Transcriptome sequencing and profiling of expressed genes in cambial zone and differentiating xylem of Japanese cedar (Cryptomeria japonica)

Conserved autophagy and diverse cell wall composition: unifying features of vascular tissues in evolutionarily distinct plants

BACKGROUND AND AIMS

The formation of multifunctional vascular tissues represents a significant advancement in plant evolution. Differentiation of conductive cells is specific, involving two main pathways, namely protoplast clearance and cell wall modification. In xylogenesis, autophagy is a crucial process for complete protoplast elimination in tracheary elements, whose cell wall also undergoes strong changes. Knowledge pertaining to living sieve elements, which lose most of their protoplast during phloemogenesis, remains limited. We hypothesized that autophagy plays a crucial role, not only in complete cytoplasmic clearance in xylem but also in partial degradation in phloem. Cell wall elaborations of mature sieve elements are not so extensive. These analyses performed on evolutionarily diverse model species potentially make it possible to understand phloemogenesis to an equal extent to xylogenesis.

METHODS

We investigated the distribution of ATG8 protein, which is an autophagy marker, and cell wall components in the roots of ferns, gymnosperms and angiosperms (monocots, dicot herbaceous plants and trees). Furthermore, we conducted a bioinformatic analysis of complete data on ATG8 isoforms for Ceratopteris richardii.

KEY RESULTS

The presence of ATG8 protein was confirmed in both tracheary elements and sieve elements; however, the composition of cell wall components varied considerably among vascular tissues in the selected plants. Arabinogalactan proteins and β-1,4-galactan were detected in the roots of all studied species, suggesting their potential importance in phloem formation or function. In contrast, no evolutionary pattern was observed for xyloglucan, arabinan or homogalacturonan.

CONCLUSIONS

Our findings indicate that the involvement of autophagy in plants is universal during the development of tracheary elements that are dead at maturity and sieve elements that remain alive. Given the conserved nature of autophagy and its function in protoplast degradation for uninterrupted flow, autophagy might have played a vital role in the development of increasingly complex biological organizations, including the formation of vascular tissues. However, different cell wall compositions of xylem and phloem in different species might indicate diverse functionality and potential for substance transport, which is crucial in plant evolution.

Network Analysis of Metabolome and Transcriptome Revealed Regulation of Different Nitrogen Concentrations on Hybrid Poplar Cambium Development

Secondary development is a key biological characteristic of woody plants and the basis of wood formation. Exogenous nitrogen can affect the secondary growth of poplar, and some regulatory mechanisms have been found in the secondary xylem. However, the effect of nitrogen on cambium has not been reported. Herein, we investigated the effects of different nitrogen concentrations on cambium development using combined transcriptome and metabolome analysis. The results show that, compared with 1 mM NH4NO3 (M), the layers of hybrid poplar cambium cells decreased under the 0.15 mM NH4NO3 (L) and 0.3 mM NH4NO3 (LM) treatments. However, there was no difference in the layers of hybrid poplar cambium cells under the 3 mM NH4NO3 (HM) and 5 mM NH4NO3 (H) treatments. Totals of 2365, 824, 649 and 398 DEGs were identified in the M versus (vs.) L, M vs. LM, M vs. HM and M vs. H groups, respectively. Expression profile analysis of the DEGs showed that exogenous nitrogen affected the gene expression involved in plant hormone signal transduction, phenylpropanoid biosynthesis, the starch and sucrose metabolism pathway and the ubiquitin-mediated proteolysis pathway. In M vs. L, M vs. LM, M vs. HM and M vs. H, differential metabolites were enriched in flavonoids, lignans, coumarins and saccharides. The combined analysis of the transcriptome and metabolome showed that some genes and metabolites in plant hormone signal transduction, phenylpropanoid biosynthesis and starch and sucrose metabolism pathways may be involved in nitrogen regulation in cambium development, whose functions need to be verified. In this study, from the point of view that nitrogen influences cambium development to regulate wood formation, the network analysis of the transcriptome and metabolomics of cambium under different nitrogen supply levels was studied for the first time, revealing the potential regulatory and metabolic mechanisms involved in this process and providing new insights into the effects of nitrogen on wood development.

Two R2R3-MYB transcription factors from Chinese cedar (Cryptomeria fortunei Hooibrenk) are involved in the regulation of secondary cell wall formation

As the most abundant renewable energy source, wood comprises the secondary cell wall (SCW). SCW biosynthesis involves lignin and cellulose deposition. Increasing studies have illustrated that R2R3-MYB transcription factors (TFs) play pivotal roles in affecting lignin accumulation and SCW formation. Nevertheless, the regulatory roles of R2R3-MYBs are still unresolved in Cryptomeria fortunei Hooibrenk cambium and wood formation. To dissect the potentials of CfMYBs, we successfully cloned and intensively studied the functions of CfMYB4 and CfMYB5 in SCW formation and abiotic stress response. They both contained the conserved MYB domain capable of forming a special structure that could bind to the core motifs of downstream genes. The phylogenetic tree implied that two CfMYBs clustered into different evolutionary branches. They were predominantly expressed in the stem and were localized to the nucleus. Furthermore, CfMYB4 functioned as an activator to enhance lignin and cellulose accumulation, and increase the SCW thickness by elevating the expression levels of SCW-related genes. By contrast, CfMYB5 negatively regulated lignin and cellulose biosynthesis, and decreased SCW formation by reducing the expression of SCW biosynthetic genes. Our data not only highlight the regulatory functions of CfMYBs in lignin deposition but also provide critical insights into the development of strategies for the genetic improvement of Cryptomeria fortunei wood biomass.

Integrative analysis of transcriptome and metabolome reveals probiotic effects on cecal metabolism in broilers

BACKGROUND

Probiotics play an important role in the host and have attracted widespread attention as an alternative to antibiotics. Arbor Acres broilers were used in the present experiment and fed different doses of compound probiotics at 1, 5, and 10 g kg^-1 . The effects of compound probiotics on broiler growth performance and cecal transcriptome and metabolome were investigated.

RESULTS

We discovered 425 differentially expressed genes (DEGs; upregulated: 256; downregulated: 169) in the cecal transcriptome study. These DEGs were assigned to fat metabolic pathways, such as the peroxisome proliferator-activated receptor (PPAR) signaling pathway, according to KEGG analysis. Probiotics downregulated LPL and upregulated PPARα expression in the cecum. In metabolome analysis of the cecum of cecum, we screened 86 differential metabolites and performed KEGG enrichment analysis of these metabolites. The KEGG analysis showed that these differentially expressed metabolites were annotated to nucleotide metabolism-related pathways, such as purine metabolism. In the cecum, probiotics upregulated the content of guanine, AMP, 3'-AMP, adenylosuccinate, deoxyguanosine, and ADP-ribose, whereas they downregulated the content of 5-hydroxyisourate. Comprehensive transcriptome and metabolome analysis revealed that glycolysis, gluconeogenesis, and glycerophospholipid metabolism pathways were jointly enriched in cecum of broilers fed a probiotic-containing diet.

CONCLUSION

This study provides valuable information for studying the regulation and gene metabolism network of probiotics on cecal metabolism in broilers. © 2022 Society of Chemical Industry.

Changes in annual transcriptome dynamics of a clone of Japanese cedar (Cryptomeria japonica D. Don) planted under different climate conditions

Environmental responses are critical for plant growth and survival under different climate conditions. To elucidate the underlying biological mechanisms of environmental responses in Japanese cedar (Cryptomeria japonica D. Don), the annual transcriptome dynamics of common clonal trees (Godai1) planted at three different climate sites (Yamagata, Ibaraki, and Kumamoto Prefectures) were analyzed using microarrays. Both principal component analysis (PCA) and hierarchical clustering of the microarray data indicated the transition to dormant transcriptome status occurred earlier and the transition to active growth status later in the colder region. Interestingly, PCA also indicated that the transcriptomes of trees grown under three different conditions were similar during the growth period (June to September), whereas the transcriptomes differed between sites during the dormant period (January to March). In between-site comparisons, analyses of the annual expression profiles of genes for sites 'Yamagata vs. Kumamoto', 'Yamagata vs. Ibaraki', and 'Ibaraki vs. Kumamoto' identified 1,473, 1,137, and 925 targets exhibiting significantly different expression patterns, respectively. The total of 2,505 targets that exhibited significantly different expression patterns in all three comparisons may play important roles in enabling cuttings to adapt to local environmental conditions. Partial least-squares regression analysis and Pearson correlation coefficient analysis revealed that air temperature and day length were the dominant factors controlling the expression levels of these targets. GO and Pfam enrichment analyses indicated that these targets include genes that may contribute to environmental adaptation, such as genes related to stress and abiotic stimulus responses. This study provided fundamental information regarding transcripts that may play an important role in adaptation to environmental conditions at different planting sites.

Transcriptome and metabolome analyses reveal the regulatory effects of compound probiotics on cecal metabolism in heat-stressed broilers

The effect of compound probiotics on the caecum of broilers under heat stress was assessed in this study. A total of 400 twenty-eight-day-old AA male broilers were randomly divided into 4 treatment groups, where each group had 5 replicates of 20 broilers. The 4 treatment groups were a heat stress control group (broilers receiving a normal diet) and groups HP I, HP II, and HP Ⅲ, consisting of broilers receiving 1, 5, and 10 g of compound probiotics added to each kilogram of feed, respectively. Compound probiotics (L. casei, L. acidophilus, and B. lactis at a ratio of 1:1:2) were used to formulate a compound probiotic powder, with 1 × 10¹⁰ CFU/g of effective viable bacteria. Heat stress treatment was performed at 32 ± 1°C from 9:00 to 17:00 every day from 28 d to 42 d. In d 28 to 42, compared with the HC group, the ADG of broilers in the HP II and III groups was significantly increased (P < 0.05); the ADFI difference between groups was not significant (P > 0.05); the FCR of HP II and III broilers was significantly decreased (P < 0.05); and the FCR of the HP I group increased, but the difference was not significant (P > 0.05). Transcriptome results demonstrate that 665 differential genes were screened (DEGs; upregulated: 366, downregulated: 299). The DEGs were enriched in the B cell receptor signaling pathway, the intestinal immune network for IgA synthesis, the Fc epsilon RI signaling pathway, and other signaling pathways, according to KEGG enrichment analysis. Metabolome analysis identified 92 differential metabolites (DAMs; upregulated: 48, downregulated: 44). KEGG enrichment analysis indicated significant enrichment of Pantothenate and CoA biosynthesis and beta-Alanine metabolism. The combined transcriptome and metabolome analysis revealed that the DAMs and DEGs were mostly involved in beta-alanine metabolism, arginine biosynthesis, amino sugar and nucleotide sugar, and alanine, aspartate, and glutamate metabolism. The results of this study suggest that the addition of compound probiotics has a positive effect on intestinal metabolites, improving the growth performance and contributing to the overall health of broilers under heat stress.

Wood Formation under Changing Environment: Omics Approaches to Elucidate the Mechanisms Driving the Early-to-Latewood Transition in Conifers

The global change scenarios highlight the urgency of clarifying the mechanisms driving the determination of wood traits in forest trees. Coniferous xylem is characterized by the alternation between earlywood (EW) and latewood (LW), on which proportions the wood density depend, one of the most important mechanical xylem qualities. However, the molecular mechanisms triggering the transition between the production of cells with the typical features of EW to the LW are still far from being completely elucidated. The increasing availability of omics resources for conifers, e.g., genomes and transcriptomes, would lay the basis for the comprehension of wood formation dynamics, boosting both breeding and gene-editing approaches. This review is intended to introduce the importance of wood formation dynamics and xylem traits of conifers in a changing environment. Then, an up-to-date overview of the omics resources available for conifers was reported, focusing on both genomes and transcriptomes. Later, an analysis of wood formation studies using omics approaches was conducted, with the aim of elucidating the main metabolic pathways involved in EW and LW determination. Finally, the future perspectives and the urgent needs on this research topic were highlighted.

Concerted control of the LaRAV1-LaCDKB1;3 module by temperature during dormancy release and reactivation of larch

Dormancy release and reactivation of temperate-zone trees involve the temperature-modulated expression of cell-cycle genes. However, information on the detailed regulatory mechanism is limited. Here, we compared the transcriptomes of the stems of active and dormant larch trees, emphasizing the expression patterns of cell-cycle genes and transcription factors and assessed their relationships and responses to temperatures. Twelve cell-cycle genes and 31 transcription factors were strongly expressed in the active stage. Promoter analysis suggested that these 12 genes might be regulated by transcription factors from 10 families. Altogether, 73 cases of regulation between 16 transcription factors and 12 cell-cycle genes were predicted, while the regulatory interactions between LaMYB20 and LaCYCB1;1, and LaRAV1 and LaCDKB1;3 were confirmed by yeast one-hybrid and dual-luciferase assays. Last, we found that LaRAV1 and LaCDKB1;3 had almost the same expression patterns during dormancy release and reactivation induced naturally or artificially by temperature, indicating that the LaRAV1-LaCDKB1;3 module functions in the temperature-modulated dormancy release and reactivation of larch trees. These results provide new insights into the link between temperature and cell-cycle gene expression, helping to understand the temperature control of tree growth and development in the context of climate change.

Selection and Verification of Appropriate Reference Genes for Expression Normalization in Cryptomeria fortunei under Abiotic Stress and Hormone Treatments

Cryptomeria fortunei has become one of the main timber afforestation species in subtropical high-altitude areas of China due to its fast growth, good material quality, and strong adaptability, showing broad application prospects. Quantitative real-time PCR (qRT-PCR) is the most accurate and widely used gene expression evaluation technique, and selecting appropriate reference genes (RGs) is essential for normalizing qRT-PCR results. However, suitable RGs for gene expression normalization in C. fortunei have not been reported. Here, we tested the expression stability for 12 RGs in C. fortunei under various experimental conditions (simulated abiotic stresses (cold, heat, drought, and salinity) and hormone treatments (methyl jasmonate, abscisic acid, salicylic acid, and gibberellin) and in different tissues (stems, tender needles, needles, cones, and seeds) using four algorithms (delta Ct, geNorm, NormFinder, and BestKeeper). Then, geometric mean rankings from these algorithms and the RefFinder program were used to comprehensively evaluate RG stability. The results indicated CYP, actin, UBC, and 18S as good choices for studying C. fortunei gene expression. qRT-PCR analysis of the expression patterns of three target genes (CAT and MAPK1/6) further verified that the selected RGs were suitable for gene expression normalization. This study provides an important basis for C. fortunei gene expression standardization and quantification.

Response of the ileum transcriptome to probiotic and fructo-oligosaccharides in Taiping chicken

Taiping chicken is indigenous chickens (Gallus gallus domesticus), which was one of China's excellent poultry species, is an excellent chicken in Gansu Province. As the problems caused by the overuse of antibiotics become more and more severe, people begin to look for ways to replace them. Among them, probiotics and fructo-oligosaccharides are the research hotspot to replace antibiotics. Probiotics and fructo-oligosaccharides can promote the absorption of nutrients, improve the ability to resist and prevent diseases, and improve the intestinal tissue morphology. In this study, we used RNA-Seq analysis to study the gene expression in ileum tissue after Taiping chicken was given probiotics and fructo-oligosaccharides. In total, 67 genes were differentially expressed in the ileum. Ten of the differently expressed genes were further validated by RT-qPCR. In addition, these differentially expressed genes were mainly enriched to tyrosine metabolism, AGE-RAGE signaling pathway in diabetic complications, phenylalanine metabolism, and pyrimidine metabolism. The results which this study provides contribute to our understanding application of probiotics and fructo-oligosaccharides in indigenous chickens production and provide a theoretical basis for the genetic development of indigenous chickens.

Transcriptome and microRNA Sequencing Identified miRNAs and Target Genes in Different Developmental Stages of the Vascular Cambium in Cryptomeria fortunei Hooibrenk

Cryptomeria fortunei Hooibrenk is an important fast-growing coniferous timber species that is widely used in landscaping. Recently, research on timber quality has gained substantial attention in the field of tree breeding. Wood is the secondary xylem formed by the continuous inward division and differentiation of the vascular cambium; therefore, the development of the vascular cambium is particularly important for wood quality. In this study, we analyzed the transcriptomes of the cambial zone in C. fortunei during different developmental stages using Illumina HiSeq sequencing, focusing on general transcriptome and microRNA (miRNA) data. We performed functional annotation of the differentially expressed genes (DEGs) in the different stages identified by transcriptome sequencing and generated 15 miRNA libraries yielding 4.73 Gb of clean reads. The most common length of the filtered miRNAs was 21nt, accounting for 33.1% of the total filtered reads. We annotated a total of 32 known miRNA families. Some miRNAs played roles in hormone signal transduction (miR159, miR160, and miR166), growth and development (miR166 and miR396), and the coercion response (miR394 and miR395), and degradome sequencing showed potential cleavage sites between miRNAs and target genes. Differential expression of miRNAs and target genes and functional validation of the obtained transcriptome and miRNA data provide a theoretical basis for further elucidating the molecular mechanisms of cellular growth and differentiation, as well as wood formation in the vascular cambium, which will help improve the wood quality of C. fortunei.

Champions of winter survival: cold acclimation and molecular regulation of cold hardiness in evergreen conifers

Evergreen conifers are champions of winter survival, based on their remarkable ability to acclimate to cold and develop cold hardiness. Counterintuitively, autumn cold acclimation is triggered not only by exposure to low temperature, but also by a combination of decreasing temperature, decreasing photoperiod and changes in light quality. These environmental cues control a network of signaling pathways that coordinate cold acclimation and cold hardiness in overwintering conifers, leading to cessation of growth, bud dormancy, freezing tolerance and changes in energy metabolism. Advances in genomic, transcriptomic and metabolomic tools for conifers have improved our understanding of how trees sense and respond to changes in temperature and light during cold acclimation and the development of cold hardiness, but there remain considerable gaps deserving further research in conifers. In the first section of this review, we focus on the physiological mechanisms used by evergreen conifers to adjust metabolism seasonally and to protect overwintering tissues against winter stresses. In the second section, we review how perception of low temperature and photoperiod regulate the induction of cold acclimation. Finally, we explore the evolutionary context of cold acclimation in conifers and evaluate challenges imposed on them by changing climate and discuss emerging areas of research in the field.

Transcriptomic Profiling of Cryptomeria fortunei Hooibrenk Vascular Cambium Identifies Candidate Genes Involved in Phenylpropanoid Metabolism

Cryptomeria fortunei Hooibrenk (Chinese cedar) is a coniferous tree from southern China that has an important function in landscaping and timber production. Lignin is one of the key components of secondary cell walls, which have a crucial role in conducting water and providing mechanical support for the upward growth of plants. It is mainly biosynthesized via the phenylpropanoid metabolic pathway, of which the molecular mechanism remains so far unresolved in C. fortunei. In order to obtain further insight into this pathway, we performed transcriptome sequencing of the C. fortunei cambial zone at 5 successive growth stages. We generated 78,673 unigenes from transcriptome data, of which 45,214 (57.47%) were successfully annotated in the non-redundant protein database (NR). A total of 8975 unigenes were identified to be significantly differentially expressed between Sample_B and Sample_A after analyzing their expression profiles. Of the differentially expressed genes (DEGs), 6817 (75.96%) and 2158 (24.04%) were up- and down-regulated, respectively. 83 DEGs were involved in phenylpropanoid metabolism, 37 DEGs that encoded v-Myb avian myeloblastosis viral oncogene homolog (MYB) transcription factor (TF), and many candidates that encoded lignin synthesizing enzymes. These findings contribute to understanding the expression pattern of C. fortunei cambial zone transcriptome. Furthermore, our results provide additional insight towards understanding the molecular mechanisms of wood formation in C. fortunei.

A protocol for Agrobacterium-mediated transformation of Japanese cedar, Sugi (Cryptomeria japonica D. Don) using embryogenic tissue explants

Sugi (Cryptomeria japonica D. Don) is the most important afforestation coniferous tree in Japan. Coniferous trees normally have a long juvenile period and require a long cultivation time for breeding. Through a traditional breeding project that began in the 1950s, first generation plus trees with excellent traits were selected primarily from artificial forests and used as seedlings. Recently, the second generation plus trees obtained by crossing between plus trees have been selected. In light of this situation, the improvement of Sugi by a transgenic approach is effective in terms of shortening the breeding period compared with conventional crossing-dependent approaches. There are three key points to an efficient Agrobacterium-mediated transformation system: (1) establishment of explants with high regeneration ability, (2) optimal co-cultivation conditions for explants and Agrobacterium, and (3) efficient elimination of Agrobacterium. Here we describe a protocol for Agrobacterium-mediated transformation of Sugi that meets the above criteria using embryogenic tissues as explants isolated from immature seeds obtained by crossing.

Transcriptome Analysis in Male Strobilus Induction by Gibberellin Treatment in Cryptomeria japonica D. Don

The plant hormone gibberellin (GA) is known to regulate elongating growth, seed germination, and the initiation of flower bud formation, and it has been postulated that GAs originally had functions in reproductive processes. Studies on the mechanism of induction of flowering by GA have been performed in Arabidopsis and other model plants. In coniferous trees, reproductive organ induction by GAs is known to occur, but there are few reports on the molecular mechanism in this system. To clarify the gene expression dynamics of the GA induction of the male strobilus in Cryptomeria japonica, we performed comprehensive gene expression analysis using a microarray. A GA-treated group and a nontreated group were allowed to set, and individual trees were sampled over a 6-week time course. A total of 881 genes exhibiting changed expression was identified. In the GA-treated group, genes related to ‘stress response’ and to ‘cell wall’ were initially enriched, and genes related to ‘transcription’ and ‘transcription factor activity’ were enriched at later stages. This analysis also clarified the dynamics of the expression of genes related to GA signaling transduction following GA treatment, permitting us to compare and contrast with the expression dynamics of genes implicated in signal transduction responses to other plant hormones. These results suggested that various plant hormones have complex influences on the male strobilus induction. Additionally, principal component analysis (PCA) using expression patterns of the genes that exhibited sequence similarity with flower bud or floral organ formation-related genes of Arabidopsis was performed. PCA suggested that gene expression leading to male strobilus formation in C. japonica became conspicuous within one week of GA treatment. Together, these findings help to clarify the evolution of the mechanism of induction of reproductive organs by GA.

Effects of day length- and temperature-regulated genes on annual transcriptome dynamics in Japanese cedar (Cryptomeria japonica D. Don), a gymnosperm indeterminate species

Seasonal phenomena in plants are primarily affected by day length and temperature. The shoot transcriptomes of trees grown in the field and a controlled-environment chamber were compared to characterize genes that control annual rhythms and the effects of day length- and temperature-regulated genes in the gymnosperm Japanese cedar (Cryptomeria japonica D. Don), which exhibits seasonally indeterminate growth. Annual transcriptome dynamics were clearly demonstrated by principal component analysis using microarray data obtained under field-grown conditions. Analysis of microarray data from trees grown in a controlled chamber identified 2,314 targets exhibiting significantly different expression patterns under short-day (SD) and long-day conditions, and 2,045 targets exhibited significantly different expression patterns at 15°C (LT; low temperature) versus 25°C. Interestingly, although growth was suppressed under both SD and LT conditions, approximately 80% of the SD- and LT-regulated targets differed, suggesting that each factor plays a unique role in the annual cycle. The top 1,000 up-regulated targets in the growth/dormant period in the field coincided with more than 50% of the SD- and LT-regulated targets, and gene co-expression network analysis of the annual transcriptome indicated a close relationship between the SD- and LT-regulated targets. These results indicate that the respective effects of day length and temperature interact to control annual transcriptome dynamics. Well-known upstream genes of signaling pathways responsive to environmental conditions, such as the core clock (LHY/CjLHYb and CCA1/CjLHYa) and PEBP family (MFT) genes, exhibited unique expression patterns in Japanese cedar compared with previous reports in other species, suggesting that these genes control differences in seasonal regulation mechanisms between species. The results of this study provide new insights into seasonal regulation of transcription in Japanese cedar.

Cloning and Functional Analysis of Lignin Biosynthesis Genes Cf4CL and CfCCoAOMT in Cryptomeria fortunei

Cryptomeria fortunei, also known as the Chinese cedar, is an important timber species in southern China. The primary component of its woody tissues is lignin, mainly present in secondary cell walls. Therefore, continuous lignin synthesis is crucial for wood formation. In this study, we aimed to discover key genes involved in lignin synthesis expressed in the vascular cambium of C. fortunei. Through transcriptome sequencing, we detected expression of two genes, 4CL and CCoAOMT, known to be homologous to enzymes involved in the lignin synthesis pathway. We studied the function of these genes through bioinformatics analysis, cloning, vascular cambium expression analysis, and transgenic cross-species functional validation studies. Our results show that Cf4CL and CfCCoAOMT do indeed function in the pathway of lignin synthesis and likely perform this function in C. fortunei. They are prime candidates for future (gene-editing) studies aimed at optimizing C. fortunei wood production.

A MYB Triad Controls Primary and Phenylpropanoid Metabolites for Pollen Coat Patterning

The pollen wall is a complex, durable structure essential for plant reproduction. A substantial portion of phenylpropanoids (e.g. flavonols) produced by pollen grain tapetal cells are deposited in the pollen wall. Transcriptional regulation of pollen wall formation has been studied extensively, and a specific regulatory mechanism for Arabidopsis (Arabidopsis thaliana) pollen flavonol biosynthesis has been postulated. Here, metabolome and transcriptome analyses of anthers from mutant and overexpression genotypes revealed that Arabidopsis MYB99, a putative ortholog of the petunia (Petunia hybrida) floral scent regulator ODORANT1 (ODO1), controls the exclusive production of tapetum diglycosylated flavonols and hydroxycinnamic acid amides. We discovered that MYB99 acts in a regulatory triad with MYB21 and MYB24, orthologs of emission of benzenoids I and II, which together with ODO1 coregulate petunia scent biosynthesis genes. Furthermore, promoter-activation assays showed that MYB99 directs precursor supply from the Calvin cycle and oxidative pentose-phosphate pathway in primary metabolism to phenylpropanoid biosynthesis by controlling TRANSKETOLASE2 expression. We provide a model depicting the relationship between the Arabidopsis MYB triad and structural genes from primary and phenylpropanoid metabolism and compare this mechanism with petunia scent control. The discovery of orthologous protein triads producing related secondary metabolites suggests that analogous regulatory modules exist in other plants and act to regulate various branches of the intricate phenylpropanoid pathway.

Xylem Cell Wall Formation in Pioneer Roots and Stems of Populus trichocarpa (Torr. & Gray)

Regulation of gene expression, as determined by the genetics of the tree species, is a major factor in determining wood quality. Therefore, the identification of genes that play a role in xylogenesis is extremely important for understanding the mechanisms shaping the plant phenotype. Efforts to develop new varieties characterized by higher yield and better wood quality will greatly benefit from recognizing and understanding the complex transcriptional network underlying wood development. The present study provides a detailed comparative description of the changes that occur in genes transcription and the biosynthesis of cell-wall-related compounds during xylogenesis in Populus trichocarpa pioneer roots and stems. Even though results of microarray analysis indicated that only approximately 10% of the differentially expressed genes were common to both organs, many fundamental mechanisms were similar; e.g. the pattern of expression of genes involved in the biosynthesis of cell wall proteins, polysaccharides, and lignins. Gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) shows that the composition of monosaccharides was also very similar, with an increasing amount of xylose building secondary cell wall hemicellulose and pectins, especially in the stems. While hemicellulose degradation was typical for stems, possibly due to the intensive level of cell wall lignification. Notably, the main component of lignins in roots were guiacyl units, while syringyl units were dominant in stems, where fibers are especially needed for support. Our study is the first comprehensive analysis, at the structural and molecular level, of xylogenesis in under- and aboveground tree parts, and clearly reveals the great complexity of molecular mechanisms underlying cell wall formation and modification during xylogenesis in different plant organs.

Genome-wide identification and profiling of microRNAs in Paulownia tomentosa cambial tissues in response to seasonal changes

MicroRNAs (miRNAs), a group of endogenous small non-coding RNAs, have been shown to play essential roles in the regulation of gene expression at the post-transcriptional level. Although Paulownia tomentosa is an ecologically and economically important timber species due to its rapid growth, few efforts have focused on small RNAs (sRNAs) in the cambial tissues during winter and summer transition. In the present study, we identified 33 known miRNA families and 29 novel miRNAs which include 20 putative novel miRNAs* in P. tomentosa cambial tissues during winter and summer transition. Through differential expression analysis, we showed that 15 known miRNAs and 8 novel miRNAs were preferentially abundant in certain stage of cambial tissues. Based on the P. tomentosa mRNA transcriptome database, 1667 and 78 potential targets were predicted for 29 known and 20 novel miRNAs, respectively and the predicted targets are mostly transcription factors and functional genes. The targets of these miRNAs were enriched in "metabolic process" and "transcription regulation" by using Gene Ontology enrichment analysis. In addition, KEGG pathway analyses revealed the involvement of miRNAs in starch and sucrose metabolism and plant-pathogen interaction metabolism pathways. Noticeably, qRT-PCR expression analysis demonstrated that 9 miRNAs and their targets were existed a negative correlation in P. tomentosa cambial tissues. This study is the first to examine known and novel miRNAs and their potential targets in P. tomentosa cambial tissues during winter and summer transition and identify several candidate genes potentially regulating cambial phase transition, and thus provide a framework for further understanding of miRNAs functions in the regulation of cambial phase transition and wood formation in trees.

Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

BACKGROUND

Adventitious root formation is an essential physiological process for successful propagation of cuttings in various plant species. Because coniferous species are highly heterozygous, propagation of cuttings is of great practical use in breeding. Although various factors influence adventitious root formation, little is known of the associated regulatory mechanisms. Whereas adventitious roots generally form from the base of cuttings, this process is accompanied by physiological changes in leaves, which supply assimilates and metabolites. Herein, we present microarray analyses of transcriptome dynamics during adventitious root formation in whole cuttings in the coniferous species, Cryptomeria japonica.

RESULTS

Temporal patterns of gene expression were determined in the base, the middle, and needles of cuttings at eight time points during adventitious root formation. Global gene expression at the base had diverged from that in the middle by 3-h post-insertion, and changed little in the subsequent 3-days post-insertion, and global gene expression in needles altered characteristically at 3- and 6-weeks post-insertion. In Gene Ontology enrichment analysis of major gene clusters based on hierarchical clustering, the expression profiles of genes related to carbohydrates, plant hormones, and other categories indicated multiple biological changes that were involved in adventitious root formation.

CONCLUSIONS

The present comprehensive transcriptome analyses indicate major transcriptional turning and contribute to the understanding of the biological processes and molecular factors that influence adventitious root formation in C. japonica.

Identification of novel putative causative genes and genetic marker for male sterility in Japanese cedar (Cryptomeria japonica D.Don)

Background

Japanese cedar (Cryptomeria japonica) is an important tree for Japanese forestry. Male-sterile marker development in Japanese cedar would facilitate selection of male-sterile plus trees, addressing the widespread social problem of pollinosis and facilitating the identification of heterozygotes, which are useful for breeding.

Results

This study used next-generation sequencing for single-nucleotide polymorphism discovery in libraries constructed from several organs, including male-sterile and male-fertile strobili. The single-nucleotide polymorphisms obtained were used to construct a high-density linkage map, which enabled identification of a locus on linkage group 9 strongly correlated with male-sterile trait. Expressed sequence tags corresponding to 11 marker loci from 5 isotigs were associated with this locus within 33.4-34.5 cM. These marker loci explained 100% of the phenotypic variation. Several homologs of these sequences are associated with male sterility in rice or Arabidopsis, including a pre-mRNA splicing factor, a DEAD-box protein, a glycosyl hydrolase, and a galactosyltransferase. These proteins are thus candidates for the causal male-sterile gene at the ms-1 locus. After we used a SNaPshot assay to develop markers for marker-assisted selection (MAS), we tested F₂ progeny between male-sterile and wild-type plus trees to validate the markers and extrapolated the testing to a larger plus-tree population. We found that two developed from one of the candidates for the causal gene were suitable for MAS.

Conclusions

More than half of the ESTs and SNPs we collected were new, enlarging the genomic basis for genetic research on Japanese cedar. We developed two SNP markers aimed at MAS that distinguished individuals carrying the male-sterile trait with 100% accuracy, as well as individuals heterozygous at the male-sterile locus, even outside the mapping population. These markers should enable practical MAS for conifer breeding.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4581-5) contains supplementary material, which is available to authorized users.

Transcriptomic analysis of wound xylem formation in Pinus canariensis

BACKGROUND

Woody plants, especially trees, usually must face several injuries caused by different agents during their lives. Healing of injuries in stem and branches, affecting the vascular cambium and xylem can take several years. In conifers, healing takes place mainly from the remaining vascular cambium in the margin of the wound. The woundwood formed in conifers during healing usually presents malformed and disordered tracheids as well as abundant traumatic resin ducts. These characteristics affect its functionality as water conductor and its technological properties.

RESULTS

In this work we analyze for the first time the transcriptomic basis of the formation of traumatic wood in conifers, and reveal some differences with normal early- and late-wood. Microarray analysis of the differentiating traumatic wood, confirmed by quantitative RT-PCR, has revealed alterations in the transcription profile of up to 1408 genes during the first period of healing. We have grouped these genes in twelve clusters, according to their transcription profiles, and have distinguished accordingly two main phases during this first healing.

CONCLUSIONS

Wounding induces a complete rearrangement of the transcriptional program in the cambial zone close to the injuries. At the first instance, radial growth is stopped, and a complete set of defensive genes, mostly related to biotic stress, are induced. Later on, cambial activity is restored in the lateral borders of the wound, even at a high rate. During this second stage certain genes related to early-wood formation, including genes involved in cell wall formation and transcription factors, are significantly overexpressed, while certain late-wood related genes are repressed. Additionally, significant alterations in the transcription profile of abundant non annotated genes are reported.

Transcriptional regulation of vascular cambium activity during the transition from juvenile to mature stages in Cunninghamia lanceolata

Cunninghamia lanceolata (Lamb.) Hook., an evergreen conifer distributed in southern China, has been recognized as the most commercially important timber species due to its rapid growth. However, the molecular mechanisms underlying growth alternation due to vascular cambium activity are poorly understood. Here, we used cryosectioning to isolate the vascular cambium tissue of C. lanceolata at three stages, namely, juvenile, transition and mature (3-, 13-, and 35-year-old trees respectively) for transcriptome-wide analysis. Through assembling and annotation of transcripts, 108,767 unigenes and some potential growth-regulated genes were identified. A total of 5213, 4873 and 2541 differentially expressed genes (DEGs) were identified in the three stages. DEGs related to cambial activity, cell division and cell wall modification were detected at various developmental stages of the vascular cambium. In addition, some putative genes involved in plant hormone biosynthesis were also differentially regulated. These results indicate that various cambium-related molecular activities result in alterations in the growth of C. lanceolata, particularly during the transition from juvenile to mature stages. The findings of the present study improve our understanding of cambium development and may aid in studies of the molecular mechanisms of wood production and provide fundamental insights into the establishment of the optimal rotation period for silvicultural trees.

Seasonal development of cambial activity in relation to xylem formation in Chinese fir

The vascular cambium is a lateral meristem which can differentiate into secondary phloem and xylem. The secondary growth of woody plants resulting from vascular cambium activity has been a focus of considerable attention, but the quantitative relationships between cambial activity and secondary xylem formation have been little studied. Our analysis of cytological changes in the cambium of Chinese fir (Cunninghamia lanceolata), revealed a significant positive correlation between vascular cambium cell numbers and cambium zone width through the seasonal cycle. Cambium cell numbers and the cambium cell radial diameter were closely related to xylem formation. Immuno-labeling showed that de-esterified homogalacturonan and (1-4)-β-d-galactan epitopes were highly abundant in cell walls of dormant-stage cambium, whereas high methylesterified homogalacturonan was strongly labeled in the active stage. Raman spectroscopy detected significant changes in the chemical composition of cell walls during the active-dormant stage transition. More pectin and less monolignols occurred in radial cell walls than in tangential walls during the dormant stage, but no significant changes were found in other stages, indicating that pectin accumulation facilitates cell wall expansion, with cambium activity transition. Our quantitative analysis of the relationship between cambial activity and xylem formation, as well as the cell wall modification during the active stage provides useful information about cambial characteristics and xylogenesis.

Determination of male strobilus developmental stages by cytological and gene expression analyses in Japanese cedar (Cryptomeria japonica)

The molecular mechanisms that control male strobilus development in conifers are largely unknown because the developmental stages and related genes have not yet been characterized. The determination of male strobilus developmental stages will contribute to genetic research and reproductive biology in conifers. Our objectives in this study were to determine the developmental stages of male strobili by cytological and transcriptome analysis, and to determine the stages at which aberrant morphology is observed in a male-sterile mutant of Cryptomeria japonica D. Don to better understand the molecular mechanisms that control male strobilus and pollen development. Male strobilus development was observed for 8 months, from initiation to pollen dispersal. A set of 19,209 expressed sequence tags (ESTs) collected from a male reproductive library and a pollen library was used for microarray analysis. We divided male strobilus development into 10 stages by cytological and transcriptome analysis. Eight clusters (7324 ESTs) exhibited major changes in transcriptome profiles during male strobili and pollen development in C. japonica Two clusters showed a gradual increase and decline in transcript abundance, respectively, while the other six clusters exhibited stage-specific changes. The stages at which the male sterility trait of Sosyun was expressed were identified using information on male strobilus and pollen developmental stages and gene expression profiles. Aberrant morphology was observed cytologically at Stage 6 (microspore stage), and differences in expression patterns compared with wild type were observed at Stage 4 (tetrad stage).

Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development

Background

Wood development is of outstanding interest both to basic research and industry due to the associated cellulose and lignin biomass production. Efforts to elucidate wood formation (which is essential for numerous aspects of both pure and applied plant science) have been made using transcriptomic analyses and/or low-resolution sampling. However, transcriptomic data do not correlate perfectly with levels of expressed proteins due to effects of post-translational modifications and variations in turnover rates. In addition, high-resolution analysis is needed to characterize key transitions. In order to identify protein profiles across the developmental region of wood formation, an in-depth and tissue specific sampling was performed.

Results

We examined protein profiles, using an ultra-performance liquid chromatography/quadrupole time of flight mass spectrometry system, in high-resolution tangential sections spanning all wood development zones in Populus tremula from undifferentiated cambium to mature phloem and xylem, including cell expansion and cell death zones. In total, we analyzed 482 sections, 20–160 μm thick, from four 47-year-old trees growing wild in Sweden. We obtained high quality expression profiles for 3,082 proteins exhibiting consistency across the replicates, considering that the trees were growing in an uncontrolled environment. A combination of Principal Component Analysis (PCA), Orthogonal Projections to Latent Structures (OPLS) modeling and an enhanced stepwise linear modeling approach identified several major transitions in global protein expression profiles, pinpointing (for example) locations of the cambial division leading to phloem and xylem cells, and secondary cell wall formation zones. We also identified key proteins and associated pathways underlying these developmental landmarks. For example, many of the lignocellulosic related proteins were upregulated in the expansion to the early developmental xylem zone, and for laccases with a rapid decrease in early xylem zones. We observed upregulation of two forms of xylem cysteine protease (Potri.002G005700.1 and Potri.005G256000.2; Pt-XCP2.1) in early xylem and their downregulation in late maturing xylem. Our data also show that Pt-KOR1.3 (Potri.003G151700.2) exhibits an expression pattern that supports the hypothesis put forward in previous studies that this is a key xyloglucanase involved in cellulose biosynthesis in primary cell walls and reduction of cellulose crystallinity in secondary walls.

Conclusion

Our novel multivariate approach highlights important processes and provides confirmatory insights into the molecular foundations of wood development.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2458-z) contains supplementary material, which is available to authorized users.

The Plant Ontology: A Tool for Plant Genomics

The use of controlled, structured vocabularies (ontologies) has become a critical tool for scientists in the post-genomic era of massive datasets. Adoption and integration of common vocabularies and annotation practices enables cross-species comparative analyses and increases data sharing and reusability. The Plant Ontology (PO; http://www.plantontology.org/ ) describes plant anatomy, morphology, and the stages of plant development, and offers a database of plant genomics annotations associated to the PO terms. The scope of the PO has grown from its original design covering only rice, maize, and Arabidopsis, and now includes terms to describe all green plants from angiosperms to green algae.This chapter introduces how the PO and other related ontologies are constructed and organized, including languages and software used for ontology development, and provides an overview of the key features. Detailed instructions illustrate how to search and browse the PO database and access the associated annotation data. Users are encouraged to provide input on the ontology through the online term request form and contribute datasets for integration in the PO database.

Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function

Conifers have been understudied at the genomic level despite their worldwide ecological and economic importance but the situation is rapidly changing with the development of next generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In just a few years, genomes of 20-24 gigabases have been sequenced for several conifers, with several others expected in the near future. Biological insights have resulted from recent sequencing initiatives as well as genetic mapping, gene expression profiling and gene discovery research over nearly two decades. We review the knowledge arising from conifer genomics research emphasizing genome evolution and the genomic basis of adaptation, and outline emerging questions and knowledge gaps. We discuss future directions in three areas with potential inputs from NGS technologies: the evolutionary impacts of adaptation in conifers based on the adaptation-by-speciation model; the contributions of genetic variability of gene expression in adaptation; and the development of a broader understanding of genetic diversity and its impacts on genome function. These research directions promise to sustain research aimed at addressing the emerging challenges of adaptation that face conifer trees.

De novo assembly and characterization of transcriptomes of early-stage fruit from two genotypes of Annona squamosa L. with contrast in seed number

Background

Annona squamosa L., a popular fruit tree, is the most widely cultivated species of the genus Annona. The lack of transcriptomic and genomic information limits the scope of genome investigations in this important shrub. It bears aggregate fruits with numerous seeds. A few rare accessions with very few seeds have been reported for Annona. A massive pyrosequencing (Roche, 454 GS FLX+) of transcriptome from early stages of fruit development (0, 4, 8 and 12 days after pollination) was performed to produce expression datasets in two genotypes, Sitaphal and NMK-1, that show a contrast in the number of seeds set in fruits. The data reported here is the first source of genome-wide differential transcriptome sequence in two genotypes of A. squamosa, and identifies several candidate genes related to seed development.

Results

Approximately 1.9 million high-quality clean reads were obtained in the cDNA library from the developing fruits of both the genotypes, with an average length of about 568 bp. Quality-reads were assembled de novo into 2074 to 11004 contigs in the developing fruit samples at different stages of development. The contig sequence data of all the four stages of each genotype were combined into larger units resulting into 14921 (Sitaphal) and 14178 (NMK-1) unigenes, with a mean size of more than 1 Kb. Assembled unigenes were functionally annotated by querying against the protein sequences of five different public databases (NCBI non redundant, Prunus persica, Vitis vinifera, Fragaria vesca, and Amborella trichopoda), with an E-value cut-off of 10⁻⁵. A total of 4588 (Sitaphal) and 2502 (NMK-1) unigenes did not match any known protein in the NR database. These sequences could be genes specific to Annona sp. or belong to untranslated regions. Several of the unigenes representing pathways related to primary and secondary metabolism, and seed and fruit development expressed at a higher level in Sitaphal, the densely seeded cultivar in comparison to the poorly seeded NMK-1. A total of 2629 (Sitaphal) and 3445 (NMK-1) Simple Sequence Repeat (SSR) motifs were identified respectively in the two genotypes. These could be potential candidates for transcript based microsatellite analysis in A. squamosa.

Conclusion

The present work provides early-stage fruit specific transcriptome sequence resource for A. squamosa. This repository will serve as a useful resource for investigating the molecular mechanisms of fruit development, and improvement of fruit related traits in A. squamosa and related species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1248-3) contains supplementary material, which is available to authorized users.

Physiological and genomic basis of mechanical-functional trade-off in plant vasculature

Some areas in plant abiotic stress research are not frequently addressed by genomic and molecular tools. One such area is the cross reaction of gravitational force with upward capillary pull of water and the mechanical-functional trade-off in plant vasculature. Although frost, drought and flooding stress greatly impact these physiological processes and consequently plant performance, the genomic and molecular basis of such trade-off is only sporadically addressed and so is its adaptive value. Embolism resistance is an important multiple stress- opposition trait and do offer scopes for critical insight to unravel and modify the input of living cells in the process and their biotechnological intervention may be of great importance. Vascular plants employ different physiological strategies to cope with embolism and variation is observed across the kingdom. The genomic resources in this area have started to emerge and open up possibilities of synthesis, validation and utilization of the new knowledge-base. This review article assesses the research till date on this issue and discusses new possibilities for bridging physiology and genomics of a plant, and foresees its implementation in crop science.