Pangeneric genome analyses reveal the evolution and diversity of the orchid genus Dendrobium.

Orchids constitute one of the most diverse families of angiosperms, yet their genome evolution and diversity remain unclear. Here we construct and analyse chromosome-scale de novo assembled genomes of 17 representative accessions spanning 12 sections in Dendrobium, one of the largest orchid genera. These accessions represent a broad spectrum of phenotypes, lineages and geographical distributions.

N-methyladenosine-mediated feedback regulation of abscisic acid perception via phase-separated ECT8 condensates in Arabidopsis.

N-methyladenosine (mA) is the most abundant internal modification in eukaryotic mRNAs, yet how plants recognize this chemical modification to swiftly adjust developmental plasticity under environmental stresses remains unclear. Here we show that mA mRNA modification and its reader protein EVOLUTIONARILY CONSERVED C-TERMINAL REGION 8 (ECT8) act together as a key checkpoint for negative feedback regulation of abscisic acid (ABA) signalling by sequestering the mA-modified ABA receptor gene PYRABACTIN RESISTANCE 1-LIKE 7 (PYL7) via phase-separated ECT8 condensates in stress granules in response to ABA. This partially depletes PYL7 mRNA from its translation in the cytoplasm, thus reducing PYL7 protein levels and compromising ABA perception.

GLABROUS INFLORESCENCE STEMS3 binds to and activates RHD2 and RHD4 genes to promote root hair elongation in Arabidopsis.

Root hairs are crucial in the uptake of essential nutrients and water in plants. This study showed that a zinc finger protein, GIS3 is involved in root hair growth in Arabidopsis. The loss-of-function gis3 and GIS3 RNAi transgenic line exhibited a significant reduction in root hairs compared to the wild type.

Shaping the landscape of N6-methyladenosine RNA methylation in Arabidopsis.

N 6-methyladenosine (m6A) modification on messenger RNAs (mRNAs) is deposited by evolutionarily conserved methyltransferases (writers). How individual m6A writers sculpt the overall landscape of the m6A methylome and the resulting biological impact in multicellular organisms remains unknown. Here, we systematically surveyed the quantitative m6A methylomes at single-nucleotide resolution and their corresponding transcriptomes in Arabidopsis (Arabidopsis thaliana) bearing respective impaired m6A writers.

FIONA1-Mediated m A Modification Regulates the Floral Transition in Arabidopsis.

N -methyladenosine (m A) mRNA modification represents the most widespread form of internal modifications in eukaryotic mRNAs. In the model plant Arabidopsis thaliana, those known methyltransferases mainly deposit m A at their target transcripts near the stop codon or in the 3' untranslated region. Here, it is reported that FIONA1 (FIO1), a human METTL16 ortholog, acts as a hitherto unknown m A methyltransferase that determines m A modifications at over 2000 Arabidopsis transcripts predominantly in the coding region.

N-methyladenosine modification underlies messenger RNA metabolism and plant development.

RNA modifications constitute an essential layer of gene regulation in living organisms. As the most prevalent internal modification on eukaryotic mRNAs, N-methyladenosine (mA) exists in many plant species and requires the evolutionarily conserved methyltransferases, demethylases, and mA binding proteins for writing, erasing, and reading mA, respectively. In plants, mA affects many aspects of mRNA metabolism, including alternative polyadenylation, secondary structure, translation, and decay, which underlies various plant developmental processes and stress responses.

TOP1α, UPF1, and TTG2 regulate seed size in a parental dosage-dependent manner.

Cues of maternal and paternal origins interact to control seed development, and the underlying molecular mechanisms are still far from clear. Here, we show that TOPOISOMERASE Iα (TOP1α), UP-FRAMESHIFT SUPPRESSOR 1 (UPF1), and TRANSPARENT TESTA GLABRA2 (TTG2) gametophytically, biparentally regulate seed size in Arabidopsis. TOP1α and UPF1 are mainly expressed in antipodal cells, and loss of their function leads to ectopic TTG2 expression in these female gametophytic cells.

Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta.

The Streptophyta include unicellular and multicellular charophyte green algae and land plants. Colonization of the terrestrial habitat by land plants is a major evolutionary event that has transformed the planet. So far, lack of genome information on unicellular charophyte algae hinders the understanding of the origin and the evolution from unicellular to multicellular life in Streptophyta.

Messenger RNA Modifications in Plants.

Over 160 distinct RNA modifications are known and collectively termed the epitranscriptome. Some of these modifications have been discovered in mRNA, uncovering a new layer of gene regulation. Transcriptome-wide mapping of epitranscriptomic codes and the discovery of their writers, erasers, and readers that dynamically install, remove, and interpret RNA modifications, respectively, are fundamental to understanding the epitranscriptome.

Spatial expression of CLAVATA3 in the shoot apical meristem suggests it is not a stem cell marker in soybean.

CLAVATA3 (CLV3), a stem cell marker in Arabidopsis thaliana, encodes a secreted peptide that maintains the stem cell population within the shoot apical meristem. This work investigated the CLV3 orthologue in a major legume crop, soybean (GmCLV3). Instead of being expressed in the three outermost layers of the meristem as in Arabidopsis, GmCLV3 was expressed deeper in the central zone beneath the fourth layer (L4) of the meristem, overlapping with the expression of soybean WUSCHEL.

Novel members of the AGAMOUS LIKE 6 subfamily of MIKCC-type MADS-box genes in soybean.

Background: The classical (C) MIKC-type MADS-box transcription factors comprise one gene family that plays diverse roles in the flowering process ranging from floral initiation to the development of floral organs. Despite their importance in regulating developmental processes that impact crop yield, they remain largely unexplored in the major legume oilseed crop, soybean.

Results: We identified 57 MIKC(c)-type transcription factors from soybean and determined the in silico gene expression profiles of the soybean MIKC(c)-type genes across different tissues.

The dynamics of soybean leaf and shoot apical meristem transcriptome undergoing floral initiation process.

Flowering process governs seed set and thus affects agricultural productivity. Soybean, a major legume crop, requires short-day photoperiod conditions for flowering. While leaf-derived signal(s) are essential for the photoperiod-induced floral initiation process at the shoot apical meristem, molecular events associated with early floral transition stages in either leaves or shoot apical meristems are not well understood.

Transcriptomic and metabolomic analysis of Yukon Thellungiella plants grown in cabinets and their natural habitat show phenotypic plasticity.

Background: Thellungiella salsuginea is an important model plant due to its natural tolerance to abiotic stresses including salt, cold, and water deficits. Microarray and metabolite profiling have shown that Thellungiella undergoes stress-responsive changes in transcript and organic solute abundance when grown under controlled environmental conditions. However, few reports assess the capacity of plants to display stress-responsive traits in natural habitats where concurrent stresses are the norm.

Genomic profiling of rice sperm cell transcripts reveals conserved and distinct elements in the flowering plant male germ lineage.

Genomic assay of sperm cell RNA provides insight into functional control, modes of regulation, and contributions of male gametes to double fertilization. Sperm cells of rice (Oryza sativa) were isolated from field-grown, disease-free plants and RNA was processed for use with the full-genome Affymetrix microarray. Comparison with Gene Expression Omnibus (GEO) reference arrays confirmed expressionally distinct gene profiles.

Comparative genomic analysis of soybean flowering genes.

Flowering is an important agronomic trait that determines crop yield. Soybean is a major oilseed legume crop used for human and animal feed. Legumes have unique vegetative and floral complexities.

Border sequences of Medicago truncatula CLE36 are specifically cleaved by endoproteases common to the extracellular fluids of Medicago and soybean.

CLE (CLAVATA3/ESR-related) peptides are developmental regulators that are secreted into the apoplast. Little is known about the role of the sequences that flank CLE peptides in terms of their biological activity or how they are targeted by proteases that are known to liberate the final active CLE peptides from their precursor sequences. The biological activity of Medicago truncatula CLE36, which possesses broadly conserved border sequences flanking the putative final active CLE36 peptide product, was assessed.

MicroRNAs in the shoot apical meristem of soybean.

Plant microRNAs (miRNAs) play crucial regulatory roles in various developmental processes. In this study, we characterize the miRNA profile of the shoot apical meristem (SAM) of an important legume crop, soybean, by integrating high-throughput sequencing data with miRNA microarray analysis. A total of 8423 non-redundant sRNAs were obtained from two libraries derived from micro-dissected SAM or mature leaf tissue.

Novel spatial expression of soybean WUSCHEL in the incipient floral primordia.

The homeobox transcription factor WUSCHEL (WUS) is known to play a critical role in the maintenance of the stem cell population in shoot and floral meristems of Arabidopsis thaliana. The corresponding gene is yet to be characterized in soybean, a vital legume crop. In this study, we isolated the soybean ortholog of WUS (GmWUS) and explored its possible conserved function by in situ hybridization analysis and ectopic expression in Arabidopsis.

In vitro propagation of Australian native ornamental plant, Scaevola.

In this chapter, we describe a robust method for the micropropagation of Australian fan flower, Scaevola, a native plant increasingly being used in the ornamental horticulture industry. Shoot segments from different species of Scaevola can be successfully multiplied following this protocol. Multiple shoots can be obtained in hormone-free Murashige and Skoog medium.

Floral initiation process at the soybean shoot apical meristem may involve multiple hormonal pathways.

Flowering and seed set underpin most of the agriculture production. In the 57 Issue of The Plant Journal, we analysed the gene expression changes in the shoot apical meristem (SAM) during the transition from vegetative to flowering phase in soybean, an important legume crop. We identified a number of genes that are actively transcribed or repressed during the transition to flowering and the annotation of which have allowed us to infer the involvement of at least three hormonal pathways: those that involve abscisic acid (ABA), auxin and jasmonic acid (JA) in the regulation of floral initiation process in soybean.

Molecular dissection of the pea shoot apical meristem.

The shoot apical meristem (SAM) is responsible for the development of all the above-ground parts of a plant. Our understanding of the SAM at the molecular level is incomplete. This study investigates the gene expression repertoire of SAMs in the garden pea (Pisum sativum).

Genomic expression profiling of mature soybean (Glycine max) pollen.

Background: Pollen, the male partner in the reproduction of flowering plants, comprises either two or three cells at maturity. The current knowledge of the pollen transcriptome is limited to the model plant systems Arabidopsis thaliana and Oryza sativa which have tri-cellular pollen grains at maturity. Comparative studies on pollen of other genera, particularly crop plants, are needed to understand the pollen gene networks that are subject to functional and evolutionary conservation.

Genome-wide analysis of gene expression in soybean shoot apical meristem.

The shoot apical meristem (SAM) contains undifferentiated stem cells that are responsible for the initiation of above-ground organs. The nature of genetic programs and the regulatory networks underlying SAM function in a major legume crop, soybean was investigated here. We used soybean GeneChip (containing 37,744 probe sets) to examine the transcript profiles associated with micro-dissected, actively growing SAMs or growth arrested axillary meristems (AMs) experiencing apical dominance, in comparison to that of non-meristem (NM) tissue.

Molecular processes underlying the floral transition in the soybean shoot apical meristem.

The transition to flowering is characterized by a shift of the shoot apical meristem (SAM) from leaf production to the initiation of a floral meristem. The flowering process is of vital importance for agriculture, but the associated events or regulatory pathways in the SAM are not well understood, especially at a system level. To address this issue, we have used a GeneChip containing 37 744 probe sets to generate a temporal profile of gene expression during the floral initiation process in the SAM of the crop legume, soybean (Glycine max).

Transcriptional profiling of the pea shoot apical meristem reveals processes underlying its function and maintenance.

Background: Despite the importance of the shoot apical meristem (SAM) in plant development and organ formation, our understanding of the molecular mechanisms controlling its function is limited. Genomic tools have the potential to unravel the molecular mysteries of the SAM, and legume systems are increasingly being used in plant-development studies owing to their unique characteristics such as nitrogen fixation, secondary metabolism, and pod development. Garden pea (Pisum sativum) is a well-established classic model species for genetics studies that has been used since the Mendel era.