Characterization of the complete chloroplast genome of Trachycarpus fortunei.
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ABSTRACT:
SUBMITTER: Feng X
PROVIDER: S-EPMC7782514 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Trachycarpus nanus is an endangered plant that is endemic to southwest of China. In the present study, the complete chloroplast genome of this species was assembled and characterized using whole genome next-generation sequencing. The complete chloroplast genome showed a circular genome of 158,713 bp size with 36.6% GC content. The genome is of typical structure and contain a pair of inverted repeat (IR) regions with 27,240 bp, separated by one large single-copy (LSC) with 86,395 bp, and one small single-copy (SSC) regions with 17,838 bp. The genome contained 132 genes, including 86 protein-coding genes, 8 rRNA genes and 38 tRNA genes. A phylogenetic tree reconstructed based on 21 chloroplast genomes reveals that Trachycarpus nanus is most related with Chamaerops humilis. The information provides important genetic basis for the species' future studies on phylogenetic and utilization.
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Project description: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.
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Project description:Chloroplast (cp) genome sequences become a useful popular tool for population and phylogeny in recent reports. Here, the complete cp genome of the Euonymus fortunei has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 157,639?bp in size, and comprises a pair of inverted repeat (IR) regions of 26,668?bp each, a large single copy (LSC) region of 85,956?bp and a small single copy (SSC) region of 18,347?bp. The total GC content is 37.2%, while the corresponding values of the LSC, SSC, and IR region are 35.1%, 31.7%, and 42.7%, respectively. The cp genome contains 126 genes, including 89 protein-coding genes, eight ribosomal RNA genes, and 29 transfer RNA genes and one pseudogene. The maximum-likelihood phylogenetic analysis showed a strong sister relationship with Euonymus japonicus in Celastraceae. Our findings provide a foundation for further investigation of cp genome evolution in E. fortunei and other higher plants.
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Project description:Alniphyllum fortunei is a subtropical tree species, a large deciduous tree with a tall and straight trunk, which is an excellent fast-growing and broad-leaved tree species with a wide range of uses we resequenced complete chloroplast (cp) genome of A. fortunei from Fujian, China. The whole genome was 154,166 bp in length, consisting of a pair of inverted repeats (IR 26,658 bp), a large single-copy region (LSC 82,438 bp), and a small single-copy region (SSC 18,367 bp). The complete genome contained 139 genes, including 89 protein-coding genes, 40 tRNA, and 8 rRNA genes. The phylogenetic analyses based on the complete chloroplast genome sequence provided solid evidence that A. fortunei has a close relationship with A. pterospermum and Bruinsmia polysperma.
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Project description:The complete chloroplast genome of an important medical fern Cyrtomium fortunei has been sequenced. Its genome is 151,699?bp in length with a pair of inverted repeats (IRs, 23,875?bp), separated by a small single copy region (SSC, 21,625?bp) and a large single copy region (LSC, 82,324?bp). It contains 132 genes, covering 88 protein coding genes, 35 tRNA genes, eight rRNA genes, and one pseudogene. Maximum likelihood analysis indicates that the phylogenetic tree is monophyletic with three clades. Cyrtomium fortunei is closely related to C. devexiscapulae, which further forms a sister clade to C. falcatum.
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Project description:Palm peroxidases are extremely stable and have uncommon substrate specificity. This study was designed to fill in the knowledge gap about the structures of a peroxidase from the windmill palm tree Trachycarpus fortunei. The complete amino acid sequence and partial glycosylation were determined by MALDI-top-down sequencing of native windmill palm tree peroxidase (WPTP), MALDI-TOF/TOF MS/MS of WPTP tryptic peptides, and cDNA sequencing. The propeptide of WPTP contained N- and C-terminal signal sequences which contained 21 and 17 amino acid residues, respectively. Mature WPTP was 306 amino acids in length, and its carbohydrate content ranged from 21% to 29%. Comparison to closely related royal palm tree peroxidase revealed structural features that may explain differences in their substrate specificity. The results can be used to guide engineering of WPTP and its novel applications.
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Project description:Erigeron breviscapus is a famous medicinal plant. However, the limited chloroplast genome information of E. breviscapus, especially for the chloroplast DNA sequence resources, has hindered the study of E. breviscapus chloroplast genome transformation. Here, the complete chloroplast (cp) genome of E. breviscapus was reported. This genome was 152,164bp in length, included 37.2% GC content and was structurally arranged into two 24,699bp inverted repeats (IRs) and two single-copy areas. The sizes of the large single-copy region and the small single-copy region were 84,657 and 18,109bp, respectively. The E. breviscapus cp genome consisted of 127 coding genes, including 83 protein coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. For those genes, 95 genes were single copy genes and 16 genes were duplicated in two inverted regions with seven tRNAs, four rRNAs, and five protein coding genes. Then, genomic DNA of E. breviscapus was used as a template, and the endogenous 5' and 3' flanking sequences of the trnI gene and trnA gene were selected as homologous recombinant fragments in vector construction and cloned through PCR. The endogenous 5' flanking sequences of the psbA gene and rrn16S gene, the endogenous 3' flanking sequences of the psbA gene, rbcL gene, and rps16 gene and one sequence element from the psbN-psbH chloroplast operon were cloned, and certain chloroplast regulatory elements were identified. Two homologous recombination fragments and all of these elements were constructed into the cloning vector pBluescript SK (+) to yield a series of chloroplast expression vectors, which harbored the reporter gene EGFP and the selectable marker aadA gene. After identification, the chloroplast expression vectors were transformed into Escherichia coli and the function of predicted regulatory elements was confirmed by a spectinomycin resistance test and fluorescence intensity measurement. The results indicated that aadA gene and EGFP gene were efficiently expressed under the regulation of predicted regulatory elements and the chloroplast expression vector had been successfully constructed, thereby providing a solid foundation for establishing subsequent E. breviscapus chloroplast transformation system and genetic improvement of E. breviscapus.
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Project description:BackgroundTrachycarpus fortunei has broad economic benefits and excellent drought resistance; however, its drought response, adaptation, and recovery processes remain unclear.MethodologyIn this study, the response, tolerance, and recovery processes of T. fortunei leaves and roots under drought stress were determined by Illumina sequencing.ResultsUnder drought stress, T. fortunei reduced its light-capturing ability and composition of its photosynthetic apparatus, thereby reducing photosynthesis to prevent photo-induced chloroplast reactive oxygen damage during dehydration. The phenylpropanoid biosynthesis process in the roots was suppressed, DHNs, LEA, Annexin D2, NAC, and other genes, which may play important roles in protecting the cell membrane's permeability in T. fortunei root tissues. During the rehydration phase, fatty acid biosynthesis in T. fortunei roots was repressed. Weighted correlation network analysis (WGCNA) screened modules that were positively or negatively correlated with physiological traits. The real-time quantitative PCR (RT-qPCR) results indicated the reliability of the transcriptomic data.ConclusionThese findings provide valuable information for identifying important components in the T. fortunei drought signaling network and enhances our understanding of the molecular mechanisms by which T. fortunei responds to drought stress.
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Project description:Abstract Salvia leucantha (Lamiaceae) is an important horticultural plant with great ornamental and economic value. Here, we report the complete chloroplast genome of this species. The chloroplast genome was determined to be 151021 bp and the GC contents was 38.0%. The sequence includes a large single copy (LSC) region of 82,262 bp, a small single copy (SSC) region of 17,537 bp, and two separated inverted regions of 25,611 bp each. It contains 130 unique genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Based on the chloroplast genomes data of 26 species in Salvia, our result indicated that S. leucantha, S. tiliifolia, S. hispanica, and S. splendens formed one clade with Bootstrap = 100%. The four species belong to Salvia subgenus Calosphace, and S. leucantha was closely related to Salvia tiliifolia and Salvia hispanica. This result will facilitate population, genetic diversity and phylogenetic studies of S. leucantha.
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Project description:Chinese windmill palms (Trachycarpus fortunei) are widely planted in karst bedrock outcrop areas in southwest China because of their high economic and ecological values. The aims of this study were to investigate the foraging ability of Chinese windmill palm seedlings planted in six different types of karst microhabitat and to identify the main environmental factors that influence root foraging ability. We planted three-year-old Chinese windmill palm seedlings in six typical karst microhabitats (i.e., rocky trough, rocky surface, rocky gully, rocky soil surface, rocky pit, and soil surface microhabitats). One year after transplanting, the seedlings were excavated to determine the morphological parameters values of new roots and the nutrient concentrations of new roots and leaves. The root foraging ability of Chinese windmill palm seedlings, defined as new root length and new root surface area, was significantly greater in the rocky trough, rocky soil surface, and soil surface microhabitats than in the rocky gully, rocky surface, and rocky pit microhabitats (p < 0.05). Redundancy analysis revealed that the main positive factor affecting the rooting ability of Chinese windmill palm seedlings was soil thickness. Chinese windmill palm seedlings improved their root absorption efficiency by increasing their root length and root surface area under soil nutrient deficiency conditions. The organic carbon, total nitrogen, and available potassium in soil positively influenced the concentration of N and K in roots. Total potassium in soil negatively influenced the biomass of new annual leaves and concentrations of N, P and K in new annual roots and leaves. Chinese windmill palm seedlings can be grown in the different karst microhabitats, especially in the rocky trough, rocky soil surface, and soil surface microhabitats, and, therefore, it is suitable for use in the regeneration of karst forests.
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