Systematic analysis of plant mitochondrial and chloroplast small RNAs suggests organelle-specific mRNA stabilization mechanisms

Land plant organellar genomes encode a small number of genes, many of which are essential for respiration and photosynthesis. Organellar gene expression is characterized by a multitude of RNA processing events that lead to stable, translatable transcripts. RNA binding proteins (RBPs), have been shown to generate and protect transcript termini and eventually induce the accumulation of short RNA footprints. We applied knowledge of such RBP-derived footprints to develop software (sRNA miner) that enables identification of RBP footprints, or other clusters of small RNAs, in organelles. We used this tool to determine mitochondrial and chloroplast cosRNAs (clustered organellar sRNAs) in Arabidopsis. We found that in mitochondria, cosRNAs coincide with transcript 3′-ends, but are largely absent from 5′-ends. In chloroplasts this bias is absent, suggesting a different mode of 5′ processing, possibly owing to different sets of RNases. Furthermore, we identified a large number of cosRNAs that represent silenced insertions of mitochondrial DNA in the nuclear genome of Arabidopsis. Steady-state RNA analyses demonstrate that cosRNAs display differential accumulation during development. Finally, we demonstrate that the chloroplast RBP PPR10 associates in vivo with its cognate cosRNA. A hypothetical role of cosRNAs as competitors of mRNAs for PPR proteins is discussed

Genome-wide Association Study (GWAS) of mesocotyl elongation based on re-sequencing approach in rice

Annotation of candidate genes anchored by associated SNPs. (XLSX 34 kb

Effects of taurine on metabolomics of bovine mammary epithelial cells under high temperature conditions

High temperature induces heat stress, adversely affecting the growth and lactation performance of cows. Research has shown the protective effect of taurine against hepatotoxicity both in vivo and in vitro. This study aimed to investigate the effect of taurine on the metabolomics of mammary epithelial cells of dairy cows under high-temperature conditions. Mammary epithelial cells were exposed to 0 mmol/L (HS, control), 8 mmol/L (HT-8), and 32 mmol/L (HT-32) of taurine, then incubated at 42°C for 6 h. Metabolomics analysis was conducted using Liquid Chromatograph Mass Spectrometer (LC–MS). Compared with the HS group, 2,873 and 3,243 metabolites were detected in the HT-8 group in positive and negative ion modes. Among these, 108 and 97 metabolites were significantly upregulated in positive and negative ion modes, while 60 and 166 metabolites were downregulated. Notably, 15 different metabolites such as palmitic acid, adenine and hypoxanthine were screened out in the HT-8 group. Compared with the HS group, 2,873 and 3,243 metabolites were, respectively, detected in the HT-32 group in the positive and negative ion modes. Among those metabolites, 206 metabolites were significantly up-regulated, while 206 metabolites were significantly downregulated in the positive mode. On the other hand, 497 metabolites were significantly upregulated in the negative mode, while 517 metabolites were reported to be downregulated. Noteworthy, 30 distinct metabolites, such as palmitic acid, phytosphingosine, hypoxanthine, nonanoic acid, and octanoic acid, were screened out in the HT-32 group. KEGG enrichment analysis showed that these metabolites were mainly involved in lipid metabolism, purine metabolism and other biological processes. Overall, our study indicates that taurine supplementation alters the metabolites primarily associated with purine metabolism, lipid metabolism and other pathways to alleviate heat stress in bovine mammary epithelial cells

Breeding report of a new blueberry cultivar Lingwu

Lingwu is a novel northern highbush blueberry cultivar derived from Patriot seedlings. In the autumn of 2011, our team collected 230 seedlings, which were subsequently planted in the spring of 2012. By the first half of July 2015, the fruits had ripened, and a superior progeny, designated as Senmao 300, was carefully selected. Upon thorough test and evaluation, this cultivar was found to bear large, oblate, light blue berries in thick and uniformly textured clusters. The fruit are characterized by sweetness, delicate texture, juiciness, and pleasant, fragrant flavor. They also exhibit medium hardness and good productivity, making them an exceptional choice for fresh consumption. From July 2017 to July 2018, a comprehensive assessment of the traits of this cultivar and its asexually propagated progeny was conducted. The results demonstrated that the cultivars overall characteristics, including plant morphology, flowering and fruiting traits, fruit yield and quality, were consistent and stable. On July 29, 2020, this cultivar was registered as Lingwu and granted a New Cultivar Right Certificate by Chinas State Forestry and Grassland Administration (SFA). This cultivar features an upright tree body with vigorous growth. The leaf blade is elongated and oval-shaped, with an average leaf area of 14.92 cm2, a leaf shape index of 1.80, and a dark green color with an entire margin. The average length of a new fruiting shoot is 11 cm, with each shoot bearing an average of 8 fruit. The fruit are oblate and densely packed on a thick and uniformly textured inflorescence that is light blue (101-A). The calyx scar is small and shriveled, and the fruit firmness is of a moderate level (2.7). The fruit have average dimensions of 1.4 cm×1.83 cm, with a maximum weight of 4.03 g and an average weight of 2.99 g per fruit. The fruit contains 9.73% soluble solids (°Brix) and has relatively high acidity levels. Fruit ripening begins in early July, making this variety particularly suitable for cultivation in regions north of the Yangtze River or high-altitude zones. For optimal growth, deep, loose soils with high fertility and good drainage are required. The soil should hold moisture without waterlogging tendencies. Preferred soil textures include loam or sandy loam with an acidic pH (4.0-5.5) and an organic matter content exceeding 3.0%. Cultivation needs 600-1200 cumulative chilling hours. Prior to planting, thorough tillage to a depth of 20-30 cm, land leveling, and soil conditioning should be carried out to meet the specified physical and chemical properties.2-or 3-year-old potted seedlings or bare-root seedlings that are at least 40 cm tall and have a main stem base diameter above 0.4 cm, are used for garden establishment. For soil and fertilizer management, soil mulching with straw, wood debris, and pine needles is applied. The thickness of the mulch should exceed 10 cm, which helps in moisturizing, increasing the soils organic matter content, and improving soils physical and chemical properties. Mulching with black sheet effectively controls weed growth. Before planting, well-fermented organic fertilizer is applied to the seedlings

Tetraploidy in Citrus wilsonii Enhances Drought Tolerance via Synergistic Regulation of Photosynthesis, Phosphorylation, and Hormonal Changes

Polyploidy varieties have been reported to exhibit higher stress tolerance relative to their diploid relatives, however, the underlying molecular and physiological mechanisms remain poorly understood. In this study, a batch of autotetraploid Citrus wilsonii were identified from a natural seedling population, and these tetraploid seedlings exhibited greater tolerance to drought stress than their diploids siblings. A global transcriptome analysis revealed that a large number of genes involved in photosynthesis response were enriched in tetraploids under drought stress, which was consistent with the changes in photosynthetic indices including Pn, gs, Tr, Ci, and chlorophyll contents. Compared with diploids, phosphorylation was also modified in the tetraploids after drought stress, as detected through tandem mass tag (TMT)-labeled proteomics. Additionally, tetraploids prioritized the regulation of plant hormone signal transduction at the transcriptional level after drought stress, which was also demonstrated by increased levels of IAA, ABA, and SA and reduced levels of GA3 and JA. Collectively, our results confirmed that the synergistic regulation of photosynthesis response, phosphorylation modification and plant hormone signaling resulted in drought tolerance of autotetraploid C. wilsonii germplasm

Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization

Background: Ruminant gut microbiota are critical in ecological adaptation, evolution, and nutrition utilization because it regulates energy metabolism, promotes nutrient absorption, and improves immune function. To study the functional roles of key gut microbiota in sheep and goats, it is essential to construct reference microbial gene catalogs and high-quality microbial genomes database. Results A total of 320 fecal samples were collected from 21 different sheep and goat breeds, originating from 32 distinct farms. Metagenomic deep sequencing and binning assembly were utilized to construct a comprehensive microbial genome information database for the gut microbiota. We successfully generated the largest reference gene catalogs for gut microbiota in sheep and goats, containing over 162 million and 82 million nonredundant predicted genes, respectively, with 49 million shared nonredundant predicted genes and 1138 shared species. We found that the rearing environment has a greater impact on microbial composition and function than the host’s species effect. Through subsequent assembly, we obtained 5810 medium- and high-quality metagenome-assembled genomes (MAGs), out of which 2661 were yet unidentified species. Among these MAGs, we identified 91 bacterial taxa that specifically colonize the sheep gut, which encode polysaccharide utilization loci for glycan and mucin degradation. Conclusions By shedding light on the co-symbiotic microbial communities in the gut of small ruminants, our study significantly enhances the understanding of their nutrient degradation and disease susceptibility. Our findings emphasize the vast potential of untapped resources in functional bacterial species within ruminants, further expanding our knowledge of how the ruminant gut microbiota recognizes and processes glycan and mucins

Diversity and aggregation patterns of plant species in a grass community

Abstract Both composition and aggregation patterns of species in a community are the outcome of community self-organizing. In this paper we conducted analysis on species diversity and aggregation patterns of plant species in a grass community, Zhuhai, China. According to the sampling survey, in total of 47 plant species, belonging to 16 families, were found. Compositae had 10 species (21.3%), seconded by Gramineae (9 species, 19.1%), Leguminosae (6 species, 12.8%), Cyperaceae (4 species, 8.5%), and Malvaceae (3 species, 6.4%). The results revealed that the means of aggregation indices I δ , I and m * /m were 21.71, 15.71 and 19.89 respectively and thus individuals of most of plant species strongly followed aggregative distribution. Iwao analysis indicated that both individuals of all species and clumps of all individuals of all species followed aggregative distribution. Taylor's power law indicated that individuals of all species followed aggregative distribution and aggregation intensity strengthened as the increase of mean density. We held that the strong aggregation intensity of a species has been resulted from the strong adaptation ability to the environment, the strong interspecific competition ability and the earlier establishment of the species. Fitting goodness of the mean, I, I δ , m * /m with probability distributions demonstrated that the mean (density), I, I δ , and m * /m over all species followed Weibull distribution rather than normal distribution. Lophatherum gracile, Paederia scandens (Lour.) Merr., Eleusine indica, and Alternanthera philoxeroides (Mart.) Griseb. were mostly aggregative, and Oxalis sp., Eleocharis plantagineiformis, Vernonia cinerea (L.) Less., and Sapium sebiferum (L.) Roxb, were mostly uniform in the spatial distribution. Importance values (IV) showed that Cynodon dactylon was the most important species, seconded by Desmodium triflorum (L.) DC., Cajanus scarabaeoides (L.) Benth., Paspalum scrobiculatum L., and Rhynchelytrum repens. Oxalis sp., Eleocharis plantagineiformis, and Vernonia cinerea (L.) Less. were the least important species in the community. Summed dominance ratio (SDR2) revealed that Cynodon dactylon and Desmodium triflorum (L.) DC. were the most dominant species in the community, followed by Rhynchelytrum repens, Paspalum scrobiculatum L., and Cajanus scarabaeoides (L.) Benth

Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice

Rice (Oryza sativa) is an important dietary source of both essential micronutrients and toxic trace elements for humans. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. Here, we describe a comprehensive study of the genetic architecture of the variation in the rice ionome performed using genome-wide association studies (GWAS) of the concentrations of 17 mineral elements in rice grain from a diverse panel of 529 accessions, each genotyped at ∼6.4 million single nucleotide polymorphism loci. We identified 72 loci associated with natural ionomic variations, 32 that are common across locations and 40 that are common within a single location. We identified candidate genes for 42 loci and provide evidence for the causal nature of three genes, the sodium transporter gene Os-HKT1;5 for sodium, Os-MOLYBDATE TRANSPORTER1;1 for molybdenum, and Grain number, plant height, and heading date7 for nitrogen. Comparison of GWAS data from rice versus Arabidopsis (Arabidopsis thaliana) also identified well-known as well as new candidates with potential for further characterization. Our study provides crucial insights into the genetic basis of ionomic variations in rice and serves as an important foundation for further studies on the genetic and molecular mechanisms controlling the rice ionome