Long noncoding RNAs (lncRNAs) have emerged as playing crucial roles in abiotic stress responsive regulation, however, the mechanism of lncRNAs underlying drought-tolerance remains largely unknown in cassava, an important tropical and sub-tropical root crop of remarkable drought tolerance. In this study, a total of 833 high-confidence lncRNAs, including 652 intergenic and 181 anti-sense lncRNAs, were identified in cassava leaves and root using strand-specific RNA-seq technology, of which 124 were drought-responsive. Trans-regulatory co-expression network revealed that lncRNAs exhibited tissue-specific expression patterns and they preferred to function differently in distinct tissues: e.g., cell-related metabolism, cell wall, and RNA regulation of transcription in folded leaf (FL); degradation of major carbohydrate (CHO) metabolism, calvin cycle and light reaction, light signaling, and tetrapyrrole synthesis in full expanded leaf (FEL); synthesis of major CHO metabolism, nitrogen-metabolism, photosynthesis, and redox in bottom leaf (BL); and hormone metabolism, secondary metabolism, calcium signaling, and abiotic stress in root (RT). In addition, 27 lncRNA-mRNA pairs referred to cis-acting regulation were identified, and these lncRNAs regulated the expression of their neighboring genes mainly through hormone metabolism, RNA regulation of transcription, and signaling of receptor kinase. Besides, 11 lncRNAs were identified acting as putative target mimics of known miRNAs in cassava. Finally, five drought-responsive lncRNAs and 13 co-expressed genes involved in trans-acting, cis-acting, or target mimic regulation were selected and confirmed by qRT-PCR. These findings provide a comprehensive view of cassava lncRNAs in response to drought stress, which will enable in-depth functional analysis in the future.

Coffea arabica L. (C. arabica) is an economically important agricultural crop and the most popular beverage worldwide. To analyze genetic diversity and provide genetic resources for the selection and breeding of superior varieties of C. arabica, 61 cultivated Arabica coffee accessions were analyzed in the study, including 12 resequencing accessions from previous research and 49 accessions that were resequenced in this study. Single nucleotide polymorphisms (SNPs) and insertion–deletions (InDels) were statistically analyzed. Based on SNP variations, a genetic structure analysis, phylogenetic tree construction, and principal component analysis were performed for the 61 coffee accessions. The results showed that a total of 805.46 Gb of raw whole-genome resequencing data was obtained from the 61 coffee accessions, with 781.29 Gb of high-quality sequencing data after filtering. In total, 7,013,820 SNP sites and 1,074,329 InDel sites were detected. The average sequencing depth ranged from 6.69× to 19.35×, and the coverage ranged from 85.49% to 96.43%. The population genetic structure and phylogenetic analysis of the 61 coffee accessions revealed four lineages, suggesting that they had at least four ancestral genetic components. Catimor exhibited the highest genetic diversity, while Geisha had the lowest genetic diversity. The selective sweep analysis indicated that among the selected genes in Catimor, disease-resistance genes were significantly more numerous than in other coffee varieties. The genome resequencing data and genetic markers identified from the 61 cultivated Arabica coffee materials provided insights into the genetic variation in Arabica coffee germplasm and facilitated extensive genetic research.

The MADS-box gene family constitutes a vital group of transcription factors that play significant roles in regulating plant growth, development, and signal transduction processes. However, research on the MADS-box genes in cassava (Manihot esculenta) has been relatively limited. To gain deeper insights into the functions of the MADS-box genes in cassava development, in this study, we undertook a comprehensive genome-wide identification of the MADS-box gene family in cassava. We identified a total of 86 MADS-box genes with complete domains in the cassava genome, designated as MeMADS01 to MeMADS86. Through bioinformatic analyses, we investigated the basic physicochemical properties, conserved motifs, chromosomal locations, and phylogenetic relationships of the cassava MADS-box genes. The MADS-box gene family of cassava exhibited conservation, as well as species-specific characteristics, with intron loss being a predominant mode of evolution for the MADS-box genes. Expression pattern variations in the MeMADS genes across different tissues offer insights into their potential functions. Time-ordered gene co-expression network (TO-GCN), transcriptome data, and RT-qPCR analysis suggested the responsiveness of the MADS-box genes to drought stress. Meanwhile, MeMADS12 might be involved in regulating flowering under drought conditions via an ABA (abscisic acid)-dependent pathway. These findings provide valuable resources for a deeper understanding of the biological roles of the MADS-box genes in cassava.

The sugar transporter (STP) gene family is a key regulator of plant development, which is crucial for the efficient transport and utilization of sugars during plant growth and development. In this study, we identified the MeSTP7 gene, which is highly expressed in cassava fibrous roots, early storage roots, and under hormonal treatment, including IAA, MeJA, ABA, and GA₃, and abiotic stressors, such as mannitol and NaCl. A strong response was observed with exoqenous IAA. Transfecting MeSTP7 into Arabidopsis promoted early seedling growth, particularly in lateral root development. The content of endogenous hormones (IAA and MeJA) as well as soluble sugars (sucrose, fructose, and glucose) was elevated in transgenic Arabidopsis. Hormone treatments with IAA, MeJA, GA₃, and ABA on transgenic Arabidopsis revealed that transgenic Arabidopsis responded positively to added 20 μM IAA. They also exhibited co-induced regulation of lateral root formation by GA₃, MeJA, and ABA. qRT-PCR analysis showed that overexpression of MeSTP7 upregulated the expression of IAA14, ARF7, and ARF19 in Arabidopsis. Under IAA treatment, the expression of these genes was similarly upregulated but downregulated under MeJA treatment. These results suggest that MeSTP7 may promote Arabidopsis seedling development by increasing the content of sucrose, glucose, and fructose in roots, which in turn influences IAA-based hormonal signaling.

Background: Lemon peels are crucial quality traits and important sources of nutraceuticals. However, the regulation of peel development remains largely misunderstood. Here, we delved into the dynamic molecular mechanisms that control smooth lemon peel formation through transcriptomics and metabolomics analyses of developing peels at five different stages, including C1 (30 DAF, day after flowering), C2 (60 DAF), C3 (90 DAF), C4 (120 DAF), and C5 (150 DAF). Results: Our analyses revealed that peel development is stage-specifically regulated, with the transition from stage C2 to stage C3 being the most critical period. Notably, major metabolic adjustments and transcriptional switches occurred between C2 and C3. Particularly, phytohormones and their related genes, flavonoids, terpenoids, phenolic acids, vitamin C, and citric acid were down-regulated at stage C3. Differentially expressed genes between the transition from C2 to C3 were mainly enriched in hydrolase activity, nucleic acid binding transcription, transcription factor activity, sequence-specific DNA binding and pathways such as plant hormone signal transduction, starch and sucrose metabolism, MAPK signaling pathway-plant, plant-pathogen interaction, and circadian rhythm-plant biosynthesis. Plant hormone signaling was crucial for peel development process. Specifically, we found that crosstalks between jasmonic acid, abscisic acid, salicylic acid, gibberellic acid, and ethylene dynamically and coordinately regulate peel development process. ABC transporter family genes and green-degrading promoting genes, including protein SGR1 ( LOC18041639 ), ervatamin-C ( LOC18051181 ), and many ethylene-responsive transcription factors were significantly induced from C2. Furthermore, we screened out stage-specific most regulated genes. Conclusions: Our findings offer molecular understanding of peel formation process and fundamental resources for the functional dissection of its regulatory networks and for genomics-assisted control of peel shape and fruit quality in lemon.

To characterize the trends in the fermentation weight loss (FWL), nutrient composition, and fermentation quality of king grass silage under different ensiling temperatures and storage periods, chopped and wilted king grass was ensiled at 15 °C, 20 °C, 25 °C, 30 °C and 35 °C for 7, 30, 60 and 120 days, respectively. Nutritional and fermentation-related parameters were predicted by near-infrared reflectance spectroscopy (NIRS) using the general Dairy One forage database. FWL was determined gravimetrically, and correlation and cluster analyses were performed for comprehensive data evaluation. The results showed that ensiling temperature, storage period, and their interaction significantly affected the FWL, nutrient composition (except for the soluble protein-to-crude protein ratio, SP/CP), and fermentation quality (except for the butyric acid, BA) of king grass silage (p < 0.05). FWL tended to increase with rising temperature and prolonged ensiling duration. With extended ensiling time, NIRS-predicted acid detergent fiber (ADF), neutral detergent fiber (NDF), ash, BA, ammonia, and SP/CP exhibited increasing trends. By contrast, NIRS-predicted dry matter, water-soluble carbohydrates (WSCs) and pH decreased significantly from day 7 to day 30 (p < 0.05). The 15 °C treatment favored the preservation of NIRS-predicted WSCs and crude protein over long-term ensiling (120 d). The NIRS-predicted ammonia under 25 °C remained at a relatively low level across the whole ensiling period; lactic acid was highest at days 7 and 60, whereas no significant difference was observed among temperatures at day 120 (p > 0.05). Both low temperature (15 °C) and high temperature (35 °C) were unfavorable for rapid pH decline. At most sampling time points, NIRS-predicted ADF and NDF contents under 30 °C and 35 °C were significantly higher than those under 15 °C (p < 0.05). Correlation analysis showed that ADF, NDF, ash, ammonia, and BA were positively correlated with each other; WSCs were negatively correlated with SP/CP, ADF, NDF, ash and acetic acid but positively correlated with pH and the lactic acid-to-acetic acid ratio. Cluster analysis classified the 13 silage quality indicators into three clusters and the 60 treatment samples into five clusters. This work offers preliminary references for developing differentiated king-grass-ensiling strategies adapted to diverse climatic regions.