Transcriptome and metabolome analyses of lignin biosynthesis mechanism of Platycladus orientalis.

Background: Platycladus orientalis, as an important plant for ecological protection, is a pioneer tree species for afforestation in arid and barren mountainous areas. Lignin has the functions of water and soil conservation, strengthening plant mechanical strength and resisting adverse environmental effects and plays an important role in the ecological protection benefits of P. orientalis. Methods: In this study, annual dynamic observations of the lignin content in roots, stems and leaves of one-year-old seedlings of a P. orientalis half-sib family were carried out, and combined transcriptome and metabolome analyses were carried out during three key stages of P. orientalis stem development. Results: The lignin contents in roots, stems and leaves of P. orientalis showed extremely significant spatiotemporal differences. In the stems, lignin was mainly distributed in the cell walls of the pith, xylem, phloem, pericyte, and epidermis, with differences in different periods. A total of 226 metabolites were detected in the stem of P. orientalis, which were divided into seven categories, including 10 synthetic precursor compounds containing lignin. Among them, the content of coniferyl alcohol was the highest, accounting for 12.27% of the total content, and caffeyl alcohol was the lowest, accounting for 7.05% only. By annotating the KEGG functions, a large number of differentially expressed genes and differential metabolites were obtained for the comparison combinations, and seven key enzymes and 24 related genes involved in the process of lignin synthesis in P. orientalis were selected. Conclusions: Based on the results of the metabolic mechanism of lignin in P. orientalis by biochemical, anatomical and molecular biological analyzes, the key regulatory pathways of lignin in P. orientalis were identified, which will be of great significance for regulating the lignin content of P. orientalis and improving the adaptability and resistance of this plant.

Multi-omics analysis reveals the ontogenesis of basal chichi in Ginkgo biloba L.

Chichi is a unique biological phenomenon observed in Ginkgo biloba L.. In this study, multi-omics analysis was used to compare basal chichi (C) with roots (R) and stems (S) to explore the regulatory mechanisms of basal chichi ontogenesis. The results showed that compared with roots and stems, the tZ, SA and ABA contents in basal chichi were the highest, and the ratio of IAA/tZ was the lowest. Nucleotides and their derivatives in basal chichi were upregulated, and phenylpropane metabolites were downregulated. Some differentially expressed genes (DEGs) strongly correlated to plant hormones were screened. We speculate that auxin and cytokinin are involved in the morphogenesis of basal chichi and that cytokinin plays a major role. The ontogenesis of basal chichi is closely related to environmental stress, and it may be a coping strategy of G. biloba in the face of environmental stress.

Transcriptome sequencing of active buds from Populus deltoides CL. and Populus × zhaiguanheibaiyang reveals phytohormones involved in branching.

Branching in woody plants affects their ecological benefits and impacts wood formation. To obtain genome-wide insights into the transcriptome changes and regulatory mechanisms associated with branching, we performed high-throughput RNA sequencing to characterize cDNA libraries generated from active buds of Populus deltoides CL. 'zhonglin2025' (BC) and Populus × zhaiguanheibaiyang (NC). NC has more branches than BC and rapid growth. We obtained a total of 198.2 million high-quality clean reads from the NC and BC libraries. We detected 3543 differentially expressed genes (DEGs) between the NC and BC libraries; 1418 were down-regulated and 2125 were up-regulated. Gene ontology functional classification of the DEGs indicated that they included 89 genes that encoded proteins related to hormone biosynthesis, 364 genes related to hormone signaling transduction, and 104 related to the auxin efflux transmembrane transporter. We validated the expression profiles of 16° by real-time quantitative PCR and found that their expression patterns were similar to those obtained from the high-throughput RNA sequencing data. We also measured the hormone content in young buds of BC and NC by high-pressure liquid chromatography. In this study, we identified global hormone regulatory patterns and differences in gene expression between NC and BC, and constructed a hormone regulatory network to explain branching in Populus buds. In addition, candidate genes that may be useful for molecular breeding of particular plant types were identified. Our results will provide a starting point for future investigations into the molecular mechanisms of branching in Populus.

Transcriptome profile analysis reveals the ontogenesis of rooted chichi in Ginkgo biloba L.

The Ginkgo biloba L. chichi is a unique organ. To explore the molecular mechanisms underlying the ontogenesis of G. biloba chichi, we used RNA-seq to analyse the transcriptome profile of rooted chichi at two developmental stages (ch1 and ch2) and nearby tissues (ck), and each sample had three biological replicates. A total of 57.74 Gb of clean bases were generated in nine cDNA libraries. These bases were de novo assembled into 68,277 unigenes with average length of 844 bp, and 51.47% of the unigenes had a match in at least one public database. The differentially expressed genes (DEGs) in ch1 vs. ck and ch2 vs. ck were 2748 and 8594, respectively. The DEGs involved in the auxin signal pathway, auxin polar transport, storage-related proteins, and the cell cycle pathway might play roles in the ontogenesis of chichi. The quantitative real-time PCR results were closely correlated with transcriptome data. The transcriptome resources generated in the current study provide gene expression profiles and differential expression profiles of G. biloba chichi and offer an essential resource to probe the molecular mechanisms underlying the ontogenesis of G. biloba chichi.

Transcriptome Profile Analysis from Different Sex Types of Ginkgo biloba L.

In plants, sex determination is a comprehensive process of correlated events, which involves genes that are differentially and/or specifically expressed in distinct developmental phases. Exploring gene expression profiles from different sex types will contribute to fully understanding sex determination in plants. In this study, we conducted RNA-sequencing of female and male buds (FB and MB) as well as ovulate strobilus and staminate strobilus (OS and SS) of Ginkgo biloba to gain insights into the genes potentially related to sex determination in this species. Approximately 60 Gb of clean reads were obtained from eight cDNA libraries. De novo assembly of the clean reads generated 108,307 unigenes with an average length of 796 bp. Among these unigenes, 51,953 (47.97%) had at least one significant match with a gene sequence in the public databases searched. A total of 4709 and 9802 differentially expressed genes (DEGs) were identified in MB vs. FB and SS vs. OS, respectively. Genes involved in plant hormone signal and transduction as well as those encoding DNA methyltransferase were found to be differentially expressed between different sex types. Their potential roles in sex determination of G. biloba were discussed. Pistil-related genes were expressed in male buds while anther-specific genes were identified in female buds, suggesting that dioecism in G. biloba was resulted from the selective arrest of reproductive primordia. High correlation of expression level was found between the RNA-Seq and quantitative real-time PCR results. The transcriptome resources that we generated allowed us to characterize gene expression profiles and examine differential expression profiles, which provided foundations for identifying functional genes associated with sex determination in G. biloba.

Identification and Characterization of MicroRNAs in Ginkgo biloba var. epiphylla Mak.

Ginkgo biloba, a dioecious plant known as a living fossil, is an ancient gymnosperm that stands distinct from other gymnosperms and angiosperms. Ginkgo biloba var. epiphylla (G. biloba var. epiphylla), with ovules borne on the leaf blade, is an unusual germplasm derived from G. biloba. MicroRNAs (miRNAs) are post-transcriptional gene regulators that play critical roles in diverse biological and metabolic processes. Currently, little is known about the miRNAs involved in the key stage of partly epiphyllous ovule germination in G. biloba var. epiphylla. Two small RNA libraries constructed from epiphyllous ovule leaves and normal leaves of G. biloba var. epiphylla were sequenced on an Illumina/Solexa platform. A total of 82 miRNA sequences belonging to 23 families and 53 putative novel miRNAs were identified in the two libraries. Differential expression analysis showed that 25 conserved and 21 novel miRNAs were differentially expressed between epiphyllous ovule leaves and normal leaves. The expression patterns of partially differentially expressed miRNAs and the transcript levels of their predicted target genes were validated by quantitative real time RT-PCR. All the expression profiles of the 21 selected miRNAs were similar to those detected by Solexa deep sequencing. Additionally, the transcript levels of almost all the putative target genes of 9 selected miRNAs were opposite to those of the corresponding miRNAs. The putative target genes of the differentially expressed miRNAs were annotated with Gene Ontology terms related to reproductive process, metabolic process and responding to stimulus. This work presents a broad range of small RNA transcriptome data obtained from epiphyllous ovule and normal leaves of G. biloba var. epiphylla, which may provide insights into the miRNA-mediated regulation in the epiphyllous ovule germination process.

[Research on systematic evolution of ginkgo biloba based on chemical composition of wood].

In the present article, the authors mensurated the infrared spectra of 22 conifer and broadleaf trees such as ginkgo biloba L., cycas revoluta thunb., Populus tomentosa Carr and so on using FTIR, analyzed the difference of a number of absorb peaks in fingerprint area, the characteristic absorb peak position of cellulose and lignin of these trees and their alternation regulations of relative intensity, then discussed the evolutional issue of ginkgo biloba. The results show that ginkgo biloba is different from cycas in the infrared spectra of wood but similar to the conifer trees, which illustrates the ginkgo biloba. is more evolutional than cycas in the timber's chemical composition but with similar affiliation to conifer trees. The content of lignin in the ginkgo biloba wood is more than that in other conifer trees, which may be a original character of ginkgo biloba. Meanwhile, the ginkgo biloba has some syringyl lignins in addition to guaiacyl, and it has the evolutional tendency for broadleaf trees.

Genetic relationships of ornamental cultivars of Ginkgo biloba analyzed by AFLP techniques.

Eight primer combinations that produced clear and a large number of polymorphic bands were screened from 64 EcoR I/Mse I primer combinations (Mse I fluorescent labeled). The genetic relationships of 21 ornamental cultivars of Ginkgo biloba L. from the United States of America, Holland, Japan, France, and China were analyzed. These primer combinations produced a total of 1 119 bands, 229 specific loci (including 54 absent bands, and 175 monomorphic bands). Among them, 983 polymorphic bands (PPB), accounting for 88%, were detected. The percentage of identification per primer combination was as high as 100%. The average PPB of 14 foreign cultivars was 35.86% and the average PPB of seven domestic cultivars was 31.51%. Genetic similarity coefficient (SC) among all cultivars varied from 0.4899 to 0.8499, and all cultivars were divided into the four clusters when SC was set at 0.7300. The cultivars from the same origin did not fall into the same group. The cultivars from France and China were classified into three groups. According to the comprehensive analyses based on specific loci, similarity coefficient, and clustering results, eight cultivars 'Fastigiata', 'Tit', 'Tubifolia', 'Daeryinxing', 'Variegata', 'Horizontalis, 'Pendula', and 'Yiyuanyeziyinxing' were considered to be important germplasms of ornamental cultivars of Ginkgo biloba.

[Quantitative genetic analysis and multiple trait selection of pharmaceutical composition on Ginkgo biloba L. leaves].

The China possesses more than 70% Ginkgo resources in the world. The purposes of this research are to collect fine seedling and grafting clones in China, to probe genetic law on flavone glycosides and terpenes on Ginkgo leaves, and select leaf-used cultivars of high-pharmaceutical composition. In this research, we have collected 87 clones from 13 provenances and have carried out randomized block experiment at Tancheng, Laizhou and Yaoxiang in Shandong Province. Flavone glycosides and terpenes were determined through HPLC method from an improved Van Beek (1991) techniques and Shimadzu Lc-10 AD (Japan). Data and breeding analyses were carried out through IBMPC and SPQG30 software. The results of variance analyses show that there are significant differences to flavone glycosides, terpenes in clones, and the law of genetic parameters on heritability (h2) and genetic variability coefficient (Gcv), is clone > sex > provenance to flavone glycosides in ginkgo leaves. The sigma g2, h2, Gcv and delta G' in male tree clone leaves are higher than female clone leaves on flavone glycosides. We have found that there is a maximum flavone content clone among males and a maximum terpene clone among females. The results of Q-cluster analyses are consistent with R-factor analyses of twenty higher terpenes clones. The results of index selection show that the ri.Y2, E(I) and CGS' of multiple traits selection including (gamma) trait are higher than single trait and multiple traits selection excluding gamma. The direct or index selection is more suited to leaf-used cultivars of Ginkgo. The genetic stability of each clone was appraised by Wricke's ecovalence method and Nassar & Huhu noparameter method. Flavone glycosides and terpenes are more than 2.09%-2.57% and 0.33%-0.41%, respectively, and we have selected four clones.