Liquidambar formosana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA762421 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15851713_1.fastq.gz | Fastqsanger.gz | |||
| SRR15851713_2.fastq.gz | Fastqsanger.gz | |||
| SRR15851714_1.fastq.gz | Fastqsanger.gz | |||
| SRR15851714_2.fastq.gz | Fastqsanger.gz | |||
| SRR15851715_1.fastq.gz | Fastqsanger.gz |
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Project description:Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Despite recent scientific headway in deciphering the difficulties of somatic embryogenesis, the overall picture of key genes, pathways, and co-expression networks regulating SE is still fragmented. Therefore, deciphering the molecular basis of somatic embryogenesis of hybrid sweetgum remains pertinent. In the present study, we analyzed the transcriptome profiles and gene expression regulation changes via RNA sequencing from three distinct developmental stages of hybrid sweetgum: non-embryogenic callus (NEC), embryogenic callus (EC), and redifferentiation. Comparative transcriptome analysis showed that 19,957 genes were differentially expressed in ten pairwise comparisons of SE. Among these, plant hormone signaling-related genes, especially the auxin and cytokinin signaling components, were significantly enriched in NEC and EC early. The K-means method was used to identify multiple transcription factors, including HB-WOX, B3-ARF, AP2/ERF, and GRFs (growth regulating factors). These transcription factors showed distinct stage- or tissue-specific expression patterns mirroring each of the 12 superclusters to which they belonged. For example, the WOX transcription factor family was expressed only at NEC and EC stages, ARF transcription factor was expressed in EC early, and GRFs was expressed in late SE. It was noteworthy that the AP2/ERF transcription factor family was expressed during the whole SE process, but almost not in roots, stems and leaves. A weighted gene co-expression network analysis (WGCNA) was used in conjunction with the gene expression profiles to recognize the genes and modules that may associate with specific tissues and stages. We constructed co-expression networks and revealed 22 gene modules. Four of these modules with properties relating to embryonic potential, early somatic embryogenesis, and somatic embryo development, as well as some hub genes, were identified for further functional studied. Through a combination analysis of WGCNA and K-means, SE-related genes including AUX22, ABI3, ARF3, ARF5, AIL1, AIL5, AGL15, WOX11, WOX9, IAA29, BBM1, MYB36, LEA6, SMR4 and others were obtained, indicating that these genes play an important role in the processes underlying the progression from EC to somatic embryos (SEs) morphogenesis. The transcriptome information provided here will form the foundation for future research on genetic transformation and epigenetic control of plant embryogenesis at a molecular level. In follow-up studies, these data could be used to construct a regulatory network for SE; Key genes obtained from coexpression network analysis at each critical stage of somatic embryo can be considered as potential candidate genes to verify these networks.
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Project description:Liquidambar formosana (Hamamelidaceae) is a tertiary relic species widely distributed in subtropical areas, and is a common endemic broad-leaved tree species in south China. Here, we report and describe for the first time the complete chloroplast genome of L. formosana based on Illumina double-ended sequencing data. The complete plastid genome was 160,425 bp, which contained inverted repeats (IR) of 26,266 bp separated by a large single-copy (LSC) and a small single-copy (SSC) of 88,971 bp and 18,922 bp, respectively. The cpDNA contains 132 genes, comprising 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the plastome is 37.9%. The phylogenetic analysis of 18 selected chloroplast genomes demonstrated that L. formosana was close to the species Sinowilsonia henryi.
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Project description:Liquidambar formosana strain:wild type Transcriptome or Gene expression
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Project description:Photosynthetic capacity and leaf life span generally determine how much carbon a plant assimilates during the growing season. Leaves of deciduous tree species start senescence in late season, but whether the senescent leaves still retain capacity of carbon assimilation remains a question. In this study, we investigated leaf phenology and photosynthesis of a subtropical broadleaf deciduous tree species Liquidambar formosana Hance in the central southern continental China. The results show that L. formosana has extended leaf senescence (more than 2 months) with a substantial number of red leaves persisting on the tree. Leaf photosynthetic capacity decreases over season, but the senescent red leaves still maintain relatively high photosynthetic capacity at 42%, 66% and 66% of the mature leaves for net photosynthesis rate, apparent quantum yield, and quantum yield at the light compensation point, respectively. These results indicate that L. formosana may still contribute to carbon sink during leaf senescence.
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