searched, 77% were categorized as complete (41% as single-copy and 36% as duplicated), 10% as fragmented and 13% as missing BUSCOs. The gene expression comparison between red and white varieties of poinsettia showed a differential regulation of the flavonoid biosynthesis pathway only at particular stages of bract development. An initial impairment of the flavonoid pathway early in the color accumulation process for the white poinsettia variety was observed, but these differences were no longer present in the subsequent stages of bract development. Nonetheless, GSTF11 and UGT79B10 showed a lower expression in the last stage of bract development for the white variety and, therefore, are potential candidates for further studies on poinsettia coloration.

CONCLUSIONS

In summary, this transcriptome analysis provides a valuable foundation for further studies on poinsettia, such as plant breeding and genetics, and highlights crucial information on the molecular mechanism of color formation.

A Practical Guide to the Study of Distribution Limits

Factors that limit the geographic distribution of species are broadly important in ecology and evolutionary biology, and understanding distribution limits is imperative for predicting how species will respond to environmental change. Good data indicate that factors such as dispersal limitation, small effective population size, and isolation are sometimes important. But empirical research highlights no single factor that explains the ubiquity of distribution limits. In this article, we outline a guide to tackling distribution limits that integrates established causes, such as dispersal limitation and spatial environmental heterogeneity, with understudied causes, such as mutational load and genetic or developmental integration of traits limiting niche expansion. We highlight how modeling and quantitative genetic and genomic analyses can provide insight into sources of distribution limits. Our practical guide provides a framework for considering the many factors likely to determine species distributions and how the different approaches can be integrated to predict distribution limits using eco-evolutionary modeling. The framework should also help predict distribution limits of invasive species and of species under climate change.

Comparative RNA-seq analysis of nickel hyperaccumulating and non-accumulating populations of Senecio coronatus (Asteraceae)

Most metal hyperaccumulating plants accumulate nickel, yet the molecular basis of Ni hyperaccumulation is not well understood. We chose Senecio coronatus to investigate this phenomenon as this species displays marked variation in shoot Ni content across ultramafic outcrops in the Barberton Greenstone Belt (South Africa), thus allowing an intraspecific comparative approach to be employed. No correlation between soil and shoot Ni contents was observed, suggesting that this variation has a genetic rather than environmental basis. This was confirmed by our observation that the accumulation phenotype of plants from two hyperaccumulator and two non-accumulator populations was maintained when the plants were grown on a soil mix from these four sites for 12 months. We analysed the genetic variation among 12 serpentine populations of S. coronatus, and used RNA-seq for de novo transcriptome assembly and analysis of gene expression in hyperaccumulator versus non-accumulator populations. Genetic analysis revealed the presence of hyperaccumulators in two well supported evolutionary lineages, indicating that Ni hyperaccumulation may have evolved more than once in this species. RNA-Seq analysis indicated that putative homologues of transporters associated with root iron uptake in plants are expressed at elevated levels in roots and shoots of hyperaccumulating populations of S. coronatus from both evolutionary lineages. We hypothesise that Ni hyperaccumulation in S. coronatus may have evolved through recruitment of these transporters, which play a role in the iron-deficiency response in other plant species.

Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation)

BACKGROUND

Fusarium circinatum is a pressing threat to the cultivation of many economically important pine tree species. Efforts to develop effective disease management strategies can be aided by investigating the molecular mechanisms involved in the host-pathogen interaction between F. circinatum and pine species. Pinus tecunumanii and Pinus patula are two closely related tropical pine species that differ widely in their resistance to F. circinatum challenge, being resistant and susceptible respectively, providing the potential for a useful pathosystem to investigate the molecular responses underlying resistance to F. circinatum. However, no genomic resources are available for P. tecunumanii. Pathogenesis-related proteins are classes of proteins that play important roles in plant-microbe interactions, e.g. chitinases; proteins that break down the major structural component of fungal cell walls. Generating a reference sequence for P. tecunumanii and characterizing pathogenesis related gene families in these two pine species is an important step towards unravelling the pine-F. circinatum interaction.

RESULTS

Eight reference based and 12 de novo assembled transcriptomes were produced, for juvenile shoot tissue from both species. EvidentialGene pipeline redundancy reduction, expression filtering, protein clustering and taxonomic filtering produced a 50 Mb shoot transcriptome consisting of 28,621 contigs for P. tecunumanii and a 72 Mb shoot transcriptome consisting of 52,735 contigs for P. patula. Predicted protein sequences encoded by the assembled transcriptomes were clustered with reference proteomes from 92 other species to identify pathogenesis related gene families in P. patula, P. tecunumanii and other pine species.

CONCLUSIONS

The P. tecunumanii transcriptome is the first gene catalogue for the species, representing an important resource for studying resistance to the pitch canker pathogen, F. circinatum. This study also constitutes, to our knowledge, the largest index of gymnosperm PR-genes to date.

The leaf transcriptome of fennel (Foeniculum vulgare Mill.) enables characterization of the t-anethole pathway and the discovery of microsatellites and single-nucleotide variants

Fennel is a plant species of both agronomic and pharmaceutical interest that is characterized by a shortage of genetic and molecular data. Taking advantage of NGS technology, we sequenced and annotated the first fennel leaf transcriptome using material from four different lines and two different bioinformatic approaches: de novo and genome-guided transcriptome assembly. A reference transcriptome for assembly was produced by combining these two approaches. Among the 79,263 transcripts obtained, 47,775 were annotated using BLASTX analysis performed against the NR protein database subset with 11,853 transcripts representing putative full-length CDS. Bioinformatic analyses revealed 1,011 transcripts encoding transcription factors, mainly from the BHLH, MYB-related, C2H2, MYB, and ERF families, and 6,411 EST-SSR regions. Single-nucleotide variants of SNPs and indels were identified among the 8 samples at a frequency of 0.5 and 0.04 variants per Kb, respectively. Finally, the assembled transcripts were screened to identify genes related to the biosynthesis of t-anethole, a compound well-known for its nutraceutical and medical properties. For each of the 11 genes encoding structural enzymes in the t-anethole biosynthetic pathway, we identified at least one transcript showing a significant match. Overall, our work represents a treasure trove of information exploitable both for marker-assisted breeding and for in-depth studies on thousands of genes, including those involved in t-anethole biosynthesis.

Epigenetic modifications preserve the hyperaccumulator Noccaea caerulescens from Ni geno-toxicity

The Ni hyperaccumulator Noccaea caerulescens has adapted to live in a naturally stressed environment, evolving a complex pattern of traits to cope with adverse conditions. Evidence is accumulating regarding the important role of epigenetic modifications in regulating plant responses to stress. In this study, we present data from the natural "open-field" adaptation of the Ni hyperaccumulator N. caerulescens to serpentine soil and provide the first evidence of the involvement of epigenetic changes in response to the high Ni content present in plant leaves. The alkaline comet assay revealed the integrity of the nuclei of leaf cells of N. caerulescens grown in a Ni-rich environment, while in the non-tolerant Arabidopsis thaliana exposed to Ni, the nuclei were severely damaged. DNA of N. caerulescens plants grown in situ were considerably hyper-methylated compared to A. thaliana plants exposed to Ni. In addition, qRT-PCR revealed that N. caerulescens MET1, DRM2, and HDA8 genes involved in epigenetic DNA and histone modification were up-regulated in the presence of high Ni content in leaves. Such epigenetic modifications may constitute a defense strategy that prevents genome instability and direct damage to the DNA structure by Ni ion, enabling plants to survive in an extreme environment. Further studies will be necessary to analyze in detail the involvement of DNA methylation and other epigenetic mechanisms in the complex process of metal hyperaccumulation and plants' adaptive response. Environ. Mol. Mutagen. 59:464-475, 2018. © 2018 Wiley Periodicals, Inc.

Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)

Rhododendron arboreum is an ecologically prominent species, which also lends commercial and medicinal benefits in the form of palatable juices and useful herbal drugs. Local abundance and survival of the species under a highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina’s platform facilitated the generation of ∼100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out of shorter transcripts predicted 113 167 non-redundant transcripts with an average length of 1164.6 bases. Of these, 71 961 transcripts were categorized based on functional annotations in the Gene Ontology database, whereby 5710 were grouped into 141 pathways and 23 746 encoded for different transcription factors. Transcriptome screening further identified 35 419 microsatellite regions, of which, 43 polymorphic loci were characterized on 30 genotypes. Seven hundred and nineteen transcripts had 811 high-quality single-nucleotide polymorphic variants with a minimum coverage of 10, a total score of 20, and SNP% of 50.

Transcriptomic analysis of boron hyperaccumulation mechanisms in Puccinellia distans

Puccinellia distans, common alkali grass, is found throughout the world and can survive in soils with boron concentrations that are lethal for other plant species. Indeed, P. distans accumulates very high levels of this element. Despite these interesting features, very little research has been performed to elucidate the boron tolerance mechanism in this species. In this study, P. distans samples were treated for three weeks with normal (0.5 mg L^-1) and elevated (500 mg L^-1) boron levels in hydroponic solution. Expressed sequence tags (ESTs) derived from shoot tissue were analyzed by RNA sequencing to identify genes up and down-regulated under boron stress. In this way, 3312 differentially expressed transcripts were detected, 67.7% of which were up-regulated and 32.3% of which were down-regulated in boron-treated plants. To partially confirm the RNA sequencing results, 32 randomly selected transcripts were analyzed for their expression levels in boron-treated plants. The results agreed with the expected direction of change (up or down-regulation). A total of 1652 transcripts had homologs in A. thaliana and/or O. sativa and mapped to 1107 different proteins. Functional annotation of these proteins indicated that the boron tolerance and hyperaccumulation mechanisms of P. distans involve many transcriptomic changes including: alterations in the malate pathway, changes in cell wall components that may allow sequestration of excess boron without toxic effects, and increased expression of at least one putative boron transporter and two putative aquaporins. Elucidation of the boron accumulation mechanism is important in developing approaches for bioremediation of boron contaminated soils.

De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)

Spiny mice of the genus Acomys display several unique physiological traits, including menstruation and scar-free wound healing; characteristics that are exceedingly rare in mammals, and of considerable interest to the scientific community. These unique attributes, and the potential for spiny mice to accurately model human diseases, are driving increased use of this genus in biomedical research, however little genetic information is accessible for this species. This project aimed to generate a draft transcriptome for the Common spiny mouse (Acomys cahirinus). Illumina sequencing of RNA from 15 organ types (male and female) produced 451 million, 150 bp paired-end reads (92.4Gbp). An extensive survey of de novo transcriptome assembly approaches using Trinity, SOAPdenovo-Trans, and Oases at multiple kmer lengths was conducted, producing 50 single-kmer assemblies from this dataset. Non-redundant transcripts from all assemblies were merged into a meta-assembly using the EvidentialGene tr2aacds pipeline, producing the largest gene catalogue to date for Acomys cahirinus. This study provides the first detailed characterization of the spiny mouse transcriptome. It validates use of the EvidentialGene tr2aacds pipeline in mammals to augment conventional de novo assembly approaches, and provides a valuable scientific resource for further investigation into the unique physiological characteristics inherent in the genus Acomys.