The complete chloroplast genome of Acanthus ilicifolius, an excellent mangrove plant.
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ABSTRACT:
SUBMITTER: Xu L
PROVIDER: S-EPMC8023608 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundAcanthus ilicifolius var. xiamenensis (Acanthaceae) is an old world mangrove species and has long been used as a folk remedy for treating various ailments in traditional medicine. The nature source of A. ilicifolius var. xiamenensis is now in short supply because of the urban development and habitat destruction. To better utilize this resource, biodiversity and bioactivity of endophytic fungi isolated from A. ilicifolius var. xiamenensis were investigated.ResultsA total of 168 fungal isolates were cultured from leaves and stems of the mangrove plant collected in January (winter) and July (summer) 2014 at Kinmen County, Taiwan. Spent culture extract of 28 isolates were found to have bioactivities against one of the following pathogenic microorganisms: the bacteria Bacillus subtilis, Staphylococcus aureus (Gram-positive) and Escherichia coli (Gram-negative) and the fungi Candida albicans and Cryptococcus neoformans. These positive extracts were mostly active against the Gram-positive bacteria and C. albicans. Corynespora cassiicola NTOU4889 and Xylaria sp. NTOU4900 inhibited growth of all 3 test bacteria whereas Phellinus noxius NTOU4917 inhibited both test fungi. A further anti-inflammatory study of culture extracts of these 28 isolates revealed that extracts with a high iNOS inhibition caused a low viability of cells, and those with a low iNOS inhibition had a high cell viability. Three extracts showed low cytotoxicity (i.e. > 100% cell viability) and high iNOS inhibition (< 15% of NO production) of cells and they were Phoma sp. 2 NTOU4338, Nodulisporium sp. NTOU4868 and Guignardia sp. NTOU4871.ConclusionThese results indicate that the endophytic fungi associated with A. ilicifolius var. xiamenensis can be a potential source of novel natural active substance.
| S-EPMC6419792 | biostudies-literature
Project description:BackgroundAcanthus is a unique genus consisting of both true mangrove and terrestrial species; thus, it represents an ideal system for studying the origin and adaptive evolution of mangrove plants to intertidal environments. However, little is known regarding the two respects of mangrove species in Acanthus. In this study, we sequenced the transcriptomes of the pooled roots and leaves tissues for a mangrove species, Acanthus ilicifolius, and its terrestrial congener, A. leucostachyus, to illustrate the origin of the mangrove species in this genus and their adaptive evolution to harsh habitats.ResultsWe obtained 73,039 and 69,580 contigs with N50 values of 741 and 1557 bp for A. ilicifolius and A. leucostachyus, respectively. Phylogenetic analyses based on four nuclear segments and three chloroplast fragments revealed that mangroves and terrestrial species in Acanthus fell into different clades, indicating a single origin of the mangrove species in Acanthus. Based on 6634 orthologs, A. ilicifolius and A. leucostachyus were found to be highly divergent, with a peak of synonymous substitution rate (Ks) distribution of 0.145 and an estimated divergence time of approximately 16.8 million years ago (MYA). The transgression in the Early to Middle Miocene may be the major reason for the entry of the mangrove lineage of Acanthus into intertidal environments. Gene ontology (GO) classifications of the full transcriptomes did not show any apparent differences between A. ilicifolius and A. leucostachyus, suggesting the absence of gene components specific to the mangrove transcriptomes. A total of 99 genes in A. ilicifolius were identified with signals of positive selection. Twenty-three of the 99 positively selected genes (PSGs) were found to be involved in salt, heat and ultraviolet stress tolerance, seed germination and embryo development under periodic inundation. These stress-tolerance related PSGs may be crucial for the adaptation of the mangrove species in this genus to stressful marine environments and may contribute to speciation in Acanthus.ConclusionsWe characterized the transcriptomes of one mangrove species of Acanthus, A. ilicifolius, and its terrestrial relative, A. leucostachyus, and provided insights into the origin of the mangrove Acanthus species and their adaptive evolution to abiotic stresses in intertidal environments.
| S-EPMC4536770 | biostudies-literature
Project description:Hibiscus tiliaceus is a semi-mangrove species that is widely distributed in tropical and subtropical coastal areas around the world. Here, the complete chloroplast (cp) genome sequence of H. tiliaceus was assembled and characterized. The cp genome was 161,748 bp in length, consisting of a large single copy (LSC) region of 89,190 bp and a small single copy (SSC) region of 19,616 bp, which were separated by a pair of 26,471 bp inverted repeat (IR) regions. The overall GC content was 36.88%. A total of 131 genes, including 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes were identified. Phylogenetic tree reconstructed by 15 complete cp genomes revealed that H. tiliaceus was sister to the congeneric species H. cannabinus.
| S-EPMC8204996 | biostudies-literature
Project description:Pluchea pteropoda Hemsl is a mangrove associate plant of Asteraceae with medicinal properties such as anti-inflammation and fever-relieving. Here, our study presented the complete chloroplast (cp) genome of Pluchea pteropoda Hemsl. The cp genome of P. pteropoda was 152,300 bp in length, including a large single copy (LSC) region of 84,127 bp, a small single copy (SSC) region of 18,093 bp and a pair of inverted repeats (IR) regions of 25,040 bp. A total of 111 unique genes were found, comprising 79 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. The GC content of the cp genome was 37.5%. Phylogenetic analysis suggested that P. pteropoda nested in Pluchea clade, which was closely related to Ageratina adenophora and Senecio scandens. The work provides beneficial data for following researches on the genetic variation, species delimitation, phylogeny and classification of Pluchea genus.
| S-EPMC8158197 | biostudies-literature
Project description:A high diversity of culturable foliar endophytic fungi is known from various mangrove plants, and the core taxa include species from Colletotrichum, Pestalotiopsis, Phoma, Phomopsis, Sporomiella, among others. Since a small fraction of fungi is able to grow in culture, this study investigated the diversity of fungi associated with leaves of Acanthus ilicifolius var. xiamenensis using both isolation and metabarcoding approaches. A total of 203 isolates were cultured from surface-sterilized leaves, representing 47 different fungal species: 30 species from the winter samples (104 isolates), and 26 species from the summer samples (99 isolates). Ascomycota was dominant in both types of leaf samples, while Basidiomycota was isolated only from the summer samples. Drechslera dematioidea (10.58%, percentage of occurrence), Colletotrichum sp. 3 (7.69%) and Alternaria sp. (7.69%) were dominant in the winter samples; Fusarium oxysporum (13.13%), Diaporthe endophytica (10.10%) and Colletotrichum sp. 1 (9.09%) in the summer samples. Overall, Corynespora cassiicola (6.90%), F. oxysporum (6.40%) and Guignardia sp. (6.40%) had the highest overall percentage of occurrence. In the metabarcoding analysis, a total of 111 operational taxonomic units (OTUs) were identified from 17 leaf samples: 96 OTUs from the winter and 70 OTUs from the summer samples. Sequences belonging to Ascomycota and Basidiomycota were detected in both samples but the former phylum was dominant over the latter. Based on read abundance, taxa having the highest percentage of occurrence included Alternaria sp. (3.46%), Cladosporium delicatulum (2.56%) and Pyrenochaetopsis leptospora (1.41%) in the winter leaves, and Aureobasidium sp. (10.72%), Cladosporium sp. (7.90%), C. delicatulum (3.45%) and Hortaea werneckii (3.21%) in the summer leaves. These latter four species also had the highest overall percentage of occurrence. Combining the results from both methods, a high diversity of fungi (at least 110 species) was found associated with leaves of A. ilicifolius var. xiamenensis. Many of the fungi identified were plant pathogens and may eventually cause diseases in the host.
| S-EPMC6625500 | biostudies-literature
Project description:This study presents the chloroplast genome of Hernandia nymphiifolia (C. Presl) Kubitzki (Hernandiaceae) one Endangered mangrove species in China, which was assembled and analyzed by de novo assembly using whole chloroplast genome sequencing data. The accessing ID of reference sequence was MG838431. The size of the complete chloroplast genome was 157,762 bp in length with a large single-copy region (LSC) of 86,641 bp, a small single-copy region (SSC) of 18,603 bp, and two inverted repeat regions (IRS) (26,260 bp). The GC content of H. nymphiifolia is 39.3%. From the chloroplast genomes, 133 genes, including 83 protein-coding genes, 42 tRNA genes, and 8 rRNA genes, were predicted. Among them, 17 genes occur in IRS, containing 6 protein-coding genes, 7 tRNA genes and 4 rRNA genes. The phylogenetic analysis with 10 eudicots species and rice as the outgroup revealed that H. nymphiifolia was clustered with 6 Ranunculales species.
| S-EPMC7799466 | biostudies-literature
Project description:Mangroves are one of the most productive and biologically diverse ecosystems, with unique plants, animals, and microorganisms adapted to the harsh coastal environments. Although fungi are widely distributed in the mangrove ecosystem and they are playing an important role in the decomposition of organic matter, their genomic profiles are still poorly understood. In this study, we isolated seven Ascomycota fungi (Westerdykella dispersa F012, Trichoderma lixii F014, Aspergillus tubingensis F023, Penicillium brefeldianum F032, Neoroussoella solani F033, Talaromyces fuscoviridis F034, and Arthrinium marii F035) from rhizospheres of two mangroves of Kandelia obovata and Acanthus ilicifolius. We sequenced and assembled the whole genome of these fungi, resulting in size ranging from 29 to 48 Mb, while contig N50 from 112 to 833 Kb. We generated six novel fungi genomes except A. tubingensis, and the gene completeness and genome completeness of all seven genomes are higher than 94%. Comparing with non-mangrove fungi, we found Carbohydrate-Binding Modules (CBM32), a subfamily of carbohydrate active enzymes, only detected in two mangrove fungi. Another two subfamilies, Glycoside Hydrolases (GH6) and Polysaccharide Lyases (PL4), were significantly different in gene copy number between K. obovata and A. ilicifolius rhizospheres (P-value 0.041 for GH6, 0.047 for PL4). These findings may indicate an important influence of mangrove environments or hosts on the ability of decomposition in rhizosphere fungi. Secondary metabolite biosynthesis gene clusters were detected and we found the mangrove fungi averagely contain 18 Type I Polyketide (t1pks) synthase, which was significantly higher than 13 in non-mangrove fungi (P-value 0.048), suggesting their potential roles in producing bioactive compounds that important for fungi development and ecology. We reported seven mangrove-associated fungal genomes in this study and compared their carbohydrate active enzymes and secondary metabolites (SM) genes with those of non-mangrove fungi, and the results suggest that there are differences in genetic information among fungi in different habitats.
| S-EPMC10512393 | biostudies-literature
Project description:Dolichandrone spathacea(L. F.) K. Schum. is an excellent tree species for coastal protection forests. In this study, the complete chloroplast genome sequence of D. spathacea was obtained through high-throughput sequencing. The length of chloroplast genome was 159,156 bp in length, containing a large single-copy region (LSC) of 86,053 bp, a small single-copy region (SSC) of 12,635 bp, and a pair of inverted repeats (IRa and IRb) regions of 30,234 bp. The chloroplast genome with 37.95% GC content, contained 134 genes, including 90 protein-coding genes, 8 rRNA genes, and 36 tRNA genes. Phylogenetic analysis with the reported chloroplast sequences shows that D. spathacea is more closely related to Spathodea campanulata.
| S-EPMC8008931 | biostudies-literature
Project description:Mangrove-associated fungi are rich sources of novel and bioactive compounds. A total of 102 fungal strains were isolated from the medicinal mangrove Acanthus ilicifolius collected from the South China Sea. Eighty-four independent culturable isolates were identified using a combination of morphological characteristics and internal transcribed spacer (ITS) sequence analyses, of which thirty-seven strains were selected for phylogenetic analysis. The identified fungi belonged to 22 genera within seven taxonomic orders of one phyla, of which four genera Verticillium, Neocosmospora, Valsa, and Pyrenochaeta were first isolated from mangroves. The cytotoxic activity of organic extracts from 55 identified fungi was evaluated against human lung cancer cell lines (A-549), human cervical carcinoma cell lines (HeLa), human hepatoma cells (HepG2), and human acute lymphoblastic leukemia cell lines (Jurkat). The crude extracts of 31 fungi (56.4%) displayed strong cytotoxicity at the concentration of 50 μg/mL. Furthermore, the fungus Penicillium sp. (HS-N-27) still showed strong cytotoxic activity at the concentration of 25 µg/mL. Integrating cytotoxic activity-guided strategy and fingerprint analysis, a well-known natural Golgi-disruptor and Arf-GEFs inhibitor, brefeldin A, was isolated from the target active strain HS-N-27. It displayed potential activity against A549, HeLa and HepG2 cell lines with the IC50 values of 101.2, 171.9 and 239.1 nM, respectively. Therefore, combining activity-guided strategy with fingerprint analysis as a discovery tool will be implemented as a systematic strategy for quick discovery of active compounds.
| S-EPMC9315649 | biostudies-literature
Project description:The chloroplast (cp) genome sequence of Rhizophora apiculata was characterized. The cp genome length was 164,343 bp in length, containing a typical structure of a large single copy (LSC) of 93,155 bp, a small single copy (SSC) of 19,376 bp, and two inverted repeats (IRs) of 25,906 bp, with a GC content of 34.9%. There were 131 genes were annotated in the cp genome, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. A phylogenetic analysis using cp genomes of mangroves and ecologically associated species resolved R. apiculata in Rhizophora with R. stylosa and R. x lamarckii. This complete chloroplast sequence offers a promising tool for further species identification and evolutionary studies of Rhizophora, as well as for mangroves.
| S-EPMC8231346 | biostudies-literature