Comparative RNA-Sequencing and DNA Methylation Analyses of Apple (Malus domestica Borkh.) Buds with Diverse Flowering Capabilities Reveal Novel Insights into the Regulatory Mechanisms of Flower Bud Formation.

In plants, DNA methylation (i.e. chromatin modification) is important for various biological processes, including growth, development and flowering. Because 'Fuji' apple trees are alternate bearing and have a long ripening period and poor-quality flower buds, we used bud types with diverse flowering capabilities to investigate the epigenetic regulatory mechanisms influencing flower bud formation. We examined the DNA methylation changes and the transcriptional responses in the selected apple bud types. We observed that in the apple genome, approximately 79.5%, 67.4% and 23.7% of the CG, CHG and CHH sequences are methylated, respectively. For each sequence context, differentially methylated regions exhibited distinct methylation patterns among the analyzed apple bud types. Global methylation and transcriptional analyses revealed that nonexpressed genes or genes expressed at low levels were highly methylated in the gene-body regions, suggesting that gene-body methylation is negatively correlated with gene expression. Moreover, genes with methylated promoters were more highly expressed than genes with unmethylated promoters, implying promoter methylation and gene expression are positively correlated. Additionally, flowering-related genes (e.g. SOC1, AP1 and SPLs) and some transcription factor genes (e.g. GATA, bHLH, bZIP and WOX) were highly expressed in spur buds (highest flowering rate), but were associated with low methylation levels in the gene-body regions. Our findings indicate a potential correlation between DNA methylation and gene expression in apple buds with diverse flowering capabilities, suggesting an epigenetic regulatory mechanism influences apple flower bud formation.

Four new species of the frogmouth genus Chaunax (Lophiiformes: Chaunacidae) from Taiwan and the Philippines.

Four new species of the genus Chaunax found in Taiwan and the Philippines are described. Chaunax albatrossae sp. nov. belongs to the C. abei species group and is distinct from its congeners in having a dark gray mouth cavity, a dark brown to black gill chamber and gill rakers and skin covered with only short, simple spinules. Three new species belong to the C. fimbriatus species group: Chaunax erythraeus sp. nov. is distinct in having a uniformly pinkish-red body and an entirely black gill chamber; Chaunax obscurus sp. nov. is distinct in having a dark gray mouth cavity and orange-red marbling on the dorsal surface that fades after fixation; and Chaunax viridiretis sp. nov. is distinguished by its green reticulate pattern with some small, bright-white patches on the dorsal surface. The diagnostic characters used to identify the chaunacids are summarized and a key to all Chaunax species found in Taiwan and adjacent waters is provided.

Epigenomic Regulatory Mechanism in Vegetative Phase Transition of Malus hupehensis.

In woody plants, phase transitions substantially affect growth and development. Although there has been considerable interest in the regulatory mechanisms underlying phase changes, the associated epigenetic modifications remain relatively uncharacterized. We examined the DNA methylation changes and the transcriptional responses in adult and juvenile Malus hupehensis leaves. The DNA methylations were 66.61% and 68.3% in the CG context, 49.12% and 52.44% in the CHG context, and 7.02% and 8.22% in the CHH context for the adult and juvenile leaves, respectively. The number of differentially methylated regions in all contexts distributed in the genic regions varied. Additionally, inhibited DNA methylation in adult leaves activated the transcription of indole-3-acetic acid related genes in the signaling, response, and transport pathways. Moreover, the opposite methylation and expression patterns were observed for the SPL and AP2 family genes between the adult and juvenile leaves. Both gene families contribute to the M. hupehensis vegetative phase transition. Furthermore, the hyper-/hypomethylation of the gene body or promoter of transcription factor genes may lead to up-/downregulated gene expression. The methylation levels of the WRKY (22), NAC (21), ERF (8), WOX (2), KNAT (6), EIN3 (2), SCL (7), ZAT (7), and HSF (4) genes were higher in the adult leaves than in the juvenile leaves, whereas the opposite pattern was observed for the TCP (2), MADS-box (11), and DOF (3) genes. An analysis of the correlation between methylation and transcription indicated the methylation of the gene body in all contexts and the methylation of the promoter in the CG and CHG contexts are negatively correlated with gene expression. However, the methylation of the promoter in the CHH context is positively correlated with gene expression. These findings reflect the diversity in the epigenetic regulation of gene expression and may be useful for elucidating the epigenetic regulatory mechanism underlying the M. hupehensis vegetative phase transition.

Chronic cement dust load induce novel damages in foliage and buds of Malus domestica.

Cement industry-derived pollutants appear to play multiple roles in stimulating abiotic stress responses in plants. Cement dust deposition on agriculture fields can affect soils, photosynthesis, transpiration and respiration of plants. Here, we characterised the acute physiological responses of Malus × domestica leaves to different cement dust concentrations. The cement dust was sprinkled over plants daily for 2 months at 10 and 20 g/plant, with 0 g/plant serving as the control. Leaf physiological responses revealed significant increases in oxidative stress and antioxidant enzyme activity levels. Additionally, ascorbic acid, soluble sugar, free amino acid, and pigment levels decreased after exposure to cement dust. Macroscopic morphometric parameters, such as weight, dry matter content, and lengths and widths of leaves and buds, were significantly reduced in the cement-treated groups. A histological analysis of leaves and buds revealed decreased cellular areas, cellular damage, and abridged leaf thickness, while an ion leakage assay confirmed the negative effects on tissue integrity. These results provide evidence that cement dust is a hazardous pollutant that induces abiotic stress responses and has degradative effects on leaf health, pigment and biochemical metabolite levels, and anatomical features. Studies to determine the elemental residues of cement dust present in edible plant parts and the adverse impacts of their consumption on human health are strongly recommended.

Genomic identification and expression analysis of nuclear pore proteins in Malus domestica.

The nuclear pore complex (NPC), comprised of individual nucleoporin (Nup) proteins, controls nucleo-cytoplasmic transport of RNA and protein, and is important for regulating plant growth and development. However, there are no reports on this complex in fruit tree species. In this study, we identified 38 apple Nups and named them based on the known Arabidopsis thaliana homologs. We also completed bioinformatics analyses of the intron and exon structural data for apple Nups. The proteins encoded by the apple Nups lacked a universally conserved domain. Moreover, a phylogenetic analysis separated the apple and A. thaliana Nups into three groups. The phylogenetic tree indicated that MdNup54 and MdNup62 are most closely related to genes in other Rosaceae species. To characterize the 38 candidate Malus domestica Nups, we measured their stage-specific expression levels. Our tests revealed these proteins were differentially expressed among diverse tissues. We analyzed the expression levels of seven apple Nups in response to an indole-3-acetic acid (IAA) treatment. The phytohormone treatment significantly inhibited apple flowering. A qRT-PCR analysis proved that an IAA treatment significantly inhibited the expression of these seven genes. A preliminary study regarding two members of the Nup62 subcomplex, MdNup54 and MdNup62, confirmed these two proteins can interact with each other. A yeast two-hybrid assay verified that MdNup54 can interact with MdKNAT4 and MdKNAT6. On the basis of the study results, we identified apple NPC and predicted its structure and function. The data generated in this investigation provide important reference material for follow-up research.

Revision of southern African species of the anglerfish genus Chaunax (Lophiiformes: Chaunacidae), with descriptions of three new species.

Species of the anglerfish genus Chaunax occurring off southern Africa are reviewed and nine species are recognized: C. africanus, C. apus, C. flammeus, C. penicillatus, C. russatus, C. suttkusi, and three newly described species. Chaunax atimovatae sp. nov. is distinguished by having numerous tiny melanophores on the skin and a mixture of bifurcate and simple spinules on its dorsal surface, scattered rounded green spots circled by yellow on its dorsal surface, 9 or 10 rakers on the second gill arch, and 2 neuromasts in the upper preopercular, 11-14 in the pectoral, 31-37 in the lateral-line proper. Chaunax heemstraorum sp. nov. is distinguished by a combination of all dermal spinules simple, large green spots on the dorsal surface, 10-12 rakers on the second gill arch; and 3 neuromasts in the upper preopercular, 13-18 in the pectoral, 37-42 in the lateral-line proper, and usually 5 on the caudal-fin base. Chaunax hollemani sp. nov. is distinguished by cirri on top of the head, head width 16.0-18.5% SL, pre-preopercle length 26.8-28.5% SL, 9 rakers on the second gill arch, and 2 neuromasts in the upper preopercular, 11-14 in the pectoral, and 33-38 in the lateral-line proper. A key to species found in the study region is provided.