Gymnocladus chinensis Baill (Fam.: Leguminosae; Trib.: Caesalpinieae) are widely distributed in China. In this study, we assembled the complete chloroplast (cp) genome of G. chinensis. The total cp genome size was 165,315 bp in length, containing a large single-copy region of 92,356 bp, a small single-copy region of 20,449bp, and a pair of inverted repeat regions of 26,255 bp. The all GC content of G. chinensis cp was 34.95%. It encodes a total of 105 unique genes, including 75 protein-coding genes, 26 tRNA genes, and four rRNA genes. Seventeen genes contain a single intron, and two genes (ycf3 and clpP) have two introns. Phylogenetic analysis results strongly supported that G. chinensis was closely related to Angylocalyx braunii.

Pinus massoniana Lamb. is an important coniferous tree species in ecological environment construction and sustainable forestry development. The function of gene gradual change and coexpression modules of needle and root parts of P. massoniana under continuous drought stress is unclear. The physiological and transcriptional expression profiles of P. massoniana seedlings from 1a half-sibling progeny during drought stress were measured and analyzed. As a result, under continuous drought conditions, needle peroxidase (POD) activity and proline content continued to increase. The malondialdehyde (MDA) content in roots continuously increased, and the root activity continuously decreased. The needles of P. massoniana seedlings may respond to drought mainly through regulating abscisic acid (ABA) and jasmonic acid (JA) hormone-related pathways. Roots may provide plant growth through fatty acid β-oxidative decomposition, and peroxisomes may contribute to the production of ROS, resulting in the upregulation of the antioxidant defense system. P. massoniana roots and needles may implement the same antioxidant mechanism through the glutathione metabolic pathway. This study provides basic data for identifying the drought response mechanisms of the needles and roots of P. massoniana.

G. sinensis thorn (called “zào jiǎo cì”, ZJC) has important medicinal and economic value, however, little is known about the molecular mechanisms behind the development of ZJC. In this study, we measured the content of soluble sugar and starch during the growth and development of the thorn, and performed transcriptome sequencing of the thorn segment, non-thorn segment, apex, and root tip at five distinct stages of thorn formation. The results showed that, with the growth of ZJC, the soluble sugar content of the roots, hypocotyls, thorn stems, thornless stems, leaves, and the starch content of the roots and leaves all firstly increased and then decreased after the basic structure of thorns was formed; the soluble sugar content and starch content of ZJC showed an overall downward trend (decreased by 59.26% and 84.56%, respectively). Myb-like, YABBY2, Growth-regulating factor 3, TCP2, Zinc transporter 8, and another 25 genes may be related to the maintenance and growth of thorns. Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) between stems with thorn and thorn-free stems found that a significant number of DEGs were annotated with terms related to the positive regulation of development, heterochronic (GO:0045962), the positive regulation of photomorphogenesis (GO:2000306), and other biological process (BP) terms. The developmental initiation regulation of ZJC may be regulated by TCP transcription factors (TFs). Eight genes were selected randomly to validate the RNA-seq results using real-time quantitative PCR (RT-qPCR) and they indicated that the transcriptome data were reliable. Our work provided a comprehensive review of the thorn development of G. sinensis.

Pinus yunnanensis var. pygmaea demonstrates obvious loss of apical dominance, inconspicuous main trunk, which can be used as an ideal material for dwarfing rootstocks. In order to find out the reasons for the lack of apical dominance of P. pygmaea, endogenous phytohormone content determination by liquid chromatography–tandem mass spectrometry (LC–MS/MS) and comparative transcriptomes were performed on the shoot apical meristem and root apical meristem of three pine species (P. massoniana, P. pygmaea, and P. elliottii). The results showed that the lack of CK and the massive accumulation of ABA and GA-related hormones may be the reasons for the loss of shoot apical dominance and the formation of multi-branching, the abnormal synthesis of diterpenoid biosynthesis may lead to the influence of GA-related synthesis, and the high expression of GA 2-oxidase (GA2ox) gene may be the cause of dwarfing. Weighted correlation network analysis (WGCNA) screened some modules that were highly expressed in the shoot apical meristem of P. pygmaea. These findings provided valuable information for identifying the network regulation of shoot apical dominance loss in P. pygmaea and enhanced the understanding of the molecular mechanism of shoot apical dominance growth differences among Pinus species.

The Gleditsia genus has various uses, including those for medicinal, edible, chemical, timber, and ornamental purposes, and the genus is widely distributed in China. However, there is still a lack of understanding about the phenotypic and growth differences seen among species within the Gleditsia genus. In this study, we compared and analyzed the various species of Gleditsia seedlings in terms of their genotypes, chromosome numbers, physiological growth, photosynthesis, hormone content, and gene expression. The results showed that the genome size of the Gleditsia genus ranges from 686.08 M to 1034.24 M and that all Gleditsia species are diploid. Among the species studied, G. fera can be divided into fast-growing genotype, exhibited several advantages in terms of leaf type and photosynthetic capacity, high levels of GA₃, and fast stem growth, making it a species with the potential for promotion and application. G. delavayi exhibited high levels of auxin and cytokinin and strong photosynthetic capacity, with rapid growth in terms of plant height. G. microphylla had the lowest levels of IAA, IBA, and NAA in the apical, and showed slow growth in terms of plant height. Weighted correlation network analysis (WGCNA) identified the hub genes associated with traits. This study lays a material and theoretical foundation for the development of new resources for Gleditsia breeding and rootstock selection and provides a basis for the mechanism of rootstock–scion interaction.

Trachycarpus fortunei (Hook.) is a typical dioecious plant, which has important economic value. There is currently no sex identification method for the early stages of T. fortunei growth. The aim of this study was to obtain expression and site differences between male and female T. fortunei transcriptomes. Using the Illumina sequencing platform, the transcriptomes of T. fortunei male and female plants were sequenced. By analyzing transcriptomic differences, the chromosomal helical binding protein (CHD1), serine/threonine protein kinase (STPK), cytochrome P450 716B1, and UPF0136 were found to be specifically expressed in T. fortunei males. After single nucleotide polymorphism (SNP) detection, a total of 12 male specific sites were found and the THUMP domain protein homologs were found to be male-biased expressed. Cytokinin dehydrogenase 6 (CKX6) was upregulated in male flowers and the lower concentrations of cytokinin (CTK) may be more conducive to male flower development. During new leaf growth, flavonoid and flavonol biosynthesis were initiated. Additionally, the flavonoids, 3′,5′-hydroxylase (F3′5′H), flavonoids 3′-hydroxylase, were upregulated, which may cause the pale yellow phenotype. Based on these data, it can be concluded that inter-sex differentially expressed genes (DEGs) and specific SNP loci may be associated with sex determination in T. fortunei.