Dataset Information

Transcriptome analysis of immature xylem in the Chinese fir at different developmental phases.

ABSTRACT: Background.Chinese fir [Cunninghamia lanceolata (Lamb.) Hook.] is one of the most important native tree species for timber production in southern China. An understanding of overall fast growing stage, stem growth stage and senescence stage cambium transcriptome variation is lacking. We used transcriptome sequencing to identify the repertoire of genes expressed during development of xylem tissue in Chinese fir, aiming to delineate the molecular mechanisms of wood formation. Results. We carried out transcriptome sequencing at three different cultivation ages (7Y, 15Y and 21Y) generating 68.71 million reads (13.88 Gbp). A total of 140,486 unigenes with a mean size of 568.64 base pairs (bp) were obtained via de novo assembly. Of these, 27,427 unigenes (19.52%) were further annotated by comparison to public protein databases. A total of 5,331 (3.79%) unigenes were mapped into 118 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Differentially expressed genes (DEG) analysis identified 3, 16 and 5,899 DEGs from the comparison of 7Y vs. 15Y, 7Y vs. 21Y and 15Y vs. 21Y, respectively, in the immature xylem tissues, including 2,638 significantly up-regulated and 3,280 significantly down-regulated genes. Besides, five NAC transcription factors, 190 MYB transcription factors, and 34 WRKY transcription factors were identified respectively from Chinese fir transcriptome. Conclusion. Our results revealed the active transcriptional pathways and identified the DEGs at different cultivation phases of Chinese fir wood formation. This transcriptome dataset will aid in understanding and carrying out future studies on the molecular basis of Chinese fir wood formation and contribute to future artificial production and applications.

SUBMITTER: Zhang Y

PROVIDER: S-EPMC4906661 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Transcriptome analysis of immature xylem in the Chinese fir at different developmental phases.

Zhang Yunxing Y Han Xiaojiao X Sang Jian J He Xuelian X Liu Mingying M Qiao Guirong G Zhuo Renying R He Guiping G Hu Jianjun J

PeerJ 20160607

Background.Chinese fir [Cunninghamia lanceolata (Lamb.) Hook.] is one of the most important native tree species for timber production in southern China. An understanding of overall fast growing stage, stem growth stage and senescence stage cambium transcriptome variation is lacking. We used transcriptome sequencing to identify the repertoire of genes expressed during development of xylem tissue in Chinese fir, aiming to delineate the molecular mechanisms of wood formation. Results. We carried ou ...[more]

PMID: 27330860

Similar Datasets

Project description:BackgroundPhosphorus is one of the essential elements for plant growth and development, but available phosphorus (Pi) content in many soil types is low. As a fast-growing tree species for timber production, Chinese fir is in great demand of Pi, and the lack of Pi in soil restricts the increase of productivity of Chinese fir plantation. Root morphology and the synthesis and secretion of organic acids play an important role in the uptake of phosphorus, but the molecular mechanisms of Chinese fir root responses to Pi deficiency are largely unexplored. In this study, seedlings of Yang 061 clone were grown under three Pi supply levels (0, 5 and 10 mg·L-1 P) and morphological attributes, organic acid content and enzyme activity were measured. The transcriptome data of Chinese fir root system were obtained and the expression levels of phosphorus responsive genes and organic acid synthesis related genes on citric acid and glyoxylate cycle pathway were determined.ResultsWe annotated 50,808 Unigenes from the transcriptome of Chinese fir roots. Among differentially expressed genes, seven genes of phosphate transporter family and 17 genes of purple acid phosphatase family were up-regulated by Pi deficiency, two proteins of SPX domain were up-regulated and one was down-regulated. The metabolic pathways of the citric acid and glyoxylate cycle pathway were mapped, and the expression characteristics of the related Unigenes under different phosphorus treatments were analyzed. The genes involved in malic acid and citric acid synthesis were up-regulated, and the activities of the related enzymes were significantly enhanced under long-term Pi stress. The contents of citric acid and malic acid in the roots of Chinese fir increased after 30 days of Pi deficiency.ConclusionChinese fir roots showed increased expression of genes related with phosphorus starvation, citrate and malate synthesis genes, increased content of organic acids, and enhanced activities of related enzymes under Pi deficiency. The results provide a new insight for revealing the molecular mechanism of adaption to Pi deficiency and the pathway of organic acid synthesis in Chinese fir roots.

Project description:BackgroundPsoroptic mange is a chronic, refractory, contagious and infectious disease mainly caused by the mange mite Psoroptes ovis, which can infect horses, sheep, buffaloes, rabbits, other domestic animals, deer, wild camels, foxes, minks, lemurs, alpacas, elks and other wild animals. Features of the disease include intense pruritus and dermatitis, depilation and hyperkeratosis, which ultimately result in emaciation or death caused by secondary bacterial infections. The infestation is usually transmitted by close contact between animals. Psoroptic mange is widespread in the world. In this paper, the transcriptome of P. ovis is described following sequencing and analysis of transcripts from samples of larvae (i.e. the Pso_L group) and nymphs and adults (i.e. the Pso_N_A group). The study describes differentially expressed genes (DEGs) and genes encoding allergens, which help understanding the biology of P. ovis and lay foundations for the development of vaccine antigens and drug target screening.MethodsThe transcriptome of P. ovis was assembled and analyzed using bioinformatic tools. The unigenes of P. ovis from each developmental stage and the unigenes differentially between developmental stages were compared with allergen protein sequences contained in the allergen database website to predict potential allergens.ResultsWe identified 38,836 unigenes, whose mean length was 825 bp. On the basis of sequence similarity with seven databases, a total of 17,366 unigenes were annotated. A total of 1,316 DEGs were identified, including 496 upregulated and 820 downregulated in the Pso_L group compared with the Pso_N_A group. We predicted 205 allergens genes in the two developmental stages similar to genes from other mites and ticks, of these, 14 were among the upregulated DEGs and 26 among the downregulated DEGs.ConclusionThis study provides a reference transcriptome of P. ovis in absence of a reference genome. The analysis of DEGs and putative allergen genes may lay the foundation for studies of functional genomics, immunity and gene expression profiles of this parasitic mite species.

Project description:Objective: In order to study the change law of Chinese fir gene expression caused by fertilization, it provides scientific basis for Chinese fir fertilization theory and practice. Method: Using Illumina HiSeq4000 high-throughput sequencing technology, sequencing sequences of four different fertilizer treatment materials (control CK1, nitrogen treatment N1, phosphorous treatment P1, and phosphorous and nitrogen mixture treatment NP1, each with three biological repeats) were obtained, and a series of comparative analysis of the differences were conducted. The experimental material was the 1-year clone cuttings of Chinese fir K62. At the end of 2017year, sand culture experiment was carried out in the plastic greenhouse of research institute of subtropical forestry,CAF. Because it was transcriptome sequencing without reference genome , sequencing reads need to be spliced into de novo, unigene and transcripts are assembled, and then functional annotation, differential expression and other project analysis are conducted. Result: In 12 samples, transcriptome sequencing produced clean reads5.0E+07nt to 7.1E+07nt, and the total splicing length was 724,341,090nt. BLASTX analysis was performed on clean reads in six databases (Nr, Swiss-prot,eggNOG, ,KEGG, Pfam, GO), and 74,288 genes were generated；The Venn diagram reveals the general overview of the gene response of different fertilization treatments: in the N1-VS-CK1 comparison group, NH4NO3 stimulation induced the opening expression of 3,295 genes, and CK1 produced 2,944 genes resistant to nitrogen; Similar results were obtained for other comparison groups. Chinese fir fertilization turns on and up-regulates the expression of some genes while shutting down or down regulating some genes of expression; Analysis of gene differential expression revealed that :720 differentially expressed genes were screened out in the N1-VS-CK1 comparison group, and 3,694 genes were found to be silenced by nitrogen application. Similar results were obtained in the other five groups: a number of differentially expressed genes were screened out, and a number of genes were silenced by nitrogen and phosphorus fertilizer; The results of the heatmap clustering graph of the six comparison groups were revealed that the genes between the same treatment and the same comparison group are basically distributed in blocks: either high expression or low expression, and vice versa. The gene distribution between different treatments in the same comparison group was complementary. To fertilize Chinese fir, it is better to mix fertilizer with different types of fertilizers; The GO enrichment and functional classification has three major categories, namely, biological process BP, cell component CC and molecular function MF, with 50 small categories; Fertilization, whether single fertilizer or multiple fertilizers, has the greatest impact on the GO terms of Chinese fir: chloroplasts, cytoskeleton, cell membrane, nucleus and cytoplasm. secondly molecular function, protein binding and biological process are affected. These results revealed that nitrogen and phosphorus can promote the absorption and metabolism of themselves and each other; KEGG enrichment analysis was performed in 6 comparison groups, and the most significant first 5 Pathway KEGG terms were selected in each comparison group, the comprehensive analysis results showed that after fertilizing Chinese fir, the most significant KEGG term was photosynthesis, nitrogen metabolism, carbon fixation and carbon metabolism, plant hormone signal transduction, plant-pathogen interaction, phenylpropanoid biosynthesis, pentose-phosphate pathway, porphyrin and chlorophyll metabolism, arginine biosynthesis and ect. Based on the above studies, the significantly up-regulated or down-regulated genes in important terms obtained by GO enrichment and classification and KEEG enrichment can be studied, and the results can guide the diagnosis of Chinese fir fertilization. Conclusion: Illumina HiSeq4000 transcriptome sequencing is a quick and cheap way to study the molecular mechanisms of non-model plants, including coniferous trees with large genomes. Chinese fir fertilization can not only turn on some genes, but also turn off some genes. The growth and development of Chinese fir will be regulated in a way that is favorable for its adaptation to the environment, competitive resources and growth and development.

Dataset Information

Transcriptome analysis of immature xylem in the Chinese fir at different developmental phases.

Publications

Transcriptome analysis of immature xylem in the Chinese fir at different developmental phases.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets