PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics.

The plastid genome (plastome) represents an indispensable molecular resource for studying plant phylogeny and evolution. Although plastome size is much smaller than that of nuclear genomes, accurately and efficiently annotating and utilizing plastome sequences remain challenging. Therefore, a streamlined phylogenomic pipeline spanning plastome annotation, phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome.

Mutations of two AhTT8 genes reduce the accumulation of anthocyanins and confer the white testa of peanut (Arachis hypogaea L.).

Anthocyanins and proanthocyanidins (PAs), which determine the color of peanut seed coats, not only offer protection to plants under biotic and abiotic stress but also contribute to human health. The white testa peanut contains lower levels of anthocyanins and PAs, yet the mechanisms underlying the white testa phenotype in peanuts remain largely unknown. In the current study, two homologous peanut AhTT8 genes, namely AhTT8_AA and AhTT8_BB, were identified as the key genes controlling the seed coat color of peanuts through BSA-seq analysis and fine mapping.

Pyridoxine dehydrogenase SePdx regulates photosynthesis via an association with the phycobilisome in a cyanobacterium.

Vitamin B6 (VitB6) deficiency is known to have a deleterious effect on photosynthesis, although the precise mechanism remains unclear. Pyridoxine dehydrogenase is a key protein involved in VitB6 biosynthesis, which facilitates the reversible reduction of pyridoxal (PL) and the oxidation of pyridoxine (PN), thereby contributing to VitB6 production. This study demonstrated the enzymatic activity of a pyridoxine dehydrogenase, SePdx, from the cyanobacterium Synechococcus elongatus PCC 7942 in the oxidation of PN.

Transcriptomic and Metabolomic Profiling of Root Tissue in Drought-Tolerant and Drought-Susceptible Wheat Genotypes in Response to Water Stress.

Wheat is the most widely grown crop in the world; its production is severely disrupted by increasing water deficit. Plant roots play a crucial role in the uptake of water and perception and transduction of water deficit signals. In the past decade, the mechanisms of drought tolerance have been frequently reported; however, the transcriptome and metabolome regulatory network of root responses to water stress has not been fully understood in wheat.

Nitrate Starvation Induces Lateral Root Organogenesis in via Auxin Signaling.

The lateral root (LR) is an essential component of the plant root system, performing important functions for nutrient and water uptake in plants and playing a pivotal role in cereal crop productivity. Nitrate (NO) is an essential nutrient for plants. In this study, wheat plants were grown in 1/2 strength Hoagland's solution containing 5 mM NO (check; CK), 0.

Growth and non-structural carbohydrates response patterns of under salt and drought stress.

Introduction: Salinity and droughts are severe abiotic stress factors that limit plant growth and development. However, the differences and similarities of non-structural carbohydrates (NSCs) responses patterns of trees under the two stress conditions remain unclear.

Methods: We determined and compared the growth, physiology, and NSCs response patterns and tested the relationships between growth and NSCs concentrations (or pool size) of seedlings planted in field under drought and salt stress with different intensities and durations.

Bicarbonate-Dependent Detoxification by Mitigating Ammonium-Induced Hypoxic Stress in Root.

Ammonium (NH) toxicity is ubiquitous in plants. To investigate the underlying mechanisms of this toxicity and bicarbonate (HCO)-dependent alleviation, wheat plants were hydroponically cultivated in half-strength Hoagland nutrient solution containing 7.5 mM NO (CK), 7.

Comparative Physiological and Transcriptome Analyses of Tolerant and Susceptible Cultivars Reveal the Molecular Mechanism of Cold Tolerance in .

is a tropical ornamental flower. The cost of production is higher under low temperature (non-freezing) conditions; therefore, it is important to increase its cold tolerance. However, the molecular mechanisms underlying the response of to cold stress remain elusive.

Comprehensive Time-Course Transcriptome Reveals the Crucial Biological Pathways Involved in the Seasonal Branch Growth in Siberian Elm ().

Timber, the most prevalent organic material on this planet, is the result of a secondary xylem emerging from vascular cambium. Yet, the intricate processes governing its seasonal generation are largely a mystery. To better understand the cyclic growth of vascular tissues in elm, we undertook an extensive study examining the anatomy, physiology, and genetic expressions in Ulmus pumila.

Patterns of deep fine root and water utilization amongst trees, shrubs and herbs in subtropical pine plantations with seasonal droughts.

Introduction: Seasonal droughts will become more severe and frequent under the context of global climate change, this would result in significant variations in the root distribution and water utilization patterns of plants. However, research on the determining factors of deep fine root and water utilization is limited.

Methods: We measured the fine root biomass and water utilization of trees, shrubs and herbs, and soil properties, light transmission, and community structure parameters in subtropical pine plantations with seasonal droughts.

C:N:P stoichiometric variations of herbs and its relationships with soil properties and species relative abundance along the Xiaokai River irrigation in the Yellow River Delta, China.

Introduction: Soil salinity is known to affect plant performance and nutrient stoichiometry by altering their ecophysiology, and thus playing a crucial role in determining plant distribution patterns and nutrient cycles in salinized ecosystems. However, there was little consensus on the effects of salinity stress on plant C, N, and P stoichiometries. Moreover, determining the relationships between species relative species abundance and plant C, N, and P stoichiometries can help to understand the different adaptive strategies between the common and rare species as well as the community assembly process.

Plastid phylogenomics sheds light on divergence time and ecological adaptations of the tribe Persicarieae (Polygonaceae).

Southwestern China, adjacent to the Qinghai-Tibetan Plateau (QTP), is known as a hotspot for plant diversity and endemism, and it is the origin and diversification center of Persicarieae. As one of the major lineages in Polygonaceae, Persicarieae represents a diverse adaptation to various habitats. As a result of morphological plasticity and poorly resolving molecular markers, phylogenetic relationships and infrageneric classification within Persicarieae have long been controversial.

Plastid phylogenomics and morphological character evolution of Chloridoideae (Poaceae).

Chloridoideae is one of the largest subfamilies of Poaceae, containing many species of great economic and ecological value; however, phylogenetic relationships among the subtribes and genera of Cynodonteae are controversial. In the present study, we combined 111 plastomes representing all five tribes, including 25 newly sequenced plastomes that are mostly from Cynodonteae. Phylogenetic analyses supported the five monophyletic tribes of Chloridoideae, including Centropodieae, Triraphideae, Eragrostideae, Zoysieae and Cynodonteae.

Comparative Transcriptome Analysis Identifies Key Defense Genes and Mechanisms in Mulberry () Leaves against Silkworms ().

As a consequence of long-term coevolution and natural selection, the leaves of mulberry () trees have become the best food source for silkworms (). Nevertheless, the molecular and genomic basis of defense response remains largely unexplored. In the present study, we assessed changes in the transcriptome changes of mulberry in response to silkworm larval feeding at 0, 3, and 6 h.

Does energy cost constitute the primary cause of ammonium toxicity in plants?

Nitrate (NO) and ammonium (NH) are the main nitrogen (N) sources and key determinants for plant growth and development. In recent decades, NH, which is a double-sided N compound, has attracted considerable amounts of attention from researchers. Elucidating the mechanisms of NH toxicity and exploring the means to overcome this toxicity are necessary to improve agricultural sustainability.

Application of chloroplast genome in the identification of Traditional Chinese Medicine Viola philippica.

Background: Viola philippica Cav. is the only source plant of "Zi Hua Di Ding", which is a Traditional Chinese Medicine (TCM) that is utilized as an antifebrile and detoxicant agent for the treatment of acute pyogenic infections. Historically, many Viola species with violet flowers have been misused in "Zi Hua Di Ding".

Plastid and mitochondrial phylogenomics reveal correlated substitution rate variation in Koenigia (Polygonoideae, Polygonaceae) and a reduced plastome for Koenigia delicatula including loss of all ndh genes.

Koenigia, a genus proposed by Linnaeus, has a contentious taxonomic history. In particular, relationships among species and the circumscription of the genus relative to Aconogonon remain uncertain. To explore phylogenetic relationships of Koenigia with other members of tribe Persicarieae and to establish the timing of major evolutionary diversification events, genome skimming of organellar sequences was used to assemble plastomes and mitochondrial genes from 15 individuals representing 13 species.

Comparative Transcriptome Analysis Reveals Candidate Genes and Pathways for Potential Branch Growth in Elm () Cultivars.

Wood plays a vital role in human life. It is important to study the thickening mechanism of tree branches and explore the mechanism of wood formation. Elm () is a strong essential wood, and it is widely used in cabinets, sculptures, and ship making.

Characterization of the complete chloroplast genome of (Poaceae), a widespread weed.

belongs to Poaceae. The complete chloroplast genome of was reported in this study. The chloroplast genome was 137,837 bp in size with a canonical quadripartite structure, including two inverted repeat regions (IR) of 21,635 bp for each, a large single-copy (LSC) region of 81,787 bp in length, and a small single-copy (SSC) region of 12,780 bp in length.

A Novel Alginate Lyase: Identification, Characterization, and Potential Application in Alginate Trisaccharide Preparation.

Alginate oligosaccharides (AOS) have many biological activities and significant applications in prebiotics, nutritional supplements, and plant growth development. Alginate lyases have unique advantages in the preparation of AOS. However, only a limited number of alginate lyases have been so far reported to have potentials in the preparation of AOS with specific degrees of polymerization.

Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Strain GY-D55.

It is highly necessary to understand the molecular mechanism underlying the salt stress response in green algae, which may contribute to finding the evolutionary cues of abiotic stress response in plants. Here, we reported a comprehensive temporal investigation of transcriptomes using data at eight different time points, from an early stage (2 h) to a late stage (up to 96 h) in GY-D55 cells. The principal component analysis (PCA) of transcriptome profiles showed that the samples of the early and late stages were well separated.

Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae).

Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, , , and In this study, the plastomes of and were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types.

Nitrate alleviates ammonium toxicity in wheat ( L.) by regulating tricarboxylic acid cycle and reducing rhizospheric acidification and oxidative damage.

Ammonium (NH) is one of the most important nutrients required by plants. However, a high concentration of NH as the sole nitrogen source suppresses plant growth. Although nitrate (NO) can alleviate NH toxicity, the mechanisms underlying this ability have not been fully elucidated.

Characterization and phylogenetic analysis of the complete plastome of L. (Amaranthaceae), an annual weeds.

The complete plastome of L., a field weed, was identified in this study. The genome size was 150,710 bp and consists of a large single-copy (LSC: 83,892 bp) region, a small single-copy (SSC: 18,100 bp) region, and two inverted repeats (IRs: 24,359 bp) regions.

Characterization and phylogenetic analysis of the complete plastome of (Plantaginaceae).

is a perennial herb, and the complete chloroplast genome (plastome) of was determined in this study. The results showed that the plastome size of was 151,178 bp, including a large single-copy region (68,533 bp), a small single-copy region (21,403 bp), and two inverted repeat regions (25,566 bp). The total GC content of the plastome was 38.