Highly dynamic, coordinated, and stage-specific profiles are revealed by a multi-omics integrative analysis during tuberous root development in cassava

Integrated transcriptomic and proteomic analysis of exogenous abscisic acid regulation on tuberous root development in Pseudostellaria heterophylla

Abscisic acid (ABA) significantly regulates plant growth and development, promoting tuberous root formation in various plants. However, the molecular mechanisms of ABA in the tuberous root development of Pseudostellaria heterophylla are not yet fully understood. This study utilized Illumina sequencing and de novo assembly strategies to obtain a reference transcriptome associated with ABA treatment. Subsequently, integrated transcriptomic and proteomic analyses were used to determine gene expression profiles in P. heterophylla tuberous roots. ABA treatment significantly increases the diameter and shortens the length of tuberous roots. Clustering analysis identified 2,256 differentially expressed genes and 679 differentially abundant proteins regulated by ABA. Gene co-expression and protein interaction networks revealed ABA positively induced 30 vital regulators. Furthermore, we identified and assigned putative functions to transcription factors (PhMYB10, PhbZIP2, PhbZIP, PhSBP) that mediate ABA signaling involved in the regulation of tuberous root development, including those related to cell wall metabolism, cell division, starch synthesis, hormone metabolism. Our findings provide valuable insights into the complex signaling networks of tuberous root development modulated by ABA. It provided potential targets for genetic manipulation to improve the yield and quality of P. heterophylla, which could significantly impact its cultivation and medicinal value.

Genome-wide identification and expression analysis of the KNOX family and its diverse roles in response to growth and abiotic tolerance in sweet potato and its two diploid relatives

KNOXs, a type of homeobox genes that encode atypical homeobox proteins, play an essential role in the regulation of growth and development, hormonal response, and abiotic stress in plants. However, the KNOX gene family has not been explored in sweet potato. In this study, through sequence alignment, genomic structure analysis, and phylogenetic characterization, 17, 12 and 11 KNOXs in sweet potato (I. batatas, 2n = 6x = 90) and its two diploid relatives I. trifida (2n = 2x = 30) and I. triloba (2n = 2x = 30) were identified. The protein physicochemical properties, chromosome localization, phylogenetic relationships, gene structure, protein interaction network, cis-elements of promoters, tissue-specific expression and expression patterns under hormone treatment and abiotic stresses of these 40 KNOX genes were systematically studied. IbKNOX4, -5, and - 6 were highly expressed in the leaves of the high-yield varieties Longshu9 and Xushu18. IbKNOX3 and IbKNOX8 in Class I were upregulated in initial storage roots compared to fibrous roots. IbKNOXs in Class M were specifically expressed in the stem tip and hardly expressed in other tissues. Moreover, IbKNOX2 and - 6, and their homologous genes were induced by PEG/mannitol and NaCl treatments. The results showed that KNOXs were involved in regulating growth and development, hormone crosstalk and abiotic stress responses between sweet potato and its two diploid relatives. This study provides a comparison of these KNOX genes in sweet potato and its two diploid relatives and a theoretical basis for functional studies.

Extensive post-transcriptional regulation revealed by integrative transcriptome and proteome analyses in salicylic acid-induced flowering in duckweed (Lemna gibba)

Duckweed is an aquatic model plant with tremendous potential in industrial and agricultural applications. Duckweed rarely flowers which significantly hinders the resource collection and heterosis utilization. Salicylic acid (SA) can significantly induce duckweed to flower; however, the underlying regulatory mechanisms remain largely unknown. In this work, transcriptome and proteome were conducted in parallel to examine the expression change of genes and proteins in Lemna gibba under SA treatment. A high-quality reference transcriptome was generated using Iso-Seq strategy, yielding 42,281 full-length transcripts. A total of 422, 423, and 417 differentially expressed genes (DEGs), as well as 213, 51, and 92 differentially expressed proteins (DEPs), were identified at flower induction, flower initiation, and flowering stages by ssRNA-seq and iTRAQ methods. Most DEGs and DEPs were only regulated at either the transcriptomic or proteomic level. Additionally, DEPs exhibited low expression correlations with the corresponding mRNAs, suggesting that post-transcriptional regulation plays a pivotal role in SA-induced flowering in L. gibba. Specifically, the genes related to photosynthesis, stress, and hormone metabolism were mainly regulated at the mRNA level, those associated with mitochondrial electron transport / ATP synthesis, nucleotide synthesis, and secondary metabolism were regulated at the protein level, while those related to redox metabolism were regulated at the mRNA and/or protein levels. The post-transcriptional regulation of genes relevant to hormone synthesis, transcription factors, and flowering was also extensively analyzed and discussed. This is the first study of integrative transcriptomic and proteomic analyses in duckweed, providing novel insights of post-transcriptional regulation in SA-induced flowering of L. gibba.

TCOD: an integrated resource for tropical crops

Tropical crops are vital for tropical agriculture, with resource scarcity, functional diversity and extensive market demand, providing considerable economic benefits for the world's tropical agriculture-producing countries. The rapid development of sequencing technology has promoted a milestone in tropical crop research, resulting in the generation of massive amount of data, which urgently needs an effective platform for data integration and sharing. However, the existing databases cannot fully satisfy researchers' requirements due to the relatively limited integration level and untimely update. Here, we present the Tropical Crop Omics Database (TCOD, https://ngdc.cncb.ac.cn/tcod), a comprehensive multi-omics data platform for tropical crops. TCOD integrates diverse omics data from 15 species, encompassing 34 chromosome-level de novo assemblies, 1 255 004 genes with functional annotations, 282 436 992 unique variants from 2048 WGS samples, 88 transcriptomic profiles from 1997 RNA-Seq samples and 13 381 germplasm items. Additionally, TCOD not only employs genes as a bridge to interconnect multi-omics data, enabling cross-species comparisons based on homology relationships, but also offers user-friendly online tools for efficient data mining and visualization. In short, TCOD integrates multi-species, multi-omics data and online tools, which will facilitate the research on genomic selective breeding and trait biology of tropical crops.

Metabolic GWAS-based dissection of genetic basis underlying nutrient quality variation and domestication of cassava storage root

BACKGROUND

Metabolites play critical roles in regulating nutritional qualities of plants, thereby influencing their consumption and human health. However, the genetic basis underlying the metabolite-based nutrient quality and domestication of root and tuber crops remain largely unknown.

RESULTS

We report a comprehensive study combining metabolic and phenotypic genome-wide association studies to dissect the genetic basis of metabolites in the storage root (SR) of cassava. We quantify 2,980 metabolic features in 299 cultivated cassava accessions. We detect 18,218 significant marker-metabolite associations via metabolic genome-wide association mapping and identify 12 candidate genes responsible for the levels of metabolites that are of potential nutritional importance. Me3GT, MeMYB4, and UGT85K4/UGT85K5, which are involved in flavone, anthocyanin, and cyanogenic glucoside metabolism, respectively, are functionally validated through in vitro enzyme assays and in vivo gene silencing analyses. We identify a cluster of cyanogenic glucoside biosynthesis genes, among which CYP79D1, CYP71E7b, and UGT85K5 are highly co-expressed and their allelic combination contributes to low linamarin content. We find MeMYB4 is responsible for variations in cyanidin 3-O-glucoside and delphinidin 3-O-rutinoside contents, thus controlling SR endothelium color. We find human selection affects quercetin 3-O-glucoside content and SR weight per plant. The candidate gene MeFLS1 is subject to selection during cassava domestication, leading to decreased quercetin 3-O-glucoside content and thus increased SR weight per plant.

CONCLUSIONS

These findings reveal the genetic basis of cassava SR metabolome variation, establish a linkage between metabolites and agronomic traits, and offer useful resources for genetically improving the nutrition of cassava and other root crops.

Genome-wide identification, characterization, and expression analysis of the sweet potato (Ipomoea batatas [L.] Lam.) ARF, Aux/IAA, GH3, and SAUR gene families

BACKGROUND

Auxins are known to have roles in the tuberization process in sweet potato (Ipomoea batatas [L.] Lam.) and these effects are mediated by various auxin signalling gene families. In this study, an analysis of the sweet potato genome was performed to identify the ARF, Aux/IAA, GH3, and SAUR auxin signalling gene family members in this crop.

RESULTS

A total of 29 ARF, 39 Aux/IAA, 13 GH3, and 200 SAUR sequences were obtained, and their biochemical properties and gene expression profiles were analysed. The sequences were relatively conserved based on exon-intron structure, motif analysis, and phylogenetic tree construction. In silico expression analyses of the genes in fibrous and storage roots indicated that many sequences were not differentially expressed in tuberizing and non-tuberizing roots. However, some ARF, Aux/IAA, and SAUR genes were up-regulated in tuberizing storage roots compared to non-tuberizing fibrous roots while many GH3 genes were down-regulated. Additionally, these genes were expressed in a variety of plant parts, with some genes being highly expressed in shoots, leaves, and stems while others had higher expression in the roots. Some of these genes are up-regulated during the plant's response to various hormone treatments and abiotic stresses. Quantitative RT-PCR confirmation of gene expression was also conducted, and the results were concordant with the in silico analyses. A protein-protein interaction network was predicted for the differentially expressed genes, suggesting that these genes likely form part of a complex regulatory network that controls tuberization. These results confirm those of existing studies that show that auxin signalling genes have numerous roles in sweet potato growth and development.

CONCLUSION

This study provides useful information on the auxin signalling gene families in Ipomoea batatas and suggests putative candidates for further studies on the role of auxin signalling in tuberization and plant development.

Trehalose metabolism coordinates transcriptional regulatory control and metabolic requirements to trigger the onset of cassava storage root initiation

Cassava storage roots (SR) are an important source of food energy and raw material for a wide range of applications. Understanding SR initiation and the associated regulation is critical to boosting tuber yield in cassava. Decades of transcriptome studies have identified key regulators relevant to SR formation, transcriptional regulation and sugar metabolism. However, there remain uncertainties over the roles of the regulators in modulating the onset of SR development owing to the limitation of the widely applied differential gene expression analysis. Here, we aimed to investigate the regulation underlying the transition from fibrous (FR) to SR based on Dynamic Network Biomarker (DNB) analysis. Gene expression analysis during cassava root initiation showed the transition period to SR happened in FR during 8 weeks after planting (FR8). Ninety-nine DNB genes associated with SR initiation and development were identified. Interestingly, the role of trehalose metabolism, especially trehalase1 (TRE1), in modulating metabolites abundance and coordinating regulatory signaling and carbon substrate availability via the connection of transcriptional regulation and sugar metabolism was highlighted. The results agree with the associated DNB characters of TRE1 reported in other transcriptome studies of cassava SR initiation and Attre1 loss of function in literature. The findings help fill the knowledge gap regarding the regulation underlying cassava SR initiation.

Integrated transcriptome, proteome and metabolome analyses revealed secondary metabolites and auxiliary carbohydrate metabolism augmenting drought tolerance in rice

Drought is one of the major consequences of climate change and a serious threat to rice production. Drought stress activates interactions among genes, proteins and metabolites at the molecular level. A comparative multi-omics analysis of drought-tolerant and drought-sensitive rice cultivars can decipher the molecular mechanisms involved in drought tolerance/response. Here, we characterized the global-level transcriptome, proteome, and metabolome profiles, and performed integrated analyses thereof in a drought-sensitive (IR64) and a drought-tolerant (Nagina 22) rice cultivar under control and drought-stress conditions. The transcriptional dynamics and its integration with proteome analysis revealed the role of transporters in regulation of drought stress. The proteome response illustrated the contribution of translational machinery to drought tolerance in N22. The metabolite profiling revealed that aromatic amino acids and soluble sugars contribute majorly to drought tolerance in rice. The integrated transcriptome, proteome and metabolome analysis performed using statistical and knowledge-based methods revealed the preference for auxiliary carbohydrate metabolism through glycolysis and pentose phosphate pathway contributed to drought tolerance in N22. In addition, L-phenylalanine and the genes/proteins responsible for its biosynthesis were also found to contribute to drought tolerance in N22. In conclusion, our study provided mechanistic insights into the drought response/adaptation mechanism and is expected to facilitate engineering of drought tolerance in rice.

Deciphering the hormone regulatory mechanisms of storage root initiation in sweet potato: challenges and future prospects

Sweet potato (Ipomoea batatas) is an economically important food crop that is grown primarily for its edible storage roots. Several researchers have consequently been conducting studies to increase sweet potato yield, and an important aspect of this research involves understanding how storage root initiation occurs. Although significant progress has been made, several challenges associated with studying this crop have resulted in lagging progress compared to other crops and thus sweet potato storage root initiation is not clearly understood. This article highlights the most important aspects of the hormone signalling processes during storage root initiation that needs to be investigated further and suggests candidate genes that should be prioritized for further study, based on their importance in storage organ formation in other crops. Lastly, ways of overcoming the challenges associated with studying this crop are suggested.

Genome-wide characterization and expression analysis of α-amylase and β-amylase genes underlying drought tolerance in cassava

BACKGROUND

Starch hydrolysates are energy sources for plant growth and development, regulate osmotic pressure and transmit signals in response to both biological and abiotic stresses. The α-amylase (AMY) and the β-amylase (BAM) are important enzymes that catalyze the hydrolysis of plant starch. Cassava (Manihot esculenta Crantz) is treated as one of the most drought-tolerant crops. However, the mechanisms of how AMY and BAM respond to drought in cassava are still unknown.

RESULTS

Six MeAMY genes and ten MeBAM genes were identified and characterized in the cassava genome. Both MeAMY and MeBAM gene families contain four genes with alternative splicing. Tandem and fragment replications play important roles in the amplification of MeAMY and MeBAM genes. Both MeBAM5 and MeBAM10 have a BZR1/BES1 domain at the N-terminus, which may have transcription factor functions. The promoter regions of MeAMY and MeBAM genes contain a large number of cis-acting elements related to abiotic stress. MeAMY1, MeAMY2, MeAMY5, and MeBAM3 are proven as critical genes in response to drought stress according to their expression patterns under drought. The starch content, soluble sugar content, and amylase activity were significantly altered in cassava under different levels of drought stress.

CONCLUSIONS

These results provide fundamental knowledge for not only further exploring the starch metabolism functions of cassava under drought stress but also offering new perspectives for understanding the mechanism of how cassava survives and develops under drought.

Integrative Analysis of the Transcriptome and Metabolome Reveals the Developmental Mechanisms and Metabolite Biosynthesis of the Tuberous Roots of Tetrastigma hemsleyanum

The tuberous root of Tetrastigma hemsleyanum Diels et Gilg (T. hemsleyanum) is a traditional Chinese medicine with a wide range of clinical applications. However, the scarcity of its wild resources, its low yield, and the variable quality that results from its artificial cultivation leads to expensive market prices that are not conducive to the further industrial development of T. hemsleyanum. In this study, transcriptomic and non-targeted metabolomic analyses were integrated to explore the underlying molecular mechanisms and metabolite biosynthesis that occur during its root development. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that differentially expressed genes (DEGs) were predominantly enriched for processes associated with flavonoid and phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction. Genes related to lignin were downregulated in tuberous roots (TRs), resulting in a decrease in lignification and the downregulation of metabolites related to flavonoids and phenylpropanoid biosynthesis. In addition, the expression levels of starch- and sucrose-related genes were upregulated in TRs. The root development of SYQ is also related to IAA, GA, ABA, and JA signaling pathways. Collectively, this study lays the foundation for analyzing the root development and quality-modulating mechanisms employed by T. hemsleyanum; this will be beneficial in conducting molecular-assisted breeding and controlling its secondary metabolite production.

MePAL6 regulates lignin accumulation to shape cassava resistance against two-spotted spider mite

INTRODUCTION

The two-spotted spider mite (TSSM) is a devastating pest of cassava production in China. Lignin is considered as an important defensive barrier against pests and diseases, several genes participate in lignin biosynthesis, however, how these genes modulate lignin accumulation in cassava and shape TSSM-resistance is largely unknown.

METHODS

To fill this knowledge gap, while under TSSM infestation, the cassava lignin biosynthesis related genes were subjected to expression pattern analysis followed by family identification, and genes with significant induction were used for further function exploration.

RESULTS

Most genes involved in lignin biosynthesis were up-regulated when the mite-resistant cassava cultivars were infested by TSSM, noticeably, the MePAL gene presented the most vigorous induction among these genes. Therefore, we paid more attention to dissect the function of MePAL gene during cassava-TSSM interaction. Gene family identification showed that there are 6 MePAL members identified in cassava genome, further phylogenetic analysis, gene duplication, cis-elements and conserved motif prediction speculated that these genes may probably contribute to biotic stress responses in cassava. The transcription profile of the 6 MePAL genes in TSSM-resistant cassava cultivar SC9 indicated a universal up-regulation pattern. To further elucidate the potential correlation between MePAL expression and TSSM-resistance, the most strongly induced gene MePAL6 were silenced using virus-induced gene silencing (VIGS) assay, we found that silencing of MePAL6 in SC9 not only simultaneously suppressed the expression of other lignin biosynthesis genes such as 4-coumarate--CoA ligase (4CL), hydroxycinnamoyltransferase (HCT) and cinnamoyl-CoA reductase (CCR), but also resulted in decrease of lignin content. Ultimately, the suppression of MePAL6 in SC9 can lead to significant deterioration of TSSM-resistance.

DISCUSSION

This study accurately identified MePAL6 as critical genes in conferring cassava resistance to TSSM, which could be considered as promising marker gene for evaluating cassava resistance to insect pest.

Single-cell transcriptome sequencing atlas of cassava tuberous root

INTRODUCTION

Single-cell transcriptome sequencing (ScRNA-seq) has emerged as an effective method for examining cell differentiation and development. In non-model plants, it hasn't been employed very much, especially in sink organs that are abundant in secondary metabolites.

RESULTS

In this study, we sequenced the single-cell transcriptomes at two developmental phases of cassava tuberous roots using the technology known as 10x Genomics (S1, S2). In total, 14,566 cells were grouped into 15 different cell types, primarily based on the marker genes of model plants known to exist. In the pseudotime study, the cell differentiation trajectory was defined, and the difference in gene expression between the two stages on the pseudotime axis was compared. The differentiation process of the vascular tissue and cerebral tissue was identified by the trajectory. We discovered the rare cell type known as the casparian strip via the use of up-regulated genes and pseudotime analysis, and we explained how it differentiates from endodermis. The successful creation of a protoplast isolation technique for organs rich in starch was also described in our study.

DISCUSSION

Together, we created the first high-resolution single-cell transcriptome atlas of cassava tuberous roots, which made significant advancements in our understanding of how these roots differentiate and develop.

A chromosome-scale genome assembly of turmeric provides insights into curcumin biosynthesis and tuber formation mechanism

Curcuma longa, known as the 'golden spice' and 'life spice', is one of the most commonly utilized spices in the world and also has medicinal, cosmetic, dye and flavoring values. Herein, we present the chromosomal-level genome for turmeric to explore the differences between tubers and rhizomes in the regulation of curcumin biosynthesis and the mechanism of tuber formation. We assembled the turmeric genome into 21 pseudochromosomes using Pacbio long reads complemented with Hi-C technologies, which has a total length of 1.11 Gb with scaffold N50 of 50.12 Mb and contains 49,612 protein-coding genes. Genomic evolutionary analysis indicated that turmeric and ginger have shared a recent WGD event. Contraction analysis of gene families showed possible roles for transcription factors, phytohormone signaling, and plant-pathogen interactions associated genes in adaptation to harsh environments. Transcriptomic data from tubers at different developmental stages indicated that candidate genes related to phytohormone signaling and carbohydrate metabolic responses may be associated with the induction of tuber formation. The difference in curcumin content between rhizomes and tubers reflected the remodeling of secondary metabolites under environmental stress, which was associated with plant defense in response to abiotic stresses. Overall, the availability of the C. longa genome provides insight into tuber formation and curcumin biosynthesis in turmeric as well as facilitating the understanding of other Curcuma species.

Integrated Transcriptomic and Proteomic Analyses Uncover the Regulatory Mechanisms of Myricaria laxiflora Under Flooding Stress

Flooding is one of the major environmental stresses that severely influence plant survival and development. However, the regulatory mechanisms underlying flooding stress remain largely unknown in Myricaria laxiflora, an endangered plant mainly distributed in the flood zone of the Yangtze River, China. In this work, transcriptome and proteome were performed in parallel in roots of M. laxiflora during nine time-points under the flooding and post-flooding recovery treatments. Overall, highly dynamic and stage-specific expression profiles of genes/proteins were observed during flooding and post-flooding recovery treatment. Genes related to auxin, cell wall, calcium signaling, and MAP kinase signaling were greatly down-regulated exclusively at the transcriptomic level during the early stages of flooding. Glycolysis and major CHO metabolism genes, which were regulated at the transcriptomic and/or proteomic levels with low expression correlations, mainly functioned during the late stages of flooding. Genes involved in reactive oxygen species (ROS) scavenging, mitochondrial metabolism, and development were also regulated exclusively at the transcriptomic level, but their expression levels were highly up-regulated upon post-flooding recovery. Moreover, the comprehensive expression profiles of genes/proteins related to redox, hormones, and transcriptional factors were also investigated. Finally, the regulatory networks of M. laxiflora in response to flooding and post-flooding recovery were discussed. The findings deepen our understanding of the molecular mechanisms of flooding stress and shed light on the genes and pathways for the preservation of M. laxiflora and other endangered plants in the flood zone.

Set up from the beginning: The origin and early development of cassava storage roots

Despite the importance of storage root (SR) organs for cassava and the other root crops yield, their developmental origin is poorly understood. Here we use multiple approaches to shed light on the initial stages of root development demonstrating that SR and fibrous roots (FR) follow different rhizogenic processes. Transcriptome analysis carried out on roots collected before, during and after root bulking highlighted early and specific activation of a number of functions essential for root swelling and identified root-specific genes able to effectively discriminate emerging FR and SR. Starch and sugars start to accumulate at a higher rate in SR before they swell but only after parenchyma tissue has been produced. Finally, using non-destructive computed tomography measurements, we show that SR (but not FR) contain, since their emergence from the stem, an inner channel structure in continuity with the stem secondary xylem, indicating that SR derive from a distinct rhizogenic process compared with FR.

Integrated Metabolomic and Transcriptomic Analyses Reveal Novel Insights of Anthocyanin Biosynthesis on Color Formation in Cassava Tuberous Roots

Yellow roots are of higher nutritional quality and better appearance than white roots in cassava, a crucial tropical and subtropical root crop. In this work, two varieties with yellow and white cassava roots were selected to explore the mechanisms of color formation by using comparative metabolome and transcriptome analyses during seven developmental stages. Compared with the white-rooted cassava, anthocyanins, catechin derivatives, coumarin derivatives, and phenolic acids accumulated at higher levels in yellow-rooted cassava. Anthocyanins were particularly enriched and displayed different accumulation patterns during tuberous root development. This was confirmed by metabolic comparisons between five yellow-rooted and five white-rooted cassava accessions. The integrative metabolomic and transcriptomic analysis further revealed a coordinate regulation of 16 metabolites and 11 co-expression genes participating in anthocyanin biosynthesis, suggesting a vital role of anthocyanin biosynthesis in yellow pigmentation in cassava tuberous roots. In addition, two transcriptional factors, i.e., MeMYB5 and MeMYB42, were also identified to co-express with these anthocyanin biosynthesis genes. These findings expand our knowledge on the role of anthocyanin biosynthesis in cassava root color formation, and offer useful information for the genetic breeding of yellow-rooted cassava in the future.

Overexpression of leucoanthocyanidin reductase or anthocyanidin reductase elevates tannins content and confers cassava resistance to two-spotted spider mite

The two-spotted spider mite (TSSM) is a destructive cassava pest. Intensive demonstration of resistance mechanism greatly facilitates the creation of TSSM-resistant cassava germplasm. Gene to metabolite network plays a crucial role in modulating plant resistance, but little is known about the genes and related metabolites which are responsible for cassava resistance to TSSM. Here, a highly resistant (HR) and a highly susceptible (HS) cassava cultivar were used, integrative and comparative transcriptomic and metabolomic analyses between these two cultivars after TSSM infestation revealed that several genes and metabolites were closely related and significantly different in abundance. In particular, the expression of leucoanthocyanidin reductase (LAR) and anthocyanidin reductase (ANR) genes showed a high positive correlation with most of the metabolites in the tannin biosynthesis pathway. Furthermore, transgenic cassava lines overexpressing either of the genes elevated tannin concentrations and conferred cassava resistance to TSSM. Additionally, different forms of tannins possessed distinct bioactivity on TSSM, of which total condensed tannins (LC₅₀ = 375.68 mg/l) showed maximum lethal effects followed by procyanidin B1 (LC₅₀ = 3537.10 mg/l). This study accurately targets LAR, ANR and specific tannin compounds as critical genes and metabolites in shaping cassava resistance to TSSM, which could be considered as biomarkers for evaluation and creation of pest-resistant cassava germplasm.

Auxin signaling and vascular cambium formation enable storage metabolism in cassava tuberous roots

Cassava storage roots are among the most important root crops worldwide, and represent one of the most consumed staple foods in sub-Saharan Africa. The vegetatively propagated tropical shrub can form many starchy tuberous roots from its stem. These storage roots are formed through the activation of secondary root growth processes. However, the underlying genetic regulation of storage root development is largely unknown. Here we report distinct structural and transcriptional changes occurring during the early phases of storage root development. A pronounced increase in auxin-related transcripts and the transcriptional activation of secondary growth factors, as well as a decrease in gibberellin-related transcripts were observed during the early stages of secondary root growth. This was accompanied by increased cell wall biosynthesis, most notably increased during the initial xylem expansion within the root vasculature. Starch storage metabolism was activated only after the formation of the vascular cambium. The formation of non-lignified xylem parenchyma cells and the activation of starch storage metabolism coincided with increased expression of the KNOX/BEL genes KNAT1, PENNYWISE, and POUND-FOOLISH, indicating their importance for proper xylem parenchyma function.

Seasonal Variation in Transcriptomic Profiling of Tetrastigma hemsleyanum Fully Developed Tuberous Roots Enriches Candidate Genes in Essential Metabolic Pathways and Phytohormone Signaling

Tetrastigma hemsleyanum Diels et Gilg (Sanyeqing, SYQ) is a perennial climbing liana and an endemic plant to southern China. Its tuberous roots (TRs) are used in traditional Chinese medicine for treating some diseases such as high fever, pneumonia, asthma, hepatitis, and cancers. However, the mechanisms underlying the development of TR and the content of flavonoids and phenylpropanoids (FPs) are not well-understood. In this study, we performed a transcriptomic analysis of 12 fully developed TR (FD-TR) samples harvested in four seasons [spring (Sp), summer (Su), autumn (Au), and winter (Wi)] using the RNA-Sequencing (RNA-Seq). We obtained a total of 78.54 Gb raw data and 65,578 unigenes. Then, the unigenes were annotated by using six databases such as non-redundant protein database (NR), Pfam, eggNOG, SWISSProt, Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene ontology (GO). The transcriptomic profiling showed closer relationships between the samples obtained in Su and Au than those obtained in Sp and Wi based on the results of both total unigenes and differentially expressed genes (DEGs). Three pathways, including the biosynthesis of FPs, metabolism of starch and sucrose, and signaling of phytohormones, were highly enriched, suggesting a gene-level seasonal variation. Based on the numbers of DEGs, brassinosteroid (BR) signal transduction factors appeared to play a key role in modulating the development of TRs while most of the auxin signaling genes were mainly activated in Wi and Sp FD-TRs. Most genes in the biosynthesis and biodegradation of starch and biodegradation of cellulose were activated in Wi FD-TRs. As determined by the high performance liquid chromatography (HPLC) and aluminum nitrate colorimetric method, the contents of total flavonoids and most detected FP components increased from Sp to Au but decreased in Wi. Enhanced expression levels of some genes in the biosynthetic pathways of FPs were detected in Su and Au samples, which corroborated well with metabolite content. Our findings provide the first transcriptomic and biochemical data on a seasonal variation in the composition of medically important metabolites in SYQ FD-TRs.