SMRT sequencing of a full-length transcriptome reveals transcript variants involved in C18 unsaturated fatty acid biosynthesis and metabolism pathways at chilling temperature in Pennisetum giganteum

Sustainable utilization of residual grass: effect of anaerobic storage days on chemical composition, fermentation performance, microbial community, and functional profiles of Pennisetum giganteum

The seasonal surplus and putrefactive property of moist forages inevitably increase the pressure on environmental protection and residual grass disposal. In the current work, the anaerobic fermentation approach was adopted to assist the sustainable recycling of leftover Pennisetum giganteum (LP), and its chemical composition, fermentation performance, bacterial community and functional profiles during anaerobic fermentation were studied. Fresh LP was spontaneously fermented for up to 60 d. At the end of anaerobic fermentation, fermented LP (FLP) displayed homolactic fermentation with low pH value, ethanol, and ammonia nitrogen concentrations but high lactic acid concentration. Weissella was dominant in 3-day FLP, yet Lactobacillus was the overwhelming genus (92.6%) in 60-day FLP. The anaerobic fermentation process promoted (P < 0.05) the metabolism of carbohydrate and nucleotide while suppressing (P < 0.05) that of lipid, cofactors, vitamins, energy, and amino acid. The results showed that the residual grass with LP as an example could be successfully fermented even if no additives were added, without signs of clostridial and fungal contamination.

Role of KOH-activated biochar on promoting anaerobic digestion of biomass from Pennisetumgianteum

Pennisetum giganteum is a promising non-food crop feedstock for biogas production due to its high productivity and bio-methane potential. However, the accumulation of volatile fatty acids (VFA) usually restricts the conversion efficiency of P. giganteum biomass (PGB) during anaerobic digestion (AD). Here, the role of KOH-activated biochar (KB) in improving the AD efficiency of PGB and the related mechanisms were investigated in detail. The results revealed that KB exhibited excellent electrical conductivity, electron transfer capacity and specific capacitance, which might be related to the decrease in the electron transfer resistance after adding KB to the AD process. In addition, the KB addition not only reinforced metabolisms of energy and VFAs but also promoted the conversion of VFAs to methane, leading to a 52% increase in the methane production rate. Bioinformatics analysis showed that Smithella and Methanosaeta were key players in the KB-mediated AD process of PGB. The stimulatory effect of methanogenesis probably resulted from the establishment of direct interspecies electron transfer (DIET) between VFA-oxidizing acetogens (e.g., Smithella) and Methanosaeta. These findings provided a key step to improve the PGB-based AD process.

A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus (JUJUNCAO) provides insights into its evolution and C4 photosynthesis

JUJUNCAO (Cenchrus fungigraminus; 2n = 4x = 28) is a Cenchrus grass with the highest biomass production among cultivated plants, and it can be used for mushroom cultivation, animal feed, and biofuel production. Here, we report a nearly complete genome assembly of JUJUNCAO and reveal that JUJUNCAO is an allopolyploid that originated ∼2.7 million years ago (mya). Its genome consists of two subgenomes, and subgenome A shares high collinear synteny with pearl millet. We also investigated the genome evolution of JUJUNCAO and suggest that the ancestral karyotype of Cenchrus split into the A and B ancestral karyotypes of JUJUNCAO. Comparative transcriptome and DNA methylome analyses revealed functional divergence of homeologous gene pairs between the two subgenomes, which was a further indication of asymmetric DNA methylation. The three types of centromeric repeat in the JUJUNCAO genome (CEN137, CEN148, and CEN156) may have evolved independently within each subgenome, with some introgressions of CEN156 from the B to the A subgenome. We investigated the photosynthetic characteristics of JUJUNCAO, revealing its typical C4 Kranz anatomy and high photosynthetic efficiency. NADP-ME and PEPCK appear to cooperate in the major C4 decarboxylation reaction of JUJUNCAO, which is different from other C4 photosynthetic subtypes and may contribute to its high photosynthetic efficiency and biomass yield. Taken together, our results provide insights into the highly efficient photosynthetic mechanism of JUJUNCAO and provide a valuable reference genome for future genetic and evolutionary studies, as well as genetic improvement of Cenchrus grasses.

Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum

BACKGROUND

Pennisetum giganteum (AABB, 2n = 4x = 28) is a C4 plant in the genus Pennisetum with origin in Africa but currently also grown in Asia and America. It is a crucial forage and potential energy grass with significant advantages in yield, stress resistance, and environmental adaptation. However, the mechanisms underlying these advantageous traits remain largely unexplored. Here, we present a high-quality genome assembly of the allotetraploid P. giganteum aiming at providing insights into biomass accumulation.

RESULTS

Our assembly has a genome size 2.03 Gb and contig N50 of 88.47 Mb that was further divided into A and B subgenomes. Genome evolution analysis revealed the evolutionary relationships across the Panicoideae subfamily lineages and identified numerous genome rearrangements that had occurred in P. giganteum. Comparative genomic analysis showed functional differentiation between the subgenomes. Transcriptome analysis found no subgenome dominance at the overall gene expression level; however, differentially expressed homoeologous genes and homoeolog-specific expressed genes between the two subgenomes were identified, suggesting that complementary effects between the A and B subgenomes contributed to biomass accumulation of P. giganteum. Besides, C4 photosynthesis-related genes were significantly expanded in P. giganteum and their sequences and expression patterns were highly conserved between the two subgenomes, implying that both subgenomes contributed greatly and almost equally to the highly efficient C4 photosynthesis in P. giganteum. We also identified key candidate genes in the C4 photosynthesis pathway that showed sustained high expression across all developmental stages of P. giganteum.

CONCLUSIONS

Our study provides important genomic resources for elucidating the genetic basis of advantageous traits in polyploid species, and facilitates further functional genomics research and genetic improvement of P. giganteum.

Dynamics of Phyllosphere Microbiota and Chemical Parameters at Various Growth Stages and Their Contribution to Anaerobic Fermentation of Pennisetum giganteum

This work evaluated the dynamic changes of phyllosphere microbiota and chemical parameters at various growth stages of Pennisetum giganteum and their effects on the bacterial community, cooccurrence networks, and functional properties during anaerobic fermentation. P. giganteum was collected at two growth stages (early vegetative stage [PA] and late vegetative stage [PB]) and was naturally fermented (NPA and NPB) for 1, 3, 7, 15, 30, and 60 days, respectively. At each time point, NPA or NPB was randomly sampled for the analysis of chemical composition, fermentation parameter, and microbial number. In addition, the fresh, 3-day, and 60-day NPA and NPB were subjected to high-throughput sequencing and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional prediction analyses. Growth stage obviously affected the phyllosphere microbiota and chemical parameters of P. giganteum. After 60 days of fermentation, NPB had a higher lactic acid concentration and ratio of lactic acid to acetic acid but a lower pH value and ammonia nitrogen concentration than NPA. Weissella and Enterobacter were dominant in 3-day NPA and Weissella was dominant in 3-day NPB, while Lactobacillus was the most abundant genus in both 60-day NPA and NPB. The complexity of bacterial cooccurrence networks in the phyllosphere decreased with P. giganteum growth. The ensiling process further decreased the complexity of bacterial networks, with the simplest bacterial correlation structures in NPB. There were great differences in the KEGG functional profiles of PA and PB. Ensiling promoted the metabolism of lipid, cofactors, vitamins, energy, and amino acids but suppressed the metabolism of carbohydrates and nucleotides. Storage time had a greater influence than growth stage on bacterial community diversity, cooccurrence networks, and functional profiles of P. giganteum silage. Differences in bacterial diversity and functionality of P. giganteum silage caused by growth stage appear to be offset by long-term storage. IMPORTANCE The phyllosphere microbiota consists of various and complex microbes, including bacteria with crucial relevance to the quality and safety of fermented food and feed. It initially derives from soil and becomes specific to its host after interaction with plants and climate. Bacteria associated with the phyllosphere are highly abundant and diverse, but we know little about their succession. Here, the phyllospheric microbiota structure was analyzed within the growth of P. giganteum. We also evaluated the effects of phyllosphere microbiota and chemical parameter changes on the anaerobic fermentation of P. giganteum. We observed remarkable differences in bacterial diversity, cooccurrence, and functionality of P. giganteum at various growth stages and storage times. The obtained results are important for understanding the fermentation mechanism and may contribute to high-efficient production without additional cost.

De novo full-length transcriptome analysis of two ecotypes of Phragmites australis (swamp reed and dune reed) provides new insights into the transcriptomic complexity of dune reed and its long-term adaptation to desert environments

BACKGROUND

The extremely harsh environment of the desert is changing dramatically every moment, and the rapid adaptive stress response in the short term requires enormous energy expenditure to mobilize widespread regulatory networks, which is all the more detrimental to the survival of the desert plants themselves. The dune reed, which has adapted to desert environments with complex and variable ecological factors, is an ideal type of plant for studying the molecular mechanisms by which Gramineae plants respond to combinatorial stress of the desert in their natural state. But so far, the data on the genetic resources of reeds is still scarce, therefore most of their research has focused on ecological and physiological studies.

RESULTS

In this study, we obtained the first De novo non-redundant Full-Length Non-Chimeric (FLNC) transcriptome databases for swamp reeds (SR), dune reeds (DR) and the All of Phragmites australis (merged of iso-seq data from SR and DR), using PacBio Iso-Seq technology and combining tools such as Iso-Seq3 and Cogent. We then identified and described long non-coding RNAs (LncRNA), transcription factor (TF) and alternative splicing (AS) events in reeds based on a transcriptome database. Meanwhile, we have identified and developed for the first time a large number of candidates expressed sequence tag-SSR (EST-SSRs) markers in reeds based on UniTransModels. In addition, through differential gene expression analysis of wild-type and homogenous cultures, we found a large number of transcription factors that may be associated with desert stress tolerance in the dune reed, and revealed that members of the Lhc family have an important role in the long-term adaptation of dune reeds to desert environments.

CONCLUSIONS

Our results provide a positive and usable genetic resource for Phragmites australis with a widespread adaptability and resistance, and provide a genetic database for subsequent reeds genome annotation and functional genomic studies.

Exploring epitranscriptomics for crop improvement and environmental stress tolerance

Climate change and stressful environmental conditions severely hamper crop growth, development and yield. Plants respond to environmental perturbations, through their plasticity provided by key-genes, governed at post-/transcriptional levels. Gene-regulation in plants is a multilevel process controlled by diverse cellular entities that includes transcription factors (TF), epigenetic regulators and non-coding RNAs beside others. There are successful studies confirming the role of epigenetic modifications (DNA-methylation/histone-modifications) in gene expression. Recent years have witnessed emergence of a highly specialized field the "Epitranscriptomics". Epitranscriptomics deals with investigating post-transcriptional RNA chemical-modifications present across the life forms that change structural, functional and biological characters of RNA. However, deeper insights on of epitranscriptomic modifications, with >140 types known so far, are to be understood fully. Researchers have identified epitranscriptome marks (writers, erasers and readers) and mapped the site-specific RNA modifications (m6A, m⁵C, 3' uridylation, etc.) responsible for fine-tuning gene expression in plants. Simultaneous advancement in sequencing platforms, upgraded bioinformatic tools and pipelines along with conventional labelled techniques have further given a statistical picture of these epitranscriptomic modifications leading to their potential applicability in crop improvement and developing climate-smart crops. We present herein the insights on epitranscriptomic machinery in plants and how epitranscriptome and epitranscriptomic modifications underlying plant growth, development and environmental stress responses/adaptations. Third-generation sequencing technology, advanced bioinformatics tools and databases being used in plant epitranscriptomics are also discussed. Emphasis is given on potential exploration of epitranscriptome engineering for crop-improvement and developing environmental stress tolerant plants covering current status, challenges and future directions.

Combination analysis of single-molecule long-read and Illumina sequencing provides insights into the anthocyanin accumulation mechanism in an ornamental grass, Pennisetum setaceum cv. Rubrum

Combination analysis of single-molecule long-read and Illumina sequencing provide full-length transcriptome information and shed new light on the anthocyanin accumulation mechanism of Pennisetum setaceum cv. 'Rubrum'. Pennisetum setaceum cv. 'Rubrum' is an ornamental grass with purple leaves widely used in landscaping. However, the current next-generation sequencing (NGS) transcriptome information of this species is not satisfactory due to the difficulties in obtaining full-length transcripts. Furthermore, the molecular mechanisms of anthocyanin accumulation in P. setaceum have not been thoroughly studied. In this study, we used PacBio full-length transcriptome sequencing (SMRT) combined with NGS technology to build and improve the transcriptomic datasets and reveal the molecular mechanism of anthocyanin accumulation in P. setaceum cv. 'Rubrum'. Therefore, 280,413 full-length non-chimeric reads sequences were obtained using the SMRT technology. We obtained 97,450 high-quality non-redundant transcripts and identified 5352 alternative splicing events. In addition, 93,066 open reading frames (ORFs), including 57,457 full ORFs and 2910 long non-coding RNA (lncRNAs) were screened out. Furthermore, 10,795 differentially expressed genes were identified using NGS. We also explored key genes, synthesis pathways, and detected lncRNA involved in anthocyanin accumulation, providing new insights into anthocyanin accumulation in P. setaceum cv. 'Rubrum'. To our best knowledge, we provided the full-length transcriptome information of P. setaceum cv. 'Rubrum' for the first time. The results of this study will provide baseline information for gene function studies and pave the way for future P. setaceum cv. 'Rubrum' breeding projects.

Bio-Matrix Pot Addition Enhanced the Vegetation Process of Iron Tailings by Pennisetum giganteum

The barrenness of large mine tailing sand reservoirs increases the risks for landslides and erosion that may be accompanied with transfer of contaminants into the surrounding environment. The tailing sand is poor in nutrients, which effectively complicates the vegetation process. We investigated direct planting of Pennisetum giganteum into tailing sand using two pit planting methods: the plants were transplanted either directly into pits filled with soil or into soil-filled bio-matrix pots made of organic material. After growing P. giganteum in iron tailing sand for 360 days, the dry weight of the plants grown in the bio-matrix pot (T2) was approximately twofold higher than that of the plants grown in soil placed directly into the sand (T1). At 360 days, the organic matter (OM) content in the soil below the pit was the lowest in the not-planted treatment (T0) and the highest in T2, the available N (AN) contents were higher in T1 and T2 than in T0, and the available P and K contents were the highest in T2. At 360 days, the Shannon diversity of the soil microbial communities was higher in T1 and T2 than in T0, and the community compositions were clearly separated from each other. The profiles of predicted C cycle catabolism functions and N fixation-related functions in T1 and T2 at 360 days were different from those in the other communities. The results showed that P. giganteum grew well in the iron tailing sand, especially in the bio-matrix pot treatment, and the increased nutrient contents and changes in microbial communities indicated that using the bio-matrix pot in planting had potential to improve the vegetation process in iron tailing sands effectively.

Using γ-ray irradiation and epiphytic microbiota inoculation to separate the effects of chemical and microbial factors on fermentation quality and bacterial community of ensiled Pennisetum giganteum

AIMS

This study aimed to separate the effects of chemical and microbial factors on the fermentation quality and bacterial community of ensiled Pennisetum giganteum.

METHODS AND RESULTS

Fresh P. giganteum of two vegetative stages (stage I, G_I ; stage II, G_II ) was treated as follows: G_I epiphytic microbiota + γ-ray presterilized G_I (M_I C_I ), G_II epiphytic microbiota + γ-ray presterilized G_I (M_II C_I ), G_I epiphytic microbiota + γ-ray presterilized G_II (M_I C_II ), and G_II epiphytic microbiota + γ-ray presterilized G_II (M_II C_II ). Triplicates per treatment were sampled after 30 days of ensiling for chemical and microbial analyses and high-throughput sequencing. Silages made from C_II (M_I C_II and M_II C_II ) had higher lactic acid concentration and the ratio of lactic to acetic acid, and lower pH and ammonia nitrogen concentration than silages produced by C_I (M_I C_I and M_II C_I ). Species differential analyses showed that the changes of chemical composition rather than epiphytic microbiota significantly affected the relative abundance of Lactobacillus, Pediococcus and Pantoea in P. giganteum silages.

CONCLUSION

These above results manifested that chemical composition was the main factor influencing the fermentation quality and bacterial community of P. giganteum silage in this study.

SIGNIFICANCE AND IMPACT OF THE STUDY

The obtained results may, therefore, be the first record to provide an in-depth understanding of the relative contributions of chemical and microbial parameters on fermentation quality and bacterial community, which is of great importance for modulating silage fermentation and improving silage quality.

Full-length transcriptome analysis of pecan (Carya illinoinensis) kernels

Pecan is rich in bioactive components such as fatty acids (FAs) and flavonoids and is an important nut type worldwide. Therefore, the molecular mechanisms of phytochemical biosynthesis in pecan are a focus of research. Recently, a draft genome and several transcriptomes have been published. However, the full-length mRNA transcripts remain unclear, and the regulatory mechanisms behind the quality components biosynthesis and accumulation have not been fully investigated. In this study, single-molecule long-read sequencing technology was used to obtain full-length transcripts of pecan kernels. In total, 37,504 isoforms of 16,702 genes were mapped to the reference genome. The numbers of known isoforms, new isoforms, and novel isoforms were 9013 (24.03%), 26,080 (69.54%), and 2411 (6.51%), respectively. Over 80% of the transcripts (30,751, 81.99%) had functional annotations. A total of 15,465 alternative splicing (AS) events and 65,761 alternative polyadenylation events were detected; wherein, the retained intron was the predominant type (5652, 36.55%) of AS. Furthermore, 1894 long noncoding RNAs and 1643 transcription factors were predicted using bioinformatics methods. Finally, the structural genes associated with FA and flavonoid biosynthesis were characterized. A high frequency of AS accuracy (70.31%) was observed in FA synthesis-associated genes. This study provides a full-length transcriptome data set of pecan kernels, which will significantly enhance the understanding of the regulatory basis of phytochemical biosynthesis during pecan kernel maturation.

Comparative Metabolomic and Transcriptomic Studies Reveal Key Metabolism Pathways Contributing to Freezing Tolerance Under Cold Stress in Kiwifruit

Cold stress poses a serious treat to cultivated kiwifruit since this plant generally has a weak ability to tolerate freezing tolerance temperatures. Surprisingly, however, the underlying mechanism of kiwifruit's freezing tolerance remains largely unexplored and unknown, especially regarding the key pathways involved in conferring this key tolerance trait. Here, we studied the metabolome and transcriptome profiles of the freezing-tolerant genotype KL (Actinidia arguta) and freezing-sensitive genotype RB (A. arguta), to identify the main pathways and important metabolites related to their freezing tolerance. A total of 565 metabolites were detected by a wide-targeting metabolomics method. Under (-25°C) cold stress, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway annotations showed that the flavonoid metabolic pathways were specifically upregulated in KL, which increased its ability to scavenge for reactive oxygen species (ROS). The transcriptome changes identified in KL were accompanied by the specific upregulation of a codeinone reductase gene, a chalcone isomerase gene, and an anthocyanin 5-aromatic acyltransferase gene. Nucleotides metabolism and phenolic acids metabolism pathways were specifically upregulated in RB, which indicated that RB had a higher energy metabolism and weaker dormancy ability. Since the LPCs (LysoPC), LPEs (LysoPE) and free fatty acids were accumulated simultaneously in both genotypes, these could serve as biomarkers of cold-induced frost damages. These key metabolism components evidently participated in the regulation of freezing tolerance of both kiwifruit genotypes. In conclusion, the results of this study demonstrated the inherent differences in the composition and activity of metabolites between KL and RB under cold stress conditions.

Temperature-Dependent Alternative Splicing of Precursor mRNAs and Its Biological Significance: A Review Focused on Post-Transcriptional Regulation of a Cold Shock Protein Gene in Hibernating Mammals

Multiple mRNA isoforms are often generated during processing such as alternative splicing of precursor mRNAs (pre-mRNA), resulting in a diversity of generated proteins. Alternative splicing is an essential mechanism for the functional complexity of eukaryotes. Temperature, which is involved in all life activities at various levels, is one of regulatory factors for controlling patterns of alternative splicing. Temperature-dependent alternative splicing is associated with various phenotypes such as flowering and circadian clock in plants and sex determination in poikilothermic animals. In some specific situations, temperature-dependent alternative splicing can be evoked even in homothermal animals. For example, the splicing pattern of mRNA for a cold shock protein, cold-inducible RNA-binding protein (CIRP or CIRBP), is changed in response to a marked drop in body temperature during hibernation of hamsters. In this review, we describe the current knowledge about mechanisms and functions of temperature-dependent alternative splicing in plants and animals. Then we discuss the physiological significance of hypothermia-induced alternative splicing of a cold shock protein gene in hibernating and non-hibernating animals.