Transcriptome characterisation of Pinus tabuliformis and evolution of genes in the Pinus phylogeny

Phylogeny and expression patterns of ERF genes that are potential reproductive inducers in hybrid larch

BACKGROUND

Larch is an important component of northern forests and a major cultivated tree species in restoration of forest cover using improved seed material. In recent years, the continuous low seed production has severely affected the production of improved variety seedlings and natural regeneration. However, research on the reproductive growth of gymnosperms is extremely scarce.

RESULTS

In this study, based on differential transcriptome analysis of two asexual reproductive phases, namely high-yield and low-yield, we further screened 5 ERF family genes that may affect the reproductive development of larch. We analyzed their genetic relationships and predicted their physicochemical properties. The expression patterns of these genes were analyzed in different tissues, developmental stages, hormone treatments, and environmental conditions in hybrid larch.

CONCLUSION

The results showed that all 5 genes were induced by low temperature and ABA, and their expression patterns in different tissues suggested a suppressive role in the development of female cones in larch. Among them, LkoERF3-like1 and LkoERF071 may be involved in the flowering age pathway. This study enriches the scarce research on reproductive development in gymnosperms and provides a theoretical basis and research direction for regulating the reproductive development of larch in seed orchards.

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.

An ethylene-induced NAC transcription factor acts as a multiple abiotic stress responsor in conifer

The proper response to various abiotic stresses is essential for plants' survival to overcome their sessile nature, especially for perennial trees with very long-life cycles. However, in conifers, the molecular mechanisms that coordinate multiple abiotic stress responses remain elusive. Here, the transcriptome response to various abiotic stresses like salt, cold, drought, heat shock and osmotic were systematically detected in Pinus tabuliformis (P. tabuliformis) seedlings. We found that four transcription factors were commonly induced by all tested stress treatments, while PtNAC3 and PtZFP30 were highly up-regulated and co-expressed. Unexpectedly, the exogenous hormone treatment assays and the content of the endogenous hormone indicates that the upregulation of PtNAC3 and PtZFP30 are mediated by ethylene. Time-course assay showed that the treatment by ethylene immediate precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), activated the expression of PtNAC3 and PtZFP30 within 8 hours. We further confirm that the PtNAC3 can directly bind to the PtZFP30 promoter region and form a cascade. Overexpression of PtNAC3 enhanced unified abiotic stress tolerance without growth penalty in transgenic Arabidopsis and promoted reproductive success under abiotic stress by shortening the lifespan, suggesting it has great potential as a biological tool applied to plant breeding for abiotic stress tolerance. This study provides novel insights into the hub nodes of the abiotic stresses response network as well as the environmental adaptation mechanism in conifers, and provides a potential biofortification tool to enhance plant unified abiotic stress tolerance.

Transcriptome and metabolome analyses of lignin biosynthesis mechanism of Platycladus orientalis

Background

Platycladus orientalis, as an important plant for ecological protection, is a pioneer tree species for afforestation in arid and barren mountainous areas. Lignin has the functions of water and soil conservation, strengthening plant mechanical strength and resisting adverse environmental effects and plays an important role in the ecological protection benefits of P. orientalis.

Methods

In this study, annual dynamic observations of the lignin content in roots, stems and leaves of one-year-old seedlings of a P. orientalis half-sib family were carried out, and combined transcriptome and metabolome analyses were carried out during three key stages of P. orientalis stem development.

Results

The lignin contents in roots, stems and leaves of P. orientalis showed extremely significant spatiotemporal differences. In the stems, lignin was mainly distributed in the cell walls of the pith, xylem, phloem, pericyte, and epidermis, with differences in different periods. A total of 226 metabolites were detected in the stem of P. orientalis, which were divided into seven categories, including 10 synthetic precursor compounds containing lignin. Among them, the content of coniferyl alcohol was the highest, accounting for 12.27% of the total content, and caffeyl alcohol was the lowest, accounting for 7.05% only. By annotating the KEGG functions, a large number of differentially expressed genes and differential metabolites were obtained for the comparison combinations, and seven key enzymes and 24 related genes involved in the process of lignin synthesis in P. orientalis were selected.

Conclusions

Based on the results of the metabolic mechanism of lignin in P. orientalis by biochemical, anatomical and molecular biological analyzes, the key regulatory pathways of lignin in P. orientalis were identified, which will be of great significance for regulating the lignin content of P. orientalis and improving the adaptability and resistance of this plant.

Involvement of PtCOL5-PtNF-YC4 in reproductive cone development and gibberellin signaling in Chinese pine

It is well documented that the CO/NF-YB/NF-YC trimer (NF-Y-CO) binds and regulates the FT promoter. However, the FT/TFL1-like (FLOWERING LOCUS T/TERMINALFLOWER1-like) genes in gymnosperms are all flowering suppressors, and the regulation model of NF-Y in gymnosperms is different from that in angiosperms. Here, using Chinese pine (Pinus tabuliformis), we identified a CONSTANS-LIKE gene, PtCOL5, the expression of which was strongly induced during cones development and it functioned as a repressor of flowering. PtNF-YC4, which interacted with PtCOL5, was highly correlated with PtCOL5 during growth and development, has been demonstrated. Moreover, PtNF-YC4 and PtCOL5 can bind to PtTFL2 promoter, and their interaction can enhance PtTFL2 expression. Interestingly, we found PtNF-YC4 and PtCOL5 were involved in gibberellin signaling and their interaction was inhibited by PtDELLA protein, thus affecting PtTFL2 expression. Collectively, PtCOL5-PtNF-YC4 was involved in reproductive cone development and gibberellin signaling in Chinese pine. Our findings uncovered reproductive cone development and signal transduction mechanism of COL-NF-Y in gymnosperms.

Ultrastructural elucidation of lignin macromolecule from different growth stages of Chinese pine

Understanding of the morphological changes at different growth stages and lignin accumulation pattern for pine biomass plays the key role in facilitating the further development of value-added utilization and downstream conversion processes. This work systematically revealed the morphological change and lignin accumulation pattern in Chinese pine branches cell walls via confocal Raman microscopy (CRM) technology. Meanwhile, the structural characteristics of isolated lignin samples from different growth stages were synthetically characterized by nuclear magnetic resonance (NMR) and gel permeation chromatography (GPC) techniques. The results indicated that the content of pith in adult pine new branch was bigger than juvenile trees. With the increase of physiological age, the branches in adult pine could accumulate more lignin both in overall content and the concentration of cell corner middle layer. Moreover, the significantly increases of molecular weights and the β-O-4, β-β linkages content revealed that the lignin macromolecule of pine would polymerize faster in the adult stage (14, 35 years). The panorama generated from the structural and chemical features of pine native lignin not only benefited to understand the biosynthetic pathways and lignin macromolecules structural variation in plant cell walls from different growth stages but also contributed to the valorization and deconstruction of biomass.

Genome-wide TCP transcription factors analysis provides insight into their new functions in seasonal and diurnal growth rhythm in Pinus tabuliformis

BACKGROUND

Pinus tabuliformis adapts to cold climate with dry winter in northern China, serving as important commercial tree species. The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTOR family(TCP)transcription factors were found to play a role in the circadian clock system in Arabidopsis. However, the role of TCP transcription factors in P. tabuliformis remains little understood.

RESULTS

In the present study, 43 TCP genes were identified from P. tabuliformis genome database. Based on the phylogeny tree and sequence similarity, the 43 TCP genes were classified into four groups. The motif results showed that different subfamilies indeed contained different motifs. Clade II genes contain motif 1, clade I genes contain motif 1, 8, 10 and clade III and IV contain more motifs, which is consistent with our grouping results. The structural analysis of PtTCP genes showed that most PtTCPs lacked introns. The distribution of clade I and clade II on the chromosome is relatively scattered, while clade III and clade IV is relatively concentrated. Co-expression network indicated that PtTCP2, PtTCP12, PtTCP36, PtTCP37, PtTCP38, PtTCP41 and PtTCP43 were co-expressed with clock genes in annual cycle and their annual cycle expression profiles both showed obvious seasonal oscillations. PtTCP2, PtTCP12, PtTCP37, PtTCP38, PtTCP40, PtTCP41, PtTCP42 and PtTCP43 were co-expressed with clock genes in diurnal cycle. Only the expression of PtTCP42 showed diurnal oscillation.

CONCLUSIONS

The TCP gene family, especially clade II, may play an important role in the regulation of the season and circadian rhythm of P. tabuliformis. In addition, the low temperature in winter may affect the diurnal oscillations.

Inflorescence Transcriptome Sequencing and Development of New EST-SSR Markers in Common Buckwheat (Fagopyrum esculentum)

Common buckwheat (Fagopyrum esculentum M.) is known for its adaptability, good nutrition, and medicinal and health care value. However, genetic studies of buckwheat have been hindered by limited genomic resources and genetic markers. In this study, Illumina HiSeq 4000 high-throughput sequencing technology was used to sequence the transcriptome of green-flower common buckwheat (Gr) with coarse pedicels and white-flower Ukrainian daliqiao (UD) with fine pedicels. A total of 118,448 unigenes were obtained, with an average length of 1248 bp and an N50 of 1850 bp. A total of 39,432 differentially expressed genes (DEGs) were identified, and the DEGs of the porphyrins and chlorophyll metabolic pathway had significantly upregulated expression in Gr. Then, a total of 17,579 sequences containing SSR loci were detected, and 20,756 EST-SSR loci were found. The distribution frequency of EST-SSR in the transcriptome was 17.52%, and the average distribution density was 8.21 kb. A total of 224 pairs of primers were randomly selected for synthesis; 35 varieties of common buckwheat and 13 varieties of Tartary buckwheat were verified through these primers. The clustering results well verified the previous conclusion that common buckwheat and Tartary buckwheat had a distant genetic relationship. The EST-SSR markers identified and developed in this study will be helpful to enrich the transcriptome information and marker-assisted selection breeding of buckwheat.

Morphological and Comparative Transcriptome Analysis of Three Species of Five-Needle Pines: Insights Into Phenotypic Evolution and Phylogeny

Pinus koraiensis, Pinus sibirica, and Pinus pumila are the major five-needle pines in northeast China, with substantial economic and ecological values. The phenotypic variation, environmental adaptability and evolutionary relationships of these three five-needle pines remain largely undecided. It is therefore important to study their genetic differentiation and evolutionary history. To obtain more genetic information, the needle transcriptomes of the three five-needle pines were sequenced and assembled. To explore the relationship of sequence information and adaptation to a high mountain environment, data on needle morphological traits [needle length (NL), needle width (NW), needle thickness (NT), and fascicle width (FW)] and 19 climatic variables describing the patterns and intensity of temperature and precipitation at six natural populations were recorded. Geographic coordinates of altitude, latitude, and longitude were also obtained. The needle morphological data was combined with transcriptome information, location, and climate data, for a comparative analysis of the three five-needle pines. We found significant differences for needle traits among the populations of the three five-needle pine species. Transcriptome analysis showed that the phenotypic variation and environmental adaptation of the needles of P. koraiensis, P. sibirica, and P. pumila were related to photosynthesis, respiration, and metabolites. Analysis of orthologs from 11 Pinus species indicated a closer genetic relationship between P. koraiensis and P. sibirica compared to P. pumila. Our study lays a foundation for genetic improvement of these five-needle pines and provides insights into the adaptation and evolution of Pinus species.

The Chinese pine genome and methylome unveil key features of conifer evolution

Conifers dominate the world's forest ecosystems and are the most widely planted tree species. Their giant and complex genomes present great challenges for assembling a complete reference genome for evolutionary and genomic studies. We present a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content. Large genes with long introns exhibited higher expressions levels. Despite a lack of recent whole-genome duplication, 91.2% of genes were duplicated through dispersed duplication, and expanded gene families are mainly related to stress responses, which may underpin conifers' adaptation, particularly in cold and/or arid conditions. The reproductive regulation network is distinct compared with angiosperms. Slow removal of TEs with high-level methylation may have contributed to genomic expansion. This study provides insights into conifer evolution and resources for advancing research on conifer adaptation and development.

MADS-box transcription factors MADS11 and DAL1 interact to mediate the vegetative-to-reproductive transition in pine

The reproductive transition is an important event that is crucial for plant survival and reproduction. Relative to the thorough understanding of the vegetative phase transition in angiosperms, a little is known about this process in perennial conifers. To gain insight into the molecular basis of the regulatory mechanism in conifers, we used temporal dynamic transcriptome analysis with samples from seven different ages of Pinus tabuliformis to identify a gene module substantially associated with aging. The results first demonstrated that the phase change in P. tabuliformis occurred as an unexpectedly rapid transition rather than a slow, gradual progression. The age-related gene module contains 33 transcription factors and was enriched in genes that belong to the MADS (MCMl, AGAMOUS, DEFICIENS, SRF)-box family, including six SOC1-like genes and DAL1 and DAL10. Expression analysis in P. tabuliformis and a late-cone-setting P. bungeana mutant showed a tight association between PtMADS11 and reproductive competence. We then confirmed that MADS11 and DAL1 coordinate the aging pathway through physical interaction. Overexpression of PtMADS11 and PtDAL1 partially rescued the flowering of 35S::miR156A and spl1,2,3,4,5,6 mutants in Arabidopsis (Arabidopsis thaliana), but only PtMADS11 could rescue the flowering of the ft-10 mutant, suggesting PtMADS11 and PtDAL1 play different roles in flowering regulatory networks in Arabidopsis. The PtMADS11 could not alter the flowering phenotype of soc1-1-2, indicating it may function differently from AtSOC1 in Arabidopsis. In this study, we identified the MADS11 gene in pine as a regulatory mediator of the juvenile-to-adult transition with functions differentiated from the angiosperm SOC1.

The Transcriptional Landscape and Hub Genes Associated with Physiological Responses to Drought Stress in Pinus tabuliformis

Drought stress has an extensive impact on regulating various physiological, metabolic, and molecular responses. In the present study, the Pinus tabuliformis transcriptome was studied to evaluate the drought-responsive genes using RNA- Sequencing approache. The results depicted that photosynthetic rate and H2O conductance started to decline under drought but recovered 24 h after re-watering; however, the intercellular CO2 concentration (Ci) increased with the onset of drought. We identified 84 drought-responsive transcription factors, 62 protein kinases, 17 transcriptional regulators, and 10 network hub genes. Additionally, we observed the expression patterns of several important gene families, including 2192 genes positively expressed in all 48 samples, and 40 genes were commonly co-expressed in all drought and recovery stages compared with the control samples. The drought-responsive transcriptome was conserved mainly between P. tabuliformis and A. thaliana, as 70% (6163) genes had a homologous in arabidopsis, out of which 52% homologous (3178 genes corresponding to 2086 genes in Arabidopsis) were also drought response genes in arabidopsis. The collaborative network exhibited 10 core hub genes integrating with ABA-dependent and independent pathways closely conserved with the ABA signaling pathway in the transcription factors module. PtNCED3 from the ABA family genes had shown significantly different expression patterns under control, mild, prolonged drought, and recovery stages. We found the expression pattern was considerably increased with the prolonged drought condition. PtNCED3 highly expressed in all drought-tested samples; more interestingly, expression pattern was higher under mild and prolonged drought. PtNCED3 is reported as one of the important regulating enzymes in ABA synthesis. The continuous accumulation of ABA in leaves increased resistance against drought was due to accumulation of PtNCED3 under drought stress in the pine needles.

Effects of graphene on morphology, microstructure and transcriptomic profiling of Pinus tabuliformis Carr. roots

Graphene has shown great potential for improving growth of many plants, but its effect on woody plants remains essentially unstudied. In this work, Pinus tabuliformis Carr. bare-rooted seedlings grown outdoors in pots were irrigated with a graphene solution over a concentration range of 0-50 mg/L for six months. Graphene was found to stimulate root growth, with a maximal effect at 25 mg/L. We then investigated root microstructure and carried out transcript profiling of root materials treated with 0 and 25 mg/L graphene. Graphene treatment resulted in plasma-wall separation and destruction of membrane integrity in root cells. More than 50 thousand of differentially expressed genes (DEGs) were obtained by RNA sequencing, among which 6477 could be annotated using other plant databases. The GO enrichment analysis and KEGG pathway analysis of the annotated DEGs indicated that abiotic stress responses, which resemble salt stress, were induced by graphene treatment in roots, while responses to biotic stimuli were inhibited. Numerous metabolic processes and hormone signal transduction pathways were altered by the treatment. The growth promotion effects of graphene may be mediated by encouraging proline synthesis, and suppression of the expression of the auxin response gene SMALL AUXIN UP-REGULATED RNA 41 (SAUR41), PYL genes which encode ABA receptors, and GSK3 homologs.

Mass spectrometry-based forest tree metabolomics

Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.

Comparative transcriptome analyses reveal two distinct transcriptional modules associated with pollen shedding time in pine

BACKGROUND

Seasonal flowering time is an ecologically and economically important trait in temperate trees. Previous studies have shown that temperature in many tree species plays a pivotal role in regulating flowering time. However, genetic control of flowering time is not synchronised in different individual trees under comparable temperature conditions, the underlying molecular mechanism is mainly to be investigated.

RESULTS

In the present study, we analysed the transcript abundance in male cones and needles from six early pollen-shedding trees (EPs) and six neighbouring late pollen-shedding trees (LPs) in Pinus tabuliformis at three consecutive time points in early spring. We found that the EPs and LPs had distinct preferred transcriptional modules in their male cones and, interestingly, the expression pattern was also consistently maintained in needles even during the winter dormancy period. Additionally, the preferred pattern in EPs was also adopted by other fast-growing tissues, such as elongating new shoots. Enhancement of nucleic acid synthesis and stress resistance pathways under cold conditions can facilitate rapid growth and maintain higher transcriptional activity.

CONCLUSIONS

During the cold winter and early spring seasons, the EPs were more sensitive to relatively warmer temperatures and showed higher transcriptomic activity than the LPs, indicating that EPs required less heat accumulation for pollen shedding than LPs. These results provided a transcriptomic-wide understanding of the temporal regulation of pollen shedding in pines.

The transcriptional activity of a temperature-sensitive transcription factor module is associated with pollen shedding time in pine

It has long been known that the pollen shedding time in pine trees is correlated with temperature, but the molecular basis for this has remained largely unknown. To better understand the mechanisms driving temperature response and to identify the hub regulators of pollen shedding time regulation in Pinus tabuliformis Carr., we identified a set of temperature-sensitive genes by carrying out a comparative transcriptome analysis using six early pollen shedding trees (EPs) and six late pollen shedding trees (LPs) during mid-winter and at three consecutive time points in early spring. We carried out a weighted gene co-expression network analysis and constructed a transcription factor (TF) collaborative network, merging the common but differentially expressed TFs of the EPs and LPs into a joint network. We found five hub genes in the core TF module whose expression was rapidly induced by low temperatures. The transcriptional activity of this TF module was strongly associated with pollen shedding time, and likely to produce the fine balance between cold hardiness and growth activity in early spring. We confirmed the key role of temperature in regulating flowering time and identified a transcription factor module associated with pollen shedding time in P. tabuliformis. This suggests that repression of growth activity by repressors is the main mechanism balancing growth and cold hardiness in pine trees in early spring. Our results provide new insights into the molecular mechanisms regulating seasonal flowering time in pines.

Comparative genomics and transcriptomics analysis reveals evolution patterns of selection in the Salix phylogeny

BACKGROUND

Willows are widely distributed in the northern hemisphere and have good adaptability to different living environment. The increasing of genome and transcriptome data provides a chance for comparative analysis to study the evolution patterns with the different origin and geographical distributions in the Salix phylogeny.

RESULTS

Transcript sequences of 10 Salicaceae species were downloaded from public databases. All pairwise of orthologues were identified by comparative analysis in these species, from which we constructed a phylogenetic tree and estimated the rate of diverse. Divergence times were estimated in the 10 Salicaceae using comparative transcriptomic analysis. All of the fast-evolving positive selection sequences were identified, and some cold-, drought-, light-, universal-, and heat- resistance genes were discovered.

CONCLUSIONS

The divergence time of subgenus Vetrix and Salix was about 17.6-16.0 Mya during the period of Middle Miocene Climate Transition (21-14 Mya). Subgenus Vetrix diverged to migratory and resident groups when the climate changed to the cool and dry trend by 14 Mya. Cold- and light- stress genes were involved in positive selection among the resident Vetrix, and which would help them to adapt the cooling stage. Universal- stress genes exhibited positive selection among the migratory group and subgenus Salix. These data are useful for comprehending the adaptive evolution and speciation in the Salix lineage.

Transcriptome sequencing of Pinus kesiya var. langbianensis and comparative analysis in the Pinus phylogeny

Background

Pines are widely distributed in the Northern Hemisphere and have a long evolutionary history. The availability of transcriptome data has facilitated comparative transcriptomics for studying the evolutionary patterns associated with the different geographical distributions of species in the Pinus phylogeny.

Results

The transcriptome of Pinus kesiya var. langbianensis was sequenced using the Illumina HiSeq 2000 platform, and a total of 68,881 unigenes were assembled by Trinity. Transcriptome sequences of another 12 conifer species were downloaded from public databases. All of the pairwise orthologues were identified by comparative transcriptome analysis in 13 conifer species, from which the rate of diversification was calculated and a phylogenetic tree inferred. All of the fast-evolving positive selection sequences were identified, and some salt-, drought-, and abscisic acid-resistance genes were discovered.

Conclusions

mRNA sequences of P. kesiya var. langbianensis were obtained by transcriptome sequencing, and a large number of simple sequence repeat and short nucleotide polymorphism loci were detected. These data can be used in molecular marker-assisted selected in pine breeding. Divergence times were estimated in the 13 conifer species using comparative transcriptomic analysis. A number of positive selection genes were found to be related to environmental factors. Salt- and abscisic acid-related genes exhibited different selection patterns between coastal and inland Pinus. Our findings help elucidate speciation patterns in the Pinus lineage.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5127-6) contains supplementary material, which is available to authorized users.

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.

RNA-seq Analysis Reveals Gene Expression Profiling of Female Fertile and Sterile Ovules of PinusTabulaeformis Carr. during Free Nuclear Mitosis of the Female Gametophyte

The development of the female gametophyte (FG) is one of the key processes of life cycle alteration between the haploid gametophyte and the diploid sporophytes in plants and it is required for successful seed development after fertilization. It is well demonstrated that free nuclear mitosis (FNM) of FG is crucial for the development of the ovule. However, studies of the molecular mechanism of ovule and FG development focused mainly on angiosperms, such as Arabidopsis thaliana and further investigation of gymnosperms remains to be completed. Here, Illumina sequencing of six transcriptomic libraries obtained from developing and abortive ovules at different stages during free nuclear mitosis of magagametophyte (FNMM) was used to acquire transcriptome data and gene expression profiles of Pinus tabulaeformis. Six cDNA libraries generated a total of 71.0 million high-quality clean reads that aligned with 63,449 unigenes and the comparison between developing and abortive ovules identified 7174 differentially expressed genes (DEGs). From the functional annotation results, DEGs involved in the cell cycle and phytohormone regulation were highlighted to reveal their biological importance in ovule development. Furthermore, validation of DEGs from the phytohormone signal transduction pathway was performed using quantitative real-time PCR analysis, revealing the dynamics of transcriptional networks and potential key components in the regulation of FG development in P. tabulaeformis were identified. These findings provide new insights into the regulatory mechanisms of ovule development in woody gymnosperms.

Complete chloroplast genome sequence and comparative analysis of loblolly pine (Pinus taeda L.) with related species

Pinaceae, the largest family of conifers, has a diversified organization of chloroplast (cp) genomes with two typical highly reduced inverted repeats (IRs). In the current study, we determined the complete sequence of the cp genome of an economically and ecologically important conifer tree, the loblolly pine (Pinus taeda L.), using Illumina paired-end sequencing and compared the sequence with those of other pine species. The results revealed a genome size of 121,531 base pairs (bp) containing a pair of 830-bp IR regions, distinguished by a small single copy (42,258 bp) and large single copy (77,614 bp) region. The chloroplast genome of P. taeda encodes 120 genes, comprising 81 protein-coding genes, four ribosomal RNA genes, and 35 tRNA genes, with 151 randomly distributed microsatellites. Approximately 6 palindromic, 34 forward, and 22 tandem repeats were found in the P. taeda cp genome. Whole cp genome comparison with those of other Pinus species exhibited an overall high degree of sequence similarity, with some divergence in intergenic spacers. Higher and lower numbers of indels and single-nucleotide polymorphism substitutions were observed relative to P. contorta and P. monophylla, respectively. Phylogenomic analyses based on the complete genome sequence revealed that 60 shared genes generated trees with the same topologies, and P. taeda was closely related to P. contorta in the subgenus Pinus. Thus, the complete P. taeda genome provided valuable resources for population and evolutionary studies of gymnosperms and can be used to identify related species.

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.

Comparative transcriptome reveal the potential adaptive evolutionary genes in Andrias davidianus

To search the evidence of molecular evolution mechanism for aquatic and cave habitat in Andrias davidianus, the evolution analysis was carried out among several species transcriptome data. The transcriptome data of Notophthalmus viridescens, Xenopus tropicalis, Cynops pyrrhogaster, Hynobius chinensis and A. davidianus were obtained from the Genbank and reassembled except Xenopus tropicalis. The BLAST search of transcriptome data obtained 1244 single-copy orthologous genes among five species. A phylogenetic tree showed A. davidianus to have the closest relationship to H. chinensis. Fourteen positively selected genes were detected in A. davidianus and N. vridescens group and fifteen in A. davidianus and H. chinensis group. Five genes were shared in the both groups which involved in the immune system, suggesting that A. davidianus adaptation to an aquatic and cave environment required rapid evolution of the immune system compared to N. viridescens and H. chinensis.

The gibberellin GID1-DELLA signalling module exists in evolutionarily ancient conifers

Gibberellins (GAs) participate in controlling various aspects of basic plant growth responses. With the exception of bryophytes, GA signalling in land plants, such as lycophytes, ferns and angiosperms, is mediated via GIBBERELLIN-INSENSITIVE DWARF1 (GID1) and DELLA proteins. To explore whether this GID1-DELLA mechanism is present in pines, we cloned an orthologue (PtGID1) of Arabidopsis AtGID1a and two putative DELLA proteins (PtDPL; PtRGA) from Pinus tabuliformis, a widespread indigenous conifer species in China, and studied their recombinant proteins. PtGID1 shares with AtGID1a the conserved HSL motifs for GA binding and an N-terminal feature that are essential for interaction with DELLA proteins. Indeed, A. thaliana 35S:PtGID1 overexpressors showed a strong GA-hypersensitive phenotype compared to the wild type. Interactions between PtGID1 and PtDELLAs, but also interactions between the conifer-angiosperm counterparts (i.e. between AtGID1 and PtDELLAs and between PtGID1 and AtDELLA), were detected in vivo. This demonstrates that pine has functional GID1-DELLA components. The Δ17-domains within PtDPL and PtRGA were identified as potential interaction sites within PtDELLAs. Our results show that PtGID1 has the ability to interact with DELLA and functions as a GA receptor. Thus, a GA-GID1-DELLA signalling module also operates in evolutionarily ancient conifers.

Testing the Hypothesis of Multiple Origins of Holoparasitism in Orobanchaceae: Phylogenetic Evidence from the Last Two Unplaced Holoparasitic Genera, Gleadovia and Phacellanthus

Orobanchaceae is the largest family among the parasitic angiosperms. It comprises non-parasites, hemi- and holoparasites, making this family an ideal test case for studying the evolution of parasitism. Previous phylogenetic analyses showed that holoparasitism had arisen at least three times from the hemiparasitic taxa in Orobanchaceae. Until now, however, not all known genera of Orobanchaceae were investigated in detail. Among them, the unknown phylogenetic positions of the holoparasites Gleadovia and Phacellanthus are the key to testing how many times holoparasitism evolved. Here, we provide clear evidence for the first time that they are members of the tribe Orobancheae, using sequence data from multiple loci (nuclear genes ITS, PHYA, PHYB, and plastid genes rps2, matK). Gleadovia is an independent lineage whereas Phacellanthus should be merged into genus Orobanche section Orobanche. Our results unambiguously support the hypothesis that there are only three origins of holoparasitism in Orobanchaceae. Divergence dating reveals for the first time that the three origins of holoparasitism were not synchronous. Our findings suggest that holoparasitism can persist in specific clades for a long time and holoparasitism may evolve independently as an adaptation to certain hosts.

A transcriptomics investigation into pine reproductive organ development

The development of reproductive structures in gymnosperms is still poorly studied because of a lack of genomic information and useful genetic tools. The hermaphroditic reproductive structure derived from unisexual gymnosperms is an even less studied aspect of seed plant evolution. To extend our understanding of the molecular mechanism of hermaphroditism and the determination of sexual identity of conifer reproductive structures in general, unisexual and bisexual cones from Pinus tabuliformis were profiled for gene expression using 60K microarrays. Expression patterns of genes during progression of sexual cone development were analysed using RNA-seq. The results showed that, overall, the transcriptomes of male structures in bisexual cones were more similar to those of female cones. However, the expression of several MADS-box genes in the bisexual cones was similar to that of male cones at the more juvenile developmental stage, while despite these expression shifts, male structures of bisexual cones and normal male cones were histologically indistinguishable and cone development was continuous. This study represents a starting point for in-depth analysis of the molecular regulation of cone development and also the origin of hermaphroditism in pine.

RNA-Seq SSRs of Moth Orchid and Screening for Molecular Markers across Genus Phalaenopsis (Orchidaceae)

Background

The moth orchid (Phalaenopsis species) is an ornamental crop that is highly commercialized worldwide. Over 30,000 cultivars of moth orchids have been registered at the Royal Horticultural Society (RHS). These cultivars were obtained by artificial pollination of interspecific hybridization. Therefore, the identification of different cultivars is highly important in the worldwide market.

Methods/Results

We used Illumina sequencing technology to analyze an important species for breeding, Phalaenopsis aphrodite subsp. formosana and develop the expressed sequence tag (EST)-simple sequence repeat (SSR) markers. After de novo assembly, the obtained sequence covered 29.1 Mb, approximately 2.2% of the P. aphrodite subsp. formosana genome (1,300 Mb), and a total of 1,439 EST-SSR loci were detected. SSR occurs in the exon region, including the 5’ untranslated region (UTR), coding region (CDS), and 3’UTR, on average every 20.22 kb. The di- and tri-nucleotide motifs (51.49% and 35.23%, respectively) were the two most frequent motifs in the P. aphrodite subsp. formosana. To validate the developed EST-SSR loci and to evaluate the transferability to the genus Phalaenopsis, thirty tri-nucleotide motifs of the EST-SSR loci were randomly selected to design EST-SSR primers and to evaluate the polymorphism and transferability across 22 native Phalaenopsis species that are usually used as parents for moth orchid breeding. Of the 30 EST-SSR loci, ten polymorphic and transferable SSR loci across the 22 native taxa can be obtained. The validated EST-SSR markers were further proven to discriminate 12 closely related Phalaenopsis cultivars. The results show that it is not difficult to obtain universal SSR markers by transcriptome deep sequencing in Phalaenopsis species.

Conclusions

This study supported that transcriptome analysis based on deep sequencing is a powerful tool to develop SSR loci in non-model species. A large number of EST-SSR loci can be isolated, and about 33.33% EST-SSR loci are universal markers across the Phalaenopsis breeding germplasm after preliminary validation. The potential universal EST-SSR markers are highly valuable for identifying all of Phalaenopsis cultivars.

Genome-Wide Identification of Genes Probably Relevant to the Uniqueness of Tea Plant (Camellia sinensis) and Its Cultivars

Tea (Camellia sinensis) is a popular beverage all over the world and a number of studies have focused on the genetic uniqueness of tea and its cultivars. However, molecular mechanisms underlying these phenomena are largely undefined. In this report, based on expression data available from public databases, we performed a series of analyses to identify genes probably relevant to the uniqueness of C. sinensis and two of its cultivars (LJ43 and ZH2). Evolutionary analyses showed that the evolutionary rates of genes involved in the pathways were not significantly different among C. sinensis, C. oleifera, and C. azalea. Interestingly, a number of gene families, including genes involved in the pathways synthesizing iconic secondary metabolites of tea plant, were significantly upregulated, expressed in C. sinensis (LJ43) when compared to C. azalea, and this may partially explain its higher content of flavonoid, theanine, and caffeine. Further investigation showed that nonsynonymous mutations may partially contribute to the differences between the two cultivars of C. sinensis, such as the chlorina and higher contents of amino acids in ZH2. Genes identified as candidates are probably relevant to the uniqueness of C. sinensis and its cultivars should be good candidates for subsequent functional analyses and marker-assisted breeding.

Transcriptome-enabled marker discovery and mapping of plastochron-related genes in Petunia spp

Background

Petunia (Petunia × hybrida), derived from a hybrid between P. axillaris and P. integrifolia, is one of the most economically important bedding plant crops and Petunia spp. serve as model systems for investigating the mechanisms underlying diverse mating systems and pollination syndromes. In addition, we have previously described genetic variation and quantitative trait loci (QTL) related to petunia development rate and morphology, which represent important breeding targets for the floriculture industry to improve crop production and performance. Despite the importance of petunia as a crop, the floriculture industry has been slow to adopt marker assisted selection to facilitate breeding strategies and there remains a limited availability of sequences and molecular markers from the genus compared to other economically important members of the Solanaceae family such as tomato, potato and pepper.

Results

Here we report the de novo assembly, annotation and characterization of transcriptomes from P. axillaris, P. exserta and P. integrifolia. Each transcriptome assembly was derived from five tissue libraries (callus, 3-week old seedlings, shoot apices, flowers of mixed developmental stages, and trichomes). A total of 74,573, 54,913, and 104,739 assembled transcripts were recovered from P. axillaris, P. exserta and P. integrifolia, respectively and following removal of multiple isoforms, 32,994 P. axillaris, 30,225 P. exserta, and 33,540 P. integrifolia high quality representative transcripts were extracted for annotation and expression analysis. The transcriptome data was mined for single nucleotide polymorphisms (SNP) and simple sequence repeat (SSR) markers, yielding 89,007 high quality SNPs and 2949 SSRs, respectively. 15,701 SNPs were computationally converted into user-friendly cleaved amplified polymorphic sequence (CAPS) markers and a subset of SNP and CAPS markers were experimentally verified. CAPS markers developed from plastochron-related homologous transcripts from P. axillaris were mapped in an interspecific Petunia population and evaluated for co-localization with QTL for development rate.

Conclusions

The high quality of the three Petunia spp. transcriptomes coupled with the utility of the SNP data will serve as a resource for further exploration of genetic diversity within the genus and will facilitate efforts to develop genetic and physical maps to aid the identification of QTL associated with traits of interest.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1931-4) contains supplementary material, which is available to authorized users.

Identification and expression profiles of sRNAs and their biogenesis and action-related genes in male and female cones of Pinus tabuliformis

Background

Small RNA (sRNA) play pivotal roles in reproductive development, and their biogenesis and action mechanisms are well characterised in angiosperm plants; however, corresponding studies in conifers are very limited. To improve our understanding of the roles of sRNA pathways in the reproductive development of conifers, the genes associated with sRNA biogenesis and action pathways were identified and analysed, and sRNA sequencing and parallel analysis of RNA ends (PARE) were performed in male and female cones of the Chinese pine (Pinus tabuliformis).

Results

Based on high-quality reference transcriptomic sequences, 21 high-confidence homologues involved in sRNA biogenesis and action in P. tabuliformis were identified, including two different DCL3 genes and one AGO4 gene. More than 75 % of genes involved in sRNA biogenesis and action have higher expression levels in female than in male cones. Twenty-six microRNA (miRNA) families and 74 targets, including 46 24-nt sRNAs with a 5’ A, which are specifically expressed in male cones or female cones and probably bind to AGO4, were identified.

Conclusions

The sRNA pathways have higher activity in female than in male cones, and the miRNA pathways are the main sRNA pathways in P. tabuliformis. The low level of 24-nt short-interfering RNAs in conifers is not caused by the absence of biogenesis-related genes or AGO-binding proteins, but most likely caused by the low accumulation of these key components. The identification of sRNAs and their targets, as well as genes associated with sRNA biogenesis and action, will provide a good starting point for investigations into the roles of sRNA pathways in cone development in conifers.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1885-6) contains supplementary material, which is available to authorized users.

Characterization of flower-bud transcriptome and development of genic SSR markers in Asian lotus (Nelumbo nucifera Gaertn.)

Background

Asian lotus (Nelumbo nucifera Gaertn.) is the national flower of India, Vietnam, and one of the top ten traditional Chinese flowers. Although lotus is highly valued for its ornamental, economic and cultural uses, genomic information, particularly the expressed sequence based (genic) markers is limited. High-throughput transcriptome sequencing provides large amounts of transcriptome data for promoting gene discovery and development of molecular markers.

Results

In this study, 68,593 unigenes were assembled from 1.34 million 454 GS-FLX sequence reads of a mixed flower-bud cDNA pool derived from three accessions of N. nucifera. A total of 5,226 SSR loci were identified, and 3,059 primer pairs were designed for marker development. Di-nucleotide repeat motifs were the most abundant type identified with a frequency of 65.2%, followed by tri- (31.7%), tetra- (2.1%), penta- (0.5%) and hexa-nucleotide repeats (0.5%). A total of 575 primer pairs were synthesized, of which 514 (89.4%) yielded PCR amplification products. In eight Nelumbo accessions, 109 markers were polymorphic. They were used to genotype a sample of 44 accessions representing diverse wild and cultivated genotypes of Nelumbo. The number of alleles per locus varied from 2 to 9 alleles and the polymorphism information content values ranged from 0.6 to 0.9. We performed genetic diversity analysis using 109 polymorphic markers. A UPGMA dendrogram was constructed based on Jaccard’s similarity coefficients revealing distinct clusters among the 44 accessions.

Conclusions

Deep transcriptome sequencing of lotus flower buds developed 3,059 genic SSRs, making a significant addition to the existing SSR markers in lotus. Among them, 109 polymorphic markers were successfully validated in 44 accessions of Nelumbo. This comprehensive set of genic SSR markers developed in our study will facilitate analyses of genetic diversity, construction of linkage maps, gene mapping, and marker-assisted selection breeding for lotus.

Transcriptome analysis of the oil-rich tea plant, Camellia oleifera, reveals candidate genes related to lipid metabolism

Background

Rapidly driven by the need for developing sustainable sources of nutritionally important fatty acids and the rising concerns about environmental impacts after using fossil oil, oil-plants have received increasing awareness nowadays. As an important oil-rich plant in China, Camellia oleifera has played a vital role in providing nutritional applications, biofuel productions and chemical feedstocks. However, the lack of C. oleifera genome sequences and little genetic information have largely hampered the urgent needs for efficient utilization of the abundant germplasms towards modern breeding efforts of this woody oil-plant.

Results

Here, using the 454 GS-FLX sequencing platform, we generated approximately 600,000 RNA-Seq reads from four tissues of C. oleifera. These reads were trimmed and assembled into 104,842 non-redundant putative transcripts with a total length of ∼38.9 Mb, representing more than 218-fold of all the C. oleifera sequences currently deposited in the GenBank (as of March 2014). Based on the BLAST similarity searches, nearly 42.6% transcripts could be annotated with known genes, conserved domains, or Gene Ontology (GO) terms. Comparisons with the cultivated tea tree, C. sinensis, identified 3,022 pairs of orthologs, of which 211 exhibited the evidence under positive selection. Pathway analysis detected the majority of genes potentially related to lipid metabolism. Evolutionary analysis of omega-6 fatty acid desaturase (FAD2) genes among 20 oil-plants unexpectedly suggests that a parallel evolution may occur between C. oleifera and Olea oleifera. Additionally, more than 2,300 simple sequence repeats (SSRs) and 20,200 single-nucleotide polymorphisms (SNPs) were detected in the C. oleifera transcriptome.

Conclusions

The generated transcriptome represents a considerable increase in the number of sequences deposited in the public databases, providing an unprecedented opportunity to discover all related-genes associated with lipid metabolic pathway in C. oleifera. It will greatly enhance the generation of new varieties of C. oleifera with increased yields and high quality.

Isolation and expression profiles of gibberellin metabolism genes in developing male and female cones of Pinus tabuliformis

Gibberellins (GAs) are important in the floral regulatory networks of angiosperm plants. Several lines of evidence suggest that GAs also play a pivotal role in conifer male and female cone development. To gain new insights into the GA metabolism pathway in conifer trees and the role of GA metabolism in male and female cone development, we identified GA metabolism genes in Pinus tabuliformis. These included one PtCPS gene, one PtKS gene, one PtKO gene, TWO PtKAO genes, one PtGA20ox gene, two PtGA3ox genes and 12 PtGA2ox genes. According to phylogenetic analysis, the GA biosynthesis pathway evolved after the divergence of mosses from ferns, but the GA-deactivating gene family underwent divided expansion after divergence of the angiosperms from gymnosperms. However, the active sites of all GA metabolism enzymes were conserved during the evolution of land plants. During male and female cone development of P. tabuliformis, the expression of most of the PtGA2ox genes, especially PtGA2ox10, was higher than GA biosynthesis genes. However, the expression of PtKAO1 in cones peaked at a very early developmental stage. The expression pattern of GA metabolism genes indicated that GAs play different roles at the early and late stages of cone development.

Development and characterization of 25 EST-SSR markers in Pinus sylvestris var. mongolica (Pinaceae)

PREMISE OF THE STUDY

A set of novel expressed sequence tag (EST) microsatellite markers was developed in Pinus sylvestris var. mongolica to promote further genetic studies in this species. •

METHODS AND RESULTS

One hundred seventy-five EST-simple sequence repeat (SSR) primers were designed and synthesized for 31,653 isotigs based on P. tabuliformis EST sequences. The primer pairs were used to identify 25 polymorphic loci in 48 individuals. The number of alleles ranged from two to eight with observed and expected heterozygosity values of 0.0435 to 0.8125 and 0.0430 to 0.7820, respectively. •

CONCLUSIONS

These new polymorphic EST-SSR markers will be useful for assessing genetic diversity, molecular breeding and genetic improvement, and conservation of P. sylvestris var. mongolica.