First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species, Pinus halepensis Mill

De novo transcriptome assembly of Dalbergia sissoo Roxb. (Fabaceae) under Botryodiplodia theobromae-induced dieback disease

Dalbergia sissoo Roxb. (Shisham) is a timber-producing species of economic, cultural, and medicinal importance in the Indian subcontinent. In the past few decades, Shisham's dieback disease caused by the fungus Botryodiplodia theobromae has become an evolving issue in the subcontinent endangering its survival. To gain insights into this issue, a standard transcriptome assembly was deployed to assess the response of D. sissoo at the transcriptomic level under the stress of B. theobromae infection. For RNA isolation, the control and infected leaf tissue samples were taken from 1-year-old greenhouse-grown D. sissoo plants after 20 days of stem-base spore inoculation. cDNA synthesis was performed from these freshly isolated RNA samples that were then sent for sequencing. About 18.14 Gb (Giga base) of data was generated using the BGISEQ-500 sequencing platform. In terms of Unigenes, 513,821 were identified after a combined assembly of all samples and then filtering the abundance. The total length of Unigenes, their average length, N50, and GC-content were 310,523,693 bp, 604 bp, 1,101 bp, and 39.95% respectively. The Unigenes were annotated using 7 functional databases i.e., 200,355 (NR: 38.99%), 164,973 (NT: 32.11%), 123,733 (Swissprot: 24.08%), 142,580 (KOG: 27.75%), 139,588 (KEGG: 27.17%), 99,752 (GO: 19.41%), and 137,281 (InterPro: 26.72%). Furthermore, the Transdecoder detected 115,762 CDS. In terms of SSR (Simple Sequence Repeat) markers, 62,863 of them were distributed on 51,508 Unigenes and on the predicted 4673 TF (Transcription Factor) coding Unigenes. A total of 16,018 up- and 19,530 down-regulated Differentially Expressed Genes (DEGs) were also identified. Moreover, the Plant Resistance Genes (PRGs) had a count of 9230. We are hopeful that in the future, these identified Unigenes, SSR markers, DEGs and PRGs will provide the prerequisites for managing Shisham dieback disease, its breeding, and in tree improvement programs.

Comprehensive Organ-Specific Profiling of Douglas Fir (Pseudotsuga menziesii) Proteome

The Douglas fir (Pseudotsuga menziesii) is a conifer native to North America that has become increasingly popular in plantations in France due to its many advantages as timber: rapid growth, quality wood, and good adaptation to climate change. Tree genetic improvement programs require knowledge of a species' genetic structure and history and the development of genetic markers. The very slow progress in this field, for Douglas fir as well as the entire genus Pinus, can be explained using the very large size of their genomes, as well as by the presence of numerous highly repeated sequences. Proteomics, therefore, provides a powerful way to access genomic information of otherwise challenging species. Here, we present the first Douglas fir proteomes acquired using nLC-MS/MS from 12 different plant organs or tissues. We identified 3975 different proteins and quantified 3462 of them, then examined the distribution of specific proteins across plant organs/tissues and their implications in various molecular processes. As the first large proteomic study of a resinous tree species with organ-specific profiling, this short note provides an important foundation for future genomic annotations of conifers and other trees.

Fire frequency, as well as stress response and developmental gene control serotiny level variation in a widespread pioneer Mediterranean conifer, Pinus halepensis

Many plants undergo adaptation to fire. Yet, as global change is increasing fire frequency worldwide, our understanding of the genetics of adaptation to fire is still limited. We studied the genetic basis of serotiny (the ability to disseminate seeds exclusively after fire) in the widespread, pioneer Mediterranean conifer Pinus halepensis Mill., by linking individual variation in serotiny presence and level to fire frequency and to genetic polymorphism in natural populations. After filtering steps, 885 single nucleotide polymorphisms (SNPs) out of 8000 SNPs used for genotyping were implemented to perform an in situ association study between genotypes and serotiny presence and level. To identify serotiny‐associated loci, we performed random forest analyses of the effect of SNPs on serotiny levels, while controlling for tree size, frequency of wildfires, and background environmental parameters. Serotiny showed a bimodal distribution, with serotinous trees more frequent in populations exposed to fire in their recent history. Twenty‐two SNPs found in genes involved in stress tolerance were associated with the presence‐absence of serotiny while 37 found in genes controlling for flowering were associated with continuous serotiny variation. This study shows the high potential of P. halepensis to adapt to changing fire regimes, benefiting from a large and flexible genetic basis of trait variation.

Elevated CO2 Alters the Physiological and Transcriptome Responses of Pinus densiflora to Long-Term CO2 Exposure

Physiological response and transcriptome changes were observed to investigate the effects on the growth, metabolism and genetic changes of Pinus densiflora grown for a long time in an environment with an elevated atmospheric CO₂ concentration. Pine trees were grown at ambient (400 ppm) and elevated (560 ppm and 720 ppm) CO₂ concentrations for 10 years in open-top chambers. The content of nonstructural carbohydrates was significantly increased in elevated CO₂. It was notable that the contents of chlorophylls significantly decreased at an elevated CO₂. The activities of antioxidants were significantly increased at an elevated CO₂ concentration of 720 ppm. We analyzed the differences in the transcriptomes of Pinus densiflora at ambient and elevated CO₂ concentrations and elucidated the functions of the differentially expressed genes (DEGs). RNA-Seq analysis identified 2415 and 4462 DEGs between an ambient and elevated CO₂ concentrations of 560 ppm and 720 ppm, respectively. Genes related to glycolysis/gluconeogenesis and starch/sucrose metabolism were unchanged or decreased at an elevated CO₂ concentration of 560 ppm and tended to increase at an elevated CO₂ concentration of 720 ppm. It was confirmed that the expression levels of genes related to photosynthesis and antioxidants were increased at an elevated CO₂ concentration of 720 ppm.

Harnessing tree-ring phenotypes to disentangle gene by environment interactions and their climate dependencies in a circum-Mediterranean pine

BACKGROUND AND AIMS

Understanding the genetic basis of adaptation and plasticity in trees constitutes a knowledge gap. We linked dendrochronology and genomics [single nucleotide polymorphisms (SNPs)] for a widespread conifer (Pinus halepensis Mill.) to characterize intraspecific growth differences elicited by climate.

METHODS

The analysis comprised 20-year tree-ring series of 130 trees structured in 23 populations evaluated in a common garden. We tested for genotype by environment interactions (G × E) of indexed ring width (RWI) and early- to latewood ratios (ELI) using factorial regression, which describes G × E as differential gene sensitivity to climate.

KEY RESULTS

The species' annual growth was positively influenced by winter temperature and spring moisture and negatively influenced by previous autumn precipitation and warm springs. Four and five climate factors explained 10 % (RWI) and 16 % (ELI) of population-specific interannual variability, respectively, with populations from drought-prone areas and with uneven precipitation experiencing larger growth reductions during dry vegetative periods. Furthermore, four and two SNPs explained 14 % (RWI) and 10 % (ELI) of interannual variability among trees, respectively. Two SNPs played a putative role in adaptation to climate: one identified from transcriptome sequencing of P. halepensis and another involved in response regulation to environmental stressors.

CONCLUSIONS

We highlight how tree-ring phenotypes, obtained from a common garden experiment, combined with a candidate-gene approach allow the quantification of genetic and environmental effects determining adaptation for a conifer with a large and complex genome.

Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences

Cephalotaxus oliveri is an endemic conifer of China, which has medicinal and ornamental value. However, the limited molecular markers and genetic information are insufficient for further genetic studies of this species. In this study, we characterized and developed the EST-SSRs from transcriptome sequences for the first time. The results showed that a total of 5089 SSRs were identified from 36446 unigenes with a density of one SSR per 11.1 kb. The most common type was trinucleotide repeats, excluding mononucleotide repeats, followed by dinucleotide repeats. AAG/CTT and AT/AT exhibited the highest frequency in the trinucleotide and dinucleotide repeats, respectively. Of the identified SSRs, 671, 1125, and 1958 SSRs were located in CDS, 3′UTR, and 5′UTR, respectively. Functional annotation showed that the SSR-containing unigenes were involved in growth and development with various biological functions. Among successfully designed primer pairs, 238 primer pairs were randomly selected for amplification and validation of EST-SSR markers and 47 primer pairs were identified as polymorphic. Finally, 28 high-polymorphic primers were used for genetic analysis and revealed a moderate level of genetic diversity. Seven natural C. oliveri sampling sites were divided into two genetic groups. Furthermore, the 28 EST-SSRs had 96.43, 71.43, and 78.57% of transferability rate in Cephalotaxus fortune, Ametotaxus argotaenia, and Pseudotaxus chienii, respectively. These markers developed in this study lay the foundation for further genetic and adaptive evolution studies in C. oliveri and related species.

Evolutionary history of the mediterranean Pinus halepensis-brutia species complex using gene-resequencing and transcriptomic approaches

Complementary gene-resequencing and transcriptomic approaches reveal contrasted evolutionary histories in a species complex. Pinus halepensis and Pinus brutia are closely related species that can intercross, but occupy different geographical ranges and bioclimates. To study the evolution of this species complex and to provide genomic resources for further research, we produce and analyze two new complementary sets of genetic resources: (i) a set of 172 re-sequenced genomic target loci analyzed in 45 individuals, and (ii) a set of 11 transcriptome assemblies. These two datasets provide insights congruent with previous studies: P. brutia displays high level of genetic diversity and no genetic sub-structure, while P. halepensis shows three main genetic clusters, the western Mediterranean and North African clusters displaying much lower genetic diversity than the eastern Mediterranean cluster, the latter cluster having similar genetic diversity to P. brutia. In addition, these datasets provide new insights on the timing of the species-complex history: the two species would have split at the end of the tertiary, and the changing climatic conditions of the Mediterranean region at the end of the Tertiary-beginning of the Quaternary, together with the distinct species tolerance to harsh climatic conditions would have resulted in different geographic distributions, demographic histories and genetic patterns of the two pines. The multiple glacial-interglacial cycles during the Quaternary would have led to the expansion of P. brutia in the Middle East, while P. halepensis would have been through bottlenecks. The last glaciations, from 0.6 Mya on, would have affected further the Western genetic pool of P. halepensis.

Bridging the genotype-phenotype gap for a Mediterranean pine by semi-automatic crown identification and multispectral imagery

Progress in high-throughput phenotyping and genomics provides the potential to understand the genetic basis of plant functional differentiation. We developed a semi-automatic methodology based on unmanned aerial vehicle (UAV) imagery for deriving tree-level phenotypes followed by genome-wide association study (GWAS). An RGB-based point cloud was used for tree crown identification in a common garden of Pinus halepensis in Spain. Crowns were combined with multispectral and thermal orthomosaics to retrieve growth traits, vegetation indices and canopy temperature. Thereafter, GWAS was performed to analyse the association between phenotypes and genomic variation at 235 single nucleotide polymorphisms (SNPs). Growth traits were associated with 12 SNPs involved in cellulose and carbohydrate metabolism. Indices related to transpiration and leaf water content were associated with six SNPs involved in stomata dynamics. Indices related to leaf pigments and leaf area were associated with 11 SNPs involved in signalling and peroxisome metabolism. About 16-20% of trait variance was explained by combinations of several SNPs, indicating polygenic control of morpho-physiological traits. Despite a limited availability of markers and individuals, this study is provides a successful proof-of-concept for the combination of high-throughput UAV-based phenotyping with cost-effective genotyping to disentangle the genetic architecture of phenotypic variation in a widespread conifer.

A 3K Axiom SNP array from a transcriptome-wide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer tree Araucaria angustifolia (Bert.) Kuntze

High-throughput SNP genotyping has become a precondition to move to higher precision and wider genome coverage genetic analysis of natural and breeding populations of non-model species. We developed a 44,318 annotated SNP catalog for Araucaria angustifolia, a grandiose subtropical conifer tree, one of the only two native Brazilian gymnosperms, critically endangered due to its valuable wood and seeds. Following transcriptome assembly and annotation, SNPs were discovered from RNA-seq and pooled RAD-seq data. From the SNP catalog, an Axiom® SNP array with 3,038 validated SNPs was developed and used to provide a comprehensive look at the genetic diversity and structure of 15 populations across the natural range of the species. RNA-seq was a far superior source of SNPs when compared to RAD-seq in terms of conversion rate to polymorphic markers on the array, likely due to the more efficient complexity reduction of the huge conifer genome. By matching microsatellite and SNP data on the same set of A. angustifolia individuals, we show that SNPs reflect more precisely the actual genome-wide patterns of genetic diversity and structure, challenging previous microsatellite-based assessments. Moreover, SNPs corroborated the known major north-south genetic cline, but allowed a more accurate attribution to regional versus among-population differentiation, indicating the potential to select ancestry-informative markers. The availability of a public, user-friendly 3K SNP array for A. angustifolia and a catalog of 44,318 SNPs predicted to provide ~29,000 informative SNPs across ~20,000 loci across the genome, will allow tackling still unsettled questions on its evolutionary history, toward a more comprehensive picture of the origin, past dynamics and future trend of the species' genetic resources. Additionally, but not less importantly, the SNP array described, unlocks the potential to adopt genomic prediction methods to accelerate the still very timid efforts of systematic tree breeding of A. angustifolia.

Ectomycorrhizal fungal diversity decreases in Mediterranean pine forests adapted to recurrent fires

Fire is a major disturbance linked to the evolutionary history and climate of Mediterranean ecosystems, where the vegetation has evolved fire-adaptive traits (e.g., serotiny in pines). In Mediterranean forests, mutualistic feedbacks between trees and ectomycorrhizal (ECM) fungi, essential for ecosystem dynamics, might be shaped by recurrent fires. We tested how the structure and function of ECM fungal communities of Pinus pinaster and Pinus halepensis vary among populations subjected to high and low fire recurrence in Mediterranean ecosystems, and analysed the relative contribution of environmental (climate, soil properties) and tree-mediated (serotiny) factors. For both pines, local and regional ECM fungal diversity were lower in areas of high than low fire recurrence, although certain fungal species were favoured in the former. A general decline of ECM root-tip enzymatic activity for P. pinaster was associated with high fire recurrence, but not for P. halepensis. Fire recurrence and fire-related factors such as climate, soil properties or tree phenotype explained these results. In addition to the main influence of climate, the tree fire-adaptive trait serotiny recovered a great portion of the variation in structure and function of ECM fungal communities associated with fire recurrence. Edaphic conditions (especially pH, tightly linked to bedrock type) were an important driver shaping ECM fungal communities, but mainly at the local scale and probably independently of the fire recurrence. Our results show that ECM fungal community shifts are associated with fire recurrence in fire-prone dry Mediterranean forests, and reveal complex feedbacks among trees, mutualistic fungi and the surrounding environment in these ecosystems.

Characterization and Application of EST-SSR Markers Developed From the Transcriptome of Amentotaxus argotaenia (Taxaceae), a Relict Vulnerable Conifer

Amentotaxus argotaenia (Taxaceae) is a vulnerable coniferous species with preference for shade and moist environment. Accurate estimation of genetic variation is crucial for its conservation, especially in the context of global warming. In this study, we acquired a transcriptome from A. argotaenia leaves using Illumina sequencing and de novo assembled 62,896 unigenes, of which 5510 EST-SSRs were detected. Twenty-two polymorphic EST-SSRs were successfully developed and further used to investigate genetic variation, linkage disequilibrium, and bottleneck signatures of A. argotaenia. The results showed that A. argotaenia had moderate genetic variation and high genetic differentiation, which may provide raw material to protect against climatic changes and accelerate local adaptation, respectively. No bottlenecks were found to occur in A. argotaenia. Our study not only showed that these EST markers are very effective in population genetic analysis but also lay a solid foundation for further investigating adaptive evolution and conservation strategies of A. argotaenia.

Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris

Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.

Looking for Local Adaptation: Convergent Microevolution in Aleppo Pine (Pinus halepensis)

Finding outlier loci underlying local adaptation is challenging and is best approached by suitable sampling design and rigorous method selection. In this study, we aimed to detect outlier loci (single nucleotide polymorphisms, SNPs) at the local scale by using Aleppo pine (Pinus halepensis), a drought resistant conifer that has colonized many habitats in the Mediterranean Basin, as the model species. We used a nested sampling approach that considered replicated altitudinal gradients for three contrasting sites. We genotyped samples at 294 SNPs located in genomic regions selected to maximize outlier detection. We then applied three different statistical methodologies-Two Bayesian outlier methods and one latent factor principal component method-To identify outlier loci. No SNP was an outlier for all three methods, while eight SNPs were detected by at least two methods and 17 were detected only by one method. From the intersection of outlier SNPs, only one presented an allelic frequency pattern associated with the elevational gradient across the three sites. In a context of multiple populations under similar selective pressures, our results underline the need for careful examination of outliers detected in genomic scans before considering them as candidates for convergent adaptation.

Gene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations

Gene copy number variations (CNVs) involved in phenotypic variations have already been shown in plants, but genomewide testing of CNVs for adaptive variation was not doable until recent technological developments. Thus, reports of the genomic architecture of adaptation involving CNVs remain scarce to date. Here, we investigated F₁ progenies of an intraprovenance cross (north-north cross, 58th parallel) and an interprovenances cross (north-south cross, 58th/49th parallels) for CNVs using comparative genomic hybridization on arrays of probes targeting gene sequences in balsam poplar (Populus balsamifera L.), a widespread North American forest tree. A total of 1,721 genes were found in varying copy numbers over the set of 19,823 tested genes. These gene CNVs presented an estimated average size of 8.3 kb and were distributed over poplar's 19 chromosomes including 22 hotspot regions. Gene CNVs number was higher for the interprovenance progeny in accordance with an expected higher genetic diversity related to the composite origin of this family. Regression analyses between gene CNVs and seven adaptive trait variations resulted in 23 significant links; among these adaptive gene CNVs, 30% were located in hotspots. One-to-five gene CNVs were found related to each of the measured adaptive traits and annotated for both biotic and abiotic stress responses. These annotations can be related to the occurrence of a higher pathogenic pressure in the southern parts of balsam poplar's distribution, and higher photosynthetic assimilation rates and water-use efficiency at high latitudes. Overall, our findings suggest that gene CNVs typically having higher mutation rates than SNPs may in fact represent efficient adaptive variations against fast-evolving pathogens.

Application of EST-SSR markers developed from the transcriptome of Torreya grandis (Taxaceae), a threatened nut-yielding conifer tree

Torreya grandis (Taxaceae) is an ancient conifer species endemic to southeast China. Because of its nutrient-rich and delicious seeds, this species has been utilized for centuries by the Chinese. However, transcriptome data and transcriptome-derived microsatellite markers for population genetics studies are still insufficient for understanding of this species’ genetic basis. In this study, a transcriptome from T. grandis leaves was generated using Illumina sequencing. A total of 69,920 unigenes were generated after de novo assembly, and annotated by searching against seven protein databases. In addition, 2,065 expressed sequence tag–simple sequence repeats (EST-SSRs) were detected, with the distribution frequency of 2.75% of total unigenes and average number of 0.03 SSRs per unigene. Among these EST-SSRs, 1,339 primer pairs were successfully designed, and 106 primer pairs were randomly selected for the development of potential molecular markers. Among them, 11 EST-SSR markers revealed a moderate level of genetic diversity, and were used to investigate the population structure of T. grandis. Two different genetic groups within this species were revealed using these EST-SSR markers, indicating that these markers developed in this study can be effectively applied to the population genetic analysis of T. grandis.

Inferring selection in instances of long-range colonization: The Aleppo pine (Pinus halepensis) in the Mediterranean Basin

Teasing apart the effects of natural selection and demography on current allele frequencies is challenging, due to both processes leaving a similar molecular footprint. In particular, when attempting to identify selection in species that have undergone a recent range expansion, the increase in genetic drift at the edges of range expansions ("allele surfing") can be a confounding factor. To address this potential issue, we first assess the long-range colonization history of the Aleppo pine across the Mediterranean Basin, using molecular markers. We then look for single nucleotide polymorphisms (SNPs) involved in local adaptation using: (a) environmental correlation methods (bayenv2), focusing on bioclimatic variables important for the species' adaptation (i.e., temperature, precipitation and water availability); and (b) FST -related methods (pcadapt). To assess the rate of false positives caused by the allele surfing effect, these results are compared with results from simulated SNP data that mimics the species' past range expansions and the effect of genetic drift, but with no selection. We find that the Aleppo pine shows a previously unsuspected complex genetic structure across its range, as well as evidence of selection acting on SNPs involved with the response to bioclimatic variables such as drought. This study uses an original approach to disentangle the confounding effects of drift and selection in range margin populations. It also contributes to the increased evidence that plant populations are able to adapt to new environments despite the expected accumulation of deleterious mutations that takes place during long-range colonizations.

Transcriptome analysis of Pinus halepensis under drought stress and during recovery

Forest trees use various strategies to cope with drought stress and these strategies involve complex molecular mechanisms. Pinus halepensis Miller (Aleppo pine) is found throughout the Mediterranean basin and is one of the most drought-tolerant pine species. In order to decipher the molecular mechanisms that P. halepensis uses to withstand drought, we performed large-scale physiological and transcriptome analyses. We selected a mature tree from a semi-arid area with suboptimal growth conditions for clonal propagation through cuttings. We then used a high-throughput experimental system to continuously monitor whole-plant transpiration rates, stomatal conductance and the vapor pressure deficit. The transcriptomes of plants were examined at six physiological stages: pre-stomatal response, partial stomatal closure, minimum transpiration, post-irrigation, partial recovery and full recovery. At each stage, data from plants exposed to the drought treatment were compared with data collected from well-irrigated control plants. A drought-stressed P. halepensis transcriptome was created using paired-end RNA-seq. In total, ~6000 differentially expressed, non-redundant transcripts were identified between drought-treated and control trees. Cluster analysis has revealed stress-induced down-regulation of transcripts related to photosynthesis, reactive oxygen species (ROS)-scavenging through the ascorbic acid (AsA)-glutathione cycle, fatty acid and cell wall biosynthesis, stomatal activity, and the biosynthesis of flavonoids and terpenoids. Up-regulated processes included chlorophyll degradation, ROS-scavenging through AsA-independent thiol-mediated pathways, abscisic acid response and accumulation of heat shock proteins, thaumatin and exordium. Recovery from drought induced strong transcription of retrotransposons, especially the retrovirus-related transposon Tnt1-94. The drought-related transcriptome illustrates this species' dynamic response to drought and recovery and unravels novel mechanisms.

Increased fire frequency promotes stronger spatial genetic structure and natural selection at regional and local scales in Pinus halepensis Mill

BACKGROUND AND AIMS

The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies.

METHODS

Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation.

KEY RESULTS

Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime.

CONCLUSIONS

An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits.

Genetic mapping of Pinus flexilis major gene (Cr4) for resistance to white pine blister rust using transcriptome-based SNP genotyping

Background

Linkage of DNA markers with phenotypic traits provides essential information to dissect clustered genes with potential phenotypic contributions in a target genome region. Pinus flexilis E. James (limber pine) is a keystone five-needle pine species in mountain-top ecosystems of North America. White pine blister rust (WPBR), caused by a non-native fungal pathogen Cronartium ribicola (J.C. Fisch.), has resulted in mortality in this conifer species and is still spreading through the distribution. The objective of this research was to develop P. flexilis transcriptome-wide single nucleotide polymorphism (SNP) markers using RNA-seq analysis for genetic mapping of the major gene (Cr4) that confers complete resistance to C. ribicola.

Results

Needle tissues of one resistant and two susceptible seedling families were subjected to RNA-seq analysis. In silico SNP markers were uncovered by mapping the RNA-seq reads back to the de novo assembled transcriptomes. A total of 110,573 in silico SNPs and 2,870 indels were identified with an average of 3.7 SNPs per Kb. These SNPs were distributed in 17,041 unigenes. Of these polymorphic P. flexilis unigenes, 6,584 were highly conserved as compared to the genome sequence of P. taeda L (loblolly pine). High-throughput genotyping arrays were designed and were used to search for Cr4-linked genic SNPs in megagametophyte populations of four maternal trees by haploid-segregation analysis. A total of 32 SNP markers in 25 genes were localized on the Cr4 linkage group (LG). Syntenic relationships of this Cr4-LG map with the model conifer species P. taeda anchored Cr4 on Pinus consensus LG8, indicating that R genes against C. ribicola have evolved independently in different five-needle pines. Functional genes close to Cr4 were annotated and their potential roles in Cr4-mediated resistance were further discussed.

Conclusions

We demonstrated a very effective, low-cost strategy for developing a SNP genetic map of a phenotypic trait of interest. SNP discovery through transcriptome comparison was integrated with high-throughput genotyping of a small set of in silico SNPs. This strategy may be applied to mapping any trait in non-model plant species that have complex genomes. Whole transcriptome sequencing provides a powerful tool for SNP discovery in conifers and other species with complex genomes, for which sequencing and annotation of complex genomes is still challenging. The genic SNP map for the consensus Cr4-LG may help future molecular breeding efforts by enabling both Cr4 positional characterization and selection of this gene against WPBR.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3079-2) contains supplementary material, which is available to authorized users.

Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding

Background

Solanum incanum is a close wild relative of S. melongena with high contents of bioactive phenolics and drought tolerance. S. aethiopicum is a cultivated African eggplant cross-compatible with S. melongena. Despite their great interest in S. melongena breeding programs, the genomic resources for these species are scarce.

Results

RNA-Seq was performed with NGS from pooled RNA of young leaf, floral bud and young fruit tissues, generating more than one hundred millions raw reads per species. The transcriptomes were assembled in 83,905 unigenes for S. incanum and in 87,084 unigenes for S. aethiopicum with an average length of 696 and 722 bp, respectively. The unigenes were structurally and functionally annotated based on comparison with public databases by using bioinformatic tools. The single nucleotide variant calling analysis (SNPs and INDELs) was performed by mapping our S. incanum and S. aethiopicum reads, as well as reads from S. melongena and S. torvum available on NCBI database (National Center for Biotechnology Information), against the eggplant genome. Both intraspecific and interspecific polymorphisms were identified and subsets of molecular markers were created for all species combinations. 36 SNVs were selected for validation in the S. incanum and S. aethiopicum accessions and 96 % were correctly amplified confirming the polymorphisms. In addition, 976 and 1,278 SSRs were identified in S. incanum and S. aethiopicum transcriptomes respectively, and a set of them were validated.

Conclusions

This work provides a broad insight into gene sequences and allelic variation in S. incanum and S. aethiopicum. This work is a first step toward better understanding of target genes involved in metabolic pathways relevant for eggplant breeding. The molecular markers detected in this study could be used across all the eggplant genepool, which is of interest for breeding programs as well as to perform marker-trait association and QTL analysis studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2631-4) contains supplementary material, which is available to authorized users.

Transcriptome sequencing, annotation and polymorphism detection in the hop bush, Dodonaea viscosa

Background

The hop bush, Dodonaea viscosa, is a trans-oceanic species distributed oversix continents. It evolved in Australia where it is found over a wide range of habitat types and is an ecologically important species. Limited genomic resources are currently available for this species, thus our understanding of its evolutionary history and ecological adaptation is restricted. Here, we present a comprehensive transcriptome dataset for future genomic studies into this species.

Methods

We performed Illumina sequencing of cDNA prepared from leaf tissue collected from seven populations of D. viscosa ssp. angustissima and spatulata distributed along an environmental gradient in South Australia. Sequenced reads were assembled to provide a transcriptome resource. Contiguous sequences (contigs) were annotated using BLAST searches against the NCBI non-redundant database and gene ontology definitions were assigned. Single nucleotide polymorphisms were detected for the establishment of a genetic marker set. A comparison between the two subspecies was also carried out.

Results

Illumina sequencing returned 268,672,818 sequence reads, which were de novoassembled into 105,125 contigs. Contigs with significant BLAST alignments (E value < 1e^-5)numbered at 44,191, with 38,311 of these having their most significant hits to sequences from land plant species. Gene Ontology terms were assigned to 28,440 contigs and KEGG analysis identified 146 pathways that the gene products from 5,070 contigs are potentially involved in. The subspecies comparison identified 8,494 fixed SNP differences across 3,979 contiguous sequences, indicating a level of genetic differentiation between them. Across all samples, 248,235 SNPs were detected.

Conclusions

We have established a significant genomic data resource for D. viscosa,providing a comprehensive transcriptomic reference. Genetic differences among morphologically distinct subspecies were found. A wide range of putative gene regions were identified along with a large set of variable SNP markers, providing a basis for studies into the evolution and ecological adaptation of D. viscosa.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1987-1) contains supplementary material, which is available to authorized users.

Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants

BACKGROUND

Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest.

METHODS

Here, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea.

RESULTS

We explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics.

CONCLUSIONS

The present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants.

Massive sequencing of Ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease

Elms, especially Ulmus minor and U. americana, are carrying out a hard battle against Dutch elm disease (DED). This vascular wilt disease, caused by Ophiostoma ulmi and O. novo-ulmi, appeared in the twentieth century and killed millions of elms across North America and Europe. Elm breeding and conservation programmes have identified a reduced number of DED tolerant genotypes. In this study, three U. minor genotypes with contrasted levels of tolerance to DED were exposed to several biotic and abiotic stresses in order to (i) obtain a de novo assembled transcriptome of U. minor using 454 pyrosequencing, (ii) perform a functional annotation of the assembled transcriptome, (iii) identify genes potentially involved in the molecular response to environmental stress, and (iv) develop gene-based markers to support breeding programmes. A total of 58,429 putative unigenes were identified after assembly and filtering of the transcriptome. 32,152 of these unigenes showed homology with proteins identified in the genome from the most common plant model species. Well-known family proteins and transcription factors involved in abiotic, biotic or both stresses were identified after functional annotation. A total of 30,693 polymorphisms were identified in 7,125 isotigs, a large number of them corresponding to single nucleotide polymorphisms (SNPs; 27,359). In a subset randomly selected for validation, 87% of the SNPs were confirmed. The material generated may be valuable for future Ulmus gene expression, population genomics and association genetics studies, especially taking into account the scarce molecular information available for this genus and the great impact that DED has on elm populations.

Evolutionary fire ecology: lessons learned from pines

Macroevolutionary studies of the genus Pinus provide the oldest current evidence of fire as an evolutionary pressure on plants and date back to ca. 125 million years ago (Ma). Microevolutionary studies show that fire traits are variable within and among populations, especially among those subject to different fire regimes. In addition, there is increasing evidence of an inherited genetic basis to variability in fire traits. Added together, pines provide compelling evidence that fire can exert an evolutionary pressure on plants and, thus, shape biodiversity. In addition, evolutionary fire ecology is providing insights to improve the management of pine forests under changing conditions. The lessons learned from pines may guide research on the evolutionary ecology of other taxa.

Differential Gene Expression Reveals Candidate Genes for Drought Stress Response in Abies alba (Pinaceae)

Increasing drought periods as a result of global climate change pose a threat to many tree species by possibly outpacing their adaptive capabilities. Revealing the genetic basis of drought stress response is therefore implemental for future conservation strategies and risk assessment. Access to informative genomic regions is however challenging, especially for conifers, partially due to their large genomes, which puts constraints on the feasibility of whole genome scans. Candidate genes offer a valuable tool to reduce the complexity of the analysis and the amount of sequencing work and costs. For this study we combined an improved drought stress phenotyping of needles via a novel terahertz water monitoring technique with Massive Analysis of cDNA Ends to identify candidate genes for drought stress response in European silver fir (Abies alba Mill.). A pooled cDNA library was constructed from the cotyledons of six drought stressed and six well-watered silver fir seedlings, respectively. Differential expression analyses of these libraries revealed 296 candidate genes for drought stress response in silver fir (247 up- and 49 down-regulated) of which a subset was validated by RT-qPCR of the twelve individual cotyledons. A majority of these genes code for currently uncharacterized proteins and hint on new genomic resources to be explored in conifers. Furthermore, we could show that some traditional reference genes from model plant species (GAPDH and eIF4A2) are not suitable for differential analysis and we propose a new reference gene, TPC1, for drought stress expression profiling in needles of conifer seedlings.

Western white pine SNP discovery and high-throughput genotyping for breeding and conservation applications

BACKGROUND

Western white pine (WWP, Pinus monticola Douglas ex D. Don) is of high interest in forest breeding and conservation because of its high susceptibility to the invasive disease white pine blister rust (WPBR, caused by the fungus Cronartium ribicola J. C. Fisch). However, WWP lacks genomic resource development and is evolutionarily far away from plants with available draft genome sequences. Here we report a single nucleotide polymorphism (SNP) study by bulked segregation-based RNA-Seq analysis.

RESULTS

A collection of resistance germplasm was used for construction of cDNA libraries and SNP genotyping. Approximately 36-89 million 2 × 100-bp reads were obtained per library and de-novo assembly generated the first shoot-tip reference transcriptome containing a total of 54,661 unique transcripts. Bioinformatic SNP detection identified >100,000 high quality SNPs in three expressed candidate gene groups: Pinus highly conserved genes (HCGs), differential expressed genes (DEGs) in plant defense response, and resistance gene analogs (RGAs). To estimate efficiency of in-silico SNP discovery, genotyping assay was developed by using Sequenom iPlex and it unveiled SNP success rates from 40.1% to 61.1%. SNP clustering analyses consistently revealed distinct populations, each composed of multiple full-sib seed families by parentage assignment in the WWP germplasm collection. Linkage disequilibrium (LD) analysis identified six genes in significant association with major gene (Cr2) resistance, including three RGAs (two NBS-LRR genes and one receptor-like protein kinase -RLK gene), two HCGs, and one DEG. At least one SNP locus provided an excellent marker for Cr2 selection across P. monticola populations.

CONCLUSIONS

The WWP shoot tip transcriptome and those validated SNP markers provide novel genomic resources for genetic, evolutionary and ecological studies. SNP loci of those candidate genes associated with resistant phenotypes can be used as positional and functional variation sites for further characterization of WWP major gene resistance against C. ribicola. Our results demonstrate that integration of RNA-seq-based transcriptome analysis and high-throughput genotyping is an effective approach for discovery of a large number of nucleotide variations and for identification of functional gene variants associated with adaptive traits in a non-model species.

Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions

Environmental salinity creates a key barrier to limit the distribution of most aquatic organisms. Adaptation to osmotic fluctuation is believed to be a factor facilitating species diversification. Adaptive evolution often involves beneficial mutations at more than one locus. Bivalves hold great interest, with numerous species living in waters, as osmoconformers, who maintain the osmotic pressure balance mostly by free amino acids. In this study, 107,076,589 reads from two groups of Crassostrea hongkongensis were produced and the assembled into 130,629 contigs. Transcripts putatively involved in stress-response, innate immunity and cell processes were identified according to Gene ontology and KEGG pathway analyses. Comparing with the transcriptome of C. gigas to characterize the diversity of transcripts between species with osmotic divergence, we identified 182,806 high-quality single nucleotide polymorphisms (SNPs) for C. hongkongensis, and 196,779 SNPs for C. gigas. Comparison of 11,602 pairs of putative orthologs allowed for identification of 14 protein-coding genes that experienced strong positive selection (Ka/Ks>1). In addition, 45 genes that may show signs of moderate positive selection (1 ≥ Ka/Ks>0.5) were also identified. Based on Ks ratios and divergence time between the two species published previously, we estimated a neutral transcriptome-wide substitution mutation rate of 1.39 × 10(-9) per site per year. Several genes were differentially expressed across the control and treated groups of each species. This is the first time to sequence the transcriptome of C. hongkongensis and provide the most comprehensive transcriptomic resource available for it. The increasing amount of transcriptome data on Crassostrea provides an excellent resource for phylogenetic analysis. A large number of SNPs identified in this work are expected to provide valuable resources for future marker and genotyping assay development. The analysis of natural selection provides an innovative view on the adaptation within species and sets the basis for future genetic and evolutionary studies.

Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations

Genomic resources are important and attainable for examining evolutionary change in divergent natural populations of nonmodel species. We utilized two next-generation sequencing (NGS) platforms, 454 and SOLiD 5500XL, to assemble low-coverage transcriptomes of the white-footed mouse (Peromyscus leucopus), a widespread and abundant native rodent in eastern North America. We sequenced liver mRNA transcripts from multiple individuals collected from urban populations in New York City and rural populations in undisturbed protected areas nearby and assembled a reference transcriptome using 1 080 065 954 SOLiD 5500XL (75 bp) reads and 3 052 640 454 GS FLX + reads. The reference contained 40 908 contigs with a N50 = 1044 bp and a total content of 30.06 Megabases (Mb). Contigs were annotated from Mus musculus (39.96% annotated) Uniprot databases. We identified 104 655 high-quality single nucleotide polymorphisms (SNPs) and 65 single sequence repeats (SSRs) with flanking primers. We also used normalized read counts to identify putative gene expression differences in 10 genes between populations. There were 19 contigs significantly differentially expressed in urban populations compared to rural populations, with gene function annotations generally related to the translation and modification of proteins and those involved in immune responses. The individual transcriptomes generated in this study will be used to investigate evolutionary responses to urbanization. The reference transcriptome provides a valuable resource for the scientific community using North American Peromyscus species as emerging model systems for ecological genetics and adaptation.