•Similar structures are found in FRIM1162 and FRIM1441 mitochondrial genomes.•ORF position differences suggest mitochondrial genome rearrangement.•Different intron patterns in Ceratocystis fimbriata ...mitochondrial genomes.•The mitochondrial uniformity gene organisation and key mutations are observed.•FRIM1162 and FRIM1441 are monophyletic C. fimbriata complex group.
The decline ofAcacia mangiumWilld. in Malaysia, especially in Sabah since 2010, is primarily due to Ceratocystiswilt and canker disease (CWCD) caused by theCeratocystis fimbriataEllis & Halst. complex. This study was aimed to investigate the mitochondrial genome architecture of two differentC. fimbriatacomplex isolates from Malaysia: one fromA. mangiumin Pahang (FRIM1162) and another fromEucalyptus pellitain Sarawak (FRIM1441). This research employed Next-Generation Sequencing (NGS) to contrast genomes from diverse hosts with nine additional mitochondrial sequences, identifying significant genetic diversity and mutational hotspots in the mitochondrial genome alignment. The mitochondrial genome-based phylogenetic analysis revealed a significant genetic relationship between the studied isolates and theC. fimbriatacomplex in the South American Subclade, indicating that theC. fimbriatacomplex discovered in Malaysia isC. manginecans. The comparative mitochondrial genome demonstrates the adaptability of the complex due to mobile genetic components and genomic rearrangements in the studiedfungal isolates. This research enhances our knowledge of the genetic diversity and evolutionary patterns within theC. fimbriatacomplex, aiding in a deeper understanding of fungal disease development and host adaption processes. The acquired insights are crucial for creating specific management strategies for CWCD, improving the overall understanding of fungal disease evolution and control.
Abstract
Wikstroemia
(Thymelaeaceae) is a diverse genus that extends from Asia to Australia and has been recorded on the Hawaiian Islands. Despite its medicinal properties and resource utilization in ...pulp production, genetic studies of the species in this important genus have been neglected. In this study, the plastome sequences of six species of
Wikstroemia
were sequenced and analysed. The plastomes ranged in size between 172,610 bp (
W. micrantha
) and 173,697 bp (
W. alternifolia
) and exhibited a typical genome structure consisting of a pair of inverted repeat (IR) regions separated by a large single-copy (LSC) region and a small single-copy (SSC) region. The six plastomes were similar in the 138 or 139 genes predicted, which consisted of 92 or 93 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC contents were identical (36.7%). Comparative genomic analyses were conducted with the inclusion of two additional published species of
Wikstroemia
in which the sequence divergence and expansion of IRs in the plastomes were determined. When compared to the coding sequences (CDSs) of
Aquilaria sinensis
, five genes, namely,
rpl
2,
rps
7,
rps
18,
ycf
1 and
ycf
2, indicated positive selection in
W. capitata
. The plastome-based phylogenetic analysis inferred that
Wikstroemia
in its current state is paraphyletic to
Stellera chamaejasme
, while the ITS-based tree analyses could not properly resolve the phylogenetic relationship between
Stellera
and
Wikstroemia
. This finding rekindled interest in the proposal to synonymize
Stellera
with
Wikstroemia
, which was previously proposed but rejected due to taxonomic conflicts. Nevertheless, this study provides valuable genomic information to aid in the taxonomic implications and phylogenomic reconstruction of Thymelaeaceae.
is an important ecosystem entity of the Malaysian mangrove forest. Since the species grows in a harsh environment, any organism that is isolated from this species would be of huge interest due to its ...potential in having novel bioactive compounds. In the present work, we isolated, identified and characterized, a total of 78 fungal isolates harboring inside the leaf tissues of
. Molecular identification using the nuclear ribosomal DNA internal transcribe spacer (ITS) sequences returned with high similarity matches to known sequences in the GenBank. Maximum likelihood analysis revealed the phylogenetic relationship of all isolates from this study. Most of the dominating fungal endophytes were from the genera
, followed by
and
. Six isolates representing the genera
, and
, were further screened for their antagonism activities. Dual culture test assay revealed their inhibition percentages against the phytopathogenic fungus
between 45-66%, and 0.8-23% when using non-volatile test assay. Of the six isolates, only
and
sp. showed antibacterial activities against the pathogenic bacteria,
, and
, with the Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) ranging from 0.5 to 2 mg/mL. The DPPH radical scavenging assay recorded a high level of antioxidant activity in
sp., 3-fold above that of
.
. We demonstrate for the first time, two members belonging to the endophytic fungal community in the tropical mangrove species that have potential use as antagonists and antibacterial agents for future biotechnological applications.
Agarwood is originated from the resinous part of Aquilaria and Gyrinops plants and has been a precious biomaterial for applications in traditional medicine, perfumery, cosmetics, and religious ...purposes all over the world. In the wild, the formation of agarwood is related to the defense mechanism of the tree in response to physical damage that allows further microbial infestation into its wood, while having the whole tree covered with agarwood would take up a long time, and it rarely happens. For Aquilaria and Gyrinops, the presence of endophytes is mainly found derived from the tree. The isolated endophytes could be important sources of natural products, while some could contribute to the formation of agarwood in the tree, which is safe for the environment and human health. This review summarized the biodiversity of fungal endophytes recorded in Aquilaria and Gyrinops and their potential effects on host trees. Till now, 67 endophytic genera have been isolated from Aquilaria and Gyrinops, and 18 ones were found responsible for the promotion of agarwood formation. Additionally, 92 compounds have been reported to be produced by the agarwood endophytes, and 52 ones displayed biological activities, most of which have anti-inflammatory, anti-bacterial, and anti-cancer activities. Nevertheless, fungal endophytes are promising agents that deserved to be further studied and scaled up to a commercial level for the production of agarwood oil, but the role of endophytes in the agarwood host trees needs to be furtherly investigated in future studies.
Aquilaria tree species are naturally distributed in the Indomalesian region and are protected against over-exploitation. They produce a fragrant non-timber product of high economic value, agarwood. ...Ambiguous species delimitation and limited genetic information within Aquilaria are among the impediments to conservation efforts. In this study, we conducted comparative analysis on eight Aquilaria species complete chloroplast (cp) genomes, of which seven were newly sequenced using Illumina HiSeq X Ten platform followed by de novo assembly. Aquilaria cp genomes possess a typical quadripartite structure including gene order and genomic structure. The length of each of the cp genome is about 174 kbp and encoded between 89 and 92 proteins, 38 tRNAs, and 8 rRNAs, with 27 duplicated in the IR (inverted repeat) region. Besides, 832 repeats (forward, reverse, palindrome and complement repeats) and nine highly variable regions were also identified. The phylogenetic analysis suggests that the topology structure of Aquilaria cp genomes were well presented with strong support values based on the cp genomes data set and matches their geographic distribution pattern. In summary, the complete cp genomes will facilitate development of species-specific molecular tools to discriminate Aquilaria species and resolve the evolutionary relationships of members of the Thymelaeaceae family.
The identification of Aquilaria species from their resinous non-wood product, the agarwood, is challenging as conventional techniques alone are unable to ascertain the species origin. Aquilaria is a ...highly protected species due to the excessive exploitation of its precious agarwood. Here, we applied the DNA barcoding technique to generate barcode sequences for Aquilaria species and later applied the barcodes to identify the source species of agarwood found in the market. We developed a reference DNA barcode library using eight candidate barcode loci (matK, rbcL, rpoB, rpoC1, psbA-trnH, trnL-trnF, ITS, and ITS2) amplified from 24 leaf accessions of seven Aquilaria species obtained from living trees. Our results indicated that all single barcodes can be easily amplified and sequenced with the selected primers. The combination of trnL-trnF+ITS and trnL-trnF+ITS2 yielded the greatest species resolution using the least number of loci combination, while matK+trnL-trnF+ITS showed potential in detecting the geographical origins of Aquilaria species. We propose trnL-trnF+ITS2 as the best candidate barcode for Aquilaria as ITS2 has a shorter sequence length compared to ITS, which eases PCR amplification especially when using degraded DNA samples such as those extracted from processed agarwood products. A blind test conducted on eight agarwood samples in different forms using the proposed barcode combination proved successful in their identification up to the species level. Such potential of DNA barcoding in identifying the source species of agarwood will contribute to the international timber trade control, by providing an effective method for species identification and product authentication.
The seeds of
Lam. and
Yuncker have been commonly used as Chinese medical material for preventing aging. Our previous studies have found that
and
possess anti-inflammatory activities in rodents. ...However, their other biological activities, such as memory-improving properties, have not yet been explored. In the present study, we examined the memory-improving effects of the extracts of
and
on scopolamine (SCOP)-induced memory deficit and explored their underlying mechanism in mice. Both
species improved SCOP-induced memory deficits in the passive avoidance test, elevated plus-maze, and spatial performance test of the Morris water maze in mice. In addition, compared with mice injected with SCOP, mice pretreated with both
species stayed for a longer time on the platform for the probe test of the Morris water maze. Moreover, both
species reduced brain acetylcholinesterase activity and malondialdehyde levels that were increased by SCOP, and the species restored the activities of antioxidant enzymes (superoxide dismutase and catalase) and the levels of glutathione that were decreased by SCOP in the brains of mice. Both
species further decreased brain interleukin-1β and tumor necrosis factor-α levels that were elevated by SCOP. We demonstrated that both
species exhibited a protective activity against SCOP-induced memory deficit, cholinergic dysfunction, oxidative damage, and neuroinflammation in mice, and
has better potential than
. In addition, we provided evidence that the seeds of
can be used as Cuscutae Semen in Traditional Chinese Medicine.
Ilex (Aquifoliaceae) are of great horticultural importance throughout the world for their foliage and decorative berries, yet a dearth of genetic information has hampered our understanding of ...phylogenetic relationships and evolutionary history. Here, we compare chloroplast genomes from across Ilex and estimate phylogenetic relationships.
We sequenced the chloroplast genomes of seven Ilex species and compared them with 34 previously published Ilex plastomes. The length of the seven newly sequenced Ilex chloroplast genomes ranged from 157,182 bp to 158,009 bp, and contained a total of 118 genes, including 83 protein-coding, 31 rRNA, and four tRNA genes. GC content ranged from 37.6 to 37.69%. Comparative analysis showed shared genomic structures and gene rearrangements. Expansion and contraction of the inverted repeat regions at the LSC/IRa and IRa/SSC junctions were observed in 22 and 26 taxa, respectively; in contrast, the IRb boundary was largely invariant. A total of 2146 simple sequence repeats and 2843 large repeats were detected in the 41 Ilex plastomes. Additionally, six genes (psaC, rbcL, trnQ, trnR, trnT, and ycf1) and two intergenic spacer regions (ndhC-trnV and petN-psbM) were identified as hypervariable, and thus potentially useful for future phylogenetic studies and DNA barcoding. We recovered consistent phylogenetic relationships regardless of inference methodology or choice of loci. We recovered five distinct, major clades, which were inconsistent with traditional taxonomic systems.
Our findings challenge traditional circumscriptions of the genus Ilex and provide new insights into the evolutionary history of this important clade. Furthermore, we detail hypervariable and repetitive regions that will be useful for future phylogenetic and population genetic studies.
Deer products from sika deer (Cervus nippon) and red deer (C. elaphus) are considered genuine and used for Traditional Chinese Medicine (TCM) materials in China. Deer has a very high economic and ...ornamental value, resulting in the formation of a characteristic deer industry in the prescription preparation of traditional Chinese medicine, health food, cosmetics, and other areas of development and utilization. Due to the high demand for deer products, the products are expensive and have limited production, but the legal use of deer is limited to only two species of sika deer and red deer; other wild deer are prohibited from hunting, so there are numerous cases of mixing and adulteration of counterfeit products and so on. There have been many reports that other animal (pig, cow, sheep, etc.) tissues or organs are often used for adulteration and confusion, resulting in poor efficacy of deer traditional medicine and trade fraud in deer products. To authenticate the deer products in a rapid and effective manner, the analysis used 22 deer products (antler, meat, bone, fetus, penis, tail, skin, and wool) that were in the form of blind samples. Total DNA extraction using a modified protocol successfully yielded DNA from the blind samples that was useful for PCR. Three candidate DNA barcoding loci, cox1, Cyt b, and rrn12, were evaluated for their discrimination strength through BLAST and phylogenetic clustering analyses. For the BLAST analysis, the 22 blind samples obtained 100% match identity across the three gene loci tested. It was revealed that 12 blind samples were correctly labeled for their species of origin, while three blind samples that were thought to originate from red deer were identified as C. nippon, and seven blind samples that were thought to originate from sika deer were identified as C. elaphus, Dama dama, and Rangifer tarandus. DNA barcoding analysis showed that all three gene loci were able to distinguish the two Cervus species and to identify the presence of adulterant species. The DNA barcoding technique was able to provide a useful and sensitive approach in identifying the species of origin in deer products.
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