Background: Most plants rely on photosynthesis; therefore, albinism in plants with leaves that are white instead of green causes slow growth, dwarfing, and even death. Although albinism has been characterized in annual model plants, little is known about albino trees. Jackfruit (Artocarpus heterophyllus) is an important tropical fruit tree species. To gain insight into the mechanisms underlying the differential growth and development between albino jackfruit mutants and green seedlings, we analyzed root, stem, and leaf tissues by combining PacBio single-molecule real-time (SMRT) sequencing, high-throughput RNA-sequencing (RNA-seq), and metabolomic analysis.Results: We identified 8,202 differentially expressed genes (DEGs), including 225 genes encoding transcription factors (TFs), from 82,572 full-length transcripts. We also identified 298 significantly changed metabolites (SCMs) in albinoA. heterophyllusseedlings from a set of 692 metabolites inA. heterophyllusseedlings. Pathway analysis revealed that these DEGs were highly enriched in metabolic pathways such as ‘photosynthesis’, ‘carbon fixation in photosynthetic organisms’, ‘glycolysis/gluconeogenesis’, and ‘TCA cycle’. Analysis of the metabolites revealed 76 SCMs associated with metabolic pathways in the albino mutants, including L-aspartic acid, citric acid, succinic acid, and fumaric acid. We selected 225 differentially expressed TF genes, 333 differentially expressed metabolic pathway genes, and 76 SCMs to construct two correlation networks. Analysis of the TF–DEG network suggested that basic helix-loop-helix (bHLH) and MYB-related TFs regulate the expression of genes involved in carbon fixation and energy metabolism to affect light responses or photomorphogenesis and normal growth. Further analysis of the DEG–SCM correlation network and the photosynthetic carbon fixation pathway suggested thatNAD-ME2(encoding a malic enzyme) and L-aspartic acid jointly inhibit carbon fixation in the albino mutants, resulting in reduced photosynthetic efficiency and inhibited plant growth.Conclusions: Our preliminarily screening identified candidate genes and metabolites specifically affected in albinoA. heterophyllusseedlings, laying the foundation for further study of the regulatory mechanism of carbon fixation during photosynthesis and energy metabolism. In addition, our findings elucidate the way genes and metabolites respond in albino trees.

Sonneratia apetala is an essential mangrove wetland restoration tree species. Studying its molecular mechanism for salt tolerance could lay a foundation for further cultivating excellent resistant germplasm. This study used a combination of PacBio isoform sequencing (Iso-seq) and BGISEQ RNA sequencing (RNA-seq) to analyze the molecular mechanism to salt stress response of one-year-old S. apetala leaves. The growth and physiological analysis showed that physiological indexes such as growth rate, net photosynthetic rate and antioxidant enzyme activity all exhibit significant changes under salt stress. From Iso-seq, a total of 295,501 full-length transcripts, with an average length of 1418 bp, were obtained. RNA-seq produced 4712 differentially expressed genes (DEGs) as compared to a control group. Of these, 930 were identified to be co-expressed during the STEM time sequence analysis. Further, 715 and 444 co-expressed DEGs were annotated by GO and KEGG analyses, respectively. Moreover, 318 of the co-expressed DEGs were annotated as essential genes that were implicated in salt stress response of S. apetala, which were involved in transcription factors, signal transduction, hormone response, ROS homeostasis, osmotic balance, cell wall synthesis or modification. These results provide candidate targets for further characterization and offer insights into the salt-tolerant mechanism of S. apetala.

Aquilaria sinensis (Lour.) Spreng. is an economically important tree specie that produces agarwood, a valuable medicinal and aromatic resin, when injured. However, its large-scale cultivation has led to confusion regarding its resources and genetic backgrounds, hindering the conservation and management of A. sinensis accessions. This study systematically developed and validated simple sequence repeat (SSR) molecular markers by using whole-genome resequencing (WGR) data from 60 A. sinensis accessions to elucidate their genetic diversity and population structure. A total of 56,657 SSR sequences (24,430 loci) were identified, which were dominated with dinucleotide repeat motifs (73.59%). After stringent quality control, 46 high-quality SSR loci were obtained, and 93 primer pairs were designed for amplification validation. Ultimately, 20 primer pairs with stable amplification and high polymorphism were selected, of which 11 exhibited high polymorphism (polymorphic information content: 0.554–0.688). These 20 primer pairs identified a total of 121 alleles, with an average of 6 alleles per locus. These primers successfully classified 149 A. sinensis accessions into three subpopulations, achieving a discrimination rate of 95.97%. The analysis of molecular variance revealed that genetic variation within the individuals accounted for 84% of the total variation. This study establishes a rapid and efficient SSR-based method by leveraging resequencing data for large-scale marker discovery in A. sinensis. It further provides a robust technical framework for the conservation and sustainable utilization of this valuable species.

Chromium (Cr) is one of the most toxic heavy metals in the environment. The tolerance to metal stress involves sophisticated regulation of gene expression networks, which involve microRNAs (miRNAs). However, the role of miRNAs in Cr stress response in Avicennia marina has not been resolved, and was addressed here. The analysis of response characteristics revealed that morpho-physiological traits such as root length, Cr accumulation level and antioxidant enzyme activity all exhibit significant changes under Cr stress. Via sRNA sequencing, a total of 27 known and 149 novel miRNAs were identified, 63 of which showed differential expression after Cr stress (q-value < 0.001). Further, 571 miRNA-target interaction pairs were identified for differentially expressed miRNAs, corresponding to 355 target genes. GO and KEGG analyses indicated that these target genes could participate in stress-related biological processes such as signal transduction, transcription regulation, protein synthesis and the MAPK signaling pathway. 54 miRNA target genes, corresponding to 37 miRNAs such as Ama-miR160, Ama-nmiR25-5p and Ama-nmiR118-5p, were enriched for “plant signal hormone transduction” (ko04075), “phenylpropanoid biosynthesis” (ko00940) and “MAPK signaling pathway” (ko04016), which indicated an important role of these miRNAs in regulating Cr stress response in A. marina. Based on the findings, a Cr stress-responsive regulatory model was developed, offering new insights into the molecular regulatory mechanisms of Cr response. In conclusion, this study shows the identity and potential role of miRNAs in the heavy metal stress response of A. marina, and provides the foundation for future research.