Comprehensive sampling from mitochondrial genomes substantiates the Neoproterozoic origin of land plants.

Molecular phylogenetics illustrates the evolution and divergence of green plants by employing sequence data from various sources. Interestingly, phylogenetic reconstruction based on mitochondrial genes tends to exhibit incongruence with those derived from nuclear and chloroplast genes. Although the uniparental inheritance and conservatively retained protein-coding genes of mitochondrial genomes inherently exclude certain potential factors that affect phylogenetic reconstruction, such as hybridization and gene loss, the utilization of mitochondrial genomes for phylogeny and divergence time estimation remains limited.

Chromatin accessibility analysis reveals functional cis-regulatory regions related to fruit development and domestication in tomato.

Non-coding DNA sequences harbor vast regulatory programs that ensure the precise spatiotemporal control of gene expression, which is essential for proper plant development and trait formation. Chromatin accessibility analysis could identify functional DNA regions within the extensive non-coding sequences and infer regulatory elements, serving as a crucial approach to unravel the mysteries of non-coding DNA sequences. Tomato fruit, a fleshy organ, provides a special system for studying fruit development and trait formation.

Tuning plant defenses in a changing world.

Two recent papers provide new insights into plant immunity. Li et al. identified an evolutionary pattern in which reduced pathogen pressure leads to a convergent reduction of immune receptors.

HFPO homologues, the novel alternatives to PFOA, impair male reproduction in mice through inducing mitochondrial dysfunction.

Hexafluoropropylene oxide (HFPO) homologues (HFPOs), presenting HFPO-dimeric acid (DA), HFPO-trimeric acid (TA) and HFPO-tetrameric acid (TeA), are emerging replacements for legacy perfluorooctanoic acid that are increasingly used for a variety of industrial applications. These novel fluorinated compounds have attracted much attention due to their environmental ubiquity and potential toxicities. However, there is a lack of clarity about their toxicological impact on male reproductive health.

The parsley genome assembly and DNA methylome shed light on apigenin biosynthesis in the Apiaceae.

Parsley [Petroselinum crispum (Mill.)] is a medicinal and edible vegetable of the Apiaceae family that is rich in apigenin. The Apiaceae family is well known for its diverse secondary metabolites.

Deciphering the biosynthetic pathway of triterpene saponins in Prunella vulgaris.

The traditional Chinese medicinal plant Prunella vulgaris contains numerous triterpene saponin metabolites, notably ursolic and oleanolic acid saponins, which have significant pharmacological values. Despite their importance, the genes responsible for synthesizing these triterpene saponins in P. vulgaris remain unidentified.

Microbial Metagenomics Revealed the Diversity and Distribution Characteristics of Groundwater Microorganisms in the Middle and Lower Reaches of the Yangtze River Basin.

Groundwater is one of the important freshwater resources on Earth and is closely related to human activities. As a good biological vector, a more diverse repertory of antibiotic resistance genes in the water environment would have a profound impact on human medical health. Therefore, this study conducted a metagenomic sequencing analysis of water samples from groundwater monitoring points in the middle and lower reaches of the Yangtze River to characterize microbial community composition and antibiotic resistance in the groundwater environment.

The gradual establishment of complex coumarin biosynthetic pathway in Apiaceae.

Complex coumarins (CCs) represent characteristic metabolites found in Apiaceae plants, possessing significant medical value. Their essential functional role is likely as protectants against pathogens and regulators responding to environmental stimuli. Utilizing genomes and transcriptomes from 34 Apiaceae plants, including our recently sequenced Peucedanum praeruptorum, we conduct comprehensive phylogenetic analyses to reconstruct the detailed evolutionary process of the CC biosynthetic pathway in Apiaceae.

The jacktree genome and population genomics provides insights for the mechanisms of the germination obstacle and the conservation of endangered ornamental plants.

Hu represents the first woody genus described by Chinese botanists, with all species classified as endangered ornamental plants endemic to China. Their characteristic spindle-shaped fruits confer high ornamental value to the plants, making them favored in gardens and parks. Nevertheless, the fruits likely pose a germination obstacle, contributing to the endangered status of this lineage.

Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of MicroTom tomato.

MicroTom has a short growth cycle and high transformation efficiency, and is a prospective model plant for studying organ development, metabolism, and plant-microbe interactions. Here, with a newly assembled reference genome for this tomato cultivar and abundant RNA-seq data derived from tissues of different organs/developmental stages/treatments, we constructed multiple gene co-expression networks, which will provide valuable clues for the identification of important genes involved in diverse regulatory pathways during plant growth, e.g.

The Saururus chinensis genome provides insights into the evolution of pollination strategies and herbaceousness in magnoliids.

Saururus chinensis, an herbaceous magnoliid without perianth, represents a clade of early-diverging angiosperms that have gone through woodiness-herbaceousness transition and pollination obstacles: the characteristic white leaves underneath inflorescence during flowering time are considered a substitute for perianth to attract insect pollinators. Here, using the newly sequenced S. chinensis genome, we revisited the phylogenetic position of magnoliids within mesangiosperms, and recovered a sister relationship for magnoliids and Chloranthales.

Plastid Phylogenomics of and the Evolution of Ten Flower Types in Tree Peony.

Andr., a member of Paeoniaceae, is native to China. In its 1600 years' cultivation, more than 2000 cultivars for different purposes (ornamental, medicinal and oil use) have been inbred.

The chromosome-level holly () genome reveals key enzymes in triterpenoid saponin biosynthesis and fruit color change.

The L. (hollies) genus of Aquifoliaceae shows high species diversity in tropical and subtropical regions of Asia and South America. Throughout the range of the genus, species have been widely used in beverage and medicine production and as ornamentals.

The genome of reveals its adaptation to saline and waterlogged habitat.

is a semi-mangrove species with strong tolerance to salt and waterlogging stress. However, the molecular basis and mechanisms that underlie this strong adaptability to harsh environments remain poorly understood. Here, we assembled a high-quality, chromosome-level genome of this semi-mangrove plant and analyzed its transcriptome under different stress treatments to reveal regulatory responses and mechanisms.

The Cycas genome and the early evolution of seed plants.

Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.