The genomic evolution of visual opsin genes in amphibians.

Among tetrapod (terrestrial) vertebrates, amphibians remain more closely tied to an amphibious lifestyle than amniotes, and their visual opsin genes may be adapted to this lifestyle. Previous studies have discussed physiological, morphological, and molecular changes in the evolution of amphibian vision. We predicted the locations of the visual opsin genes, their neighboring genes, and the tuning sites of the visual opsins, in 39 amphibian genomes. We found that all of the examined genomes lacked the Rh2 gene. The caecilian genomes have further lost the SWS1 and SWS2 genes; only the Rh1 and LWS genes were retained. The loss of the SWS1 and SWS2 genes in caecilians may be correlated with their cryptic lifestyles. The opsin gene syntenies were predicted to be highly similar to those of other bony vertebrates. Moreover, dual syntenies were identified in allotetraploid Xenopus laevis and X. borealis. Tuning site analysis showed that only some Caudata species might have UV vision. In addition, the S164A that occurred several times in LWS evolution might either functionally compensate for the Rh2 gene loss or fine-tuning visual adaptation. Our study provides the first genomic evidence for a caecilian LWS gene and a genomic viewpoint of visual opsin genes by reviewing the gains and losses of visual opsin genes, the rearrangement of syntenies, and the alteration of spectral tuning in the course of amphibians' evolution.

Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller-size coral reef zooplankton by metatranscriptomics.

PCR-based high-throughput sequencing has permitted comprehensive resolution analyses of zooplankton diversity dynamics. However, significant methodological issues still surround analyses of complex bulk community samples, not least as in prevailing PCR-based approaches. Marine drifting animals-zooplankton-play essential ecological roles in the pelagic ecosystem, transferring energy and elements to higher trophic levels, such as fishes, cetaceans and others. In the present study, we collected 48 size-fractionated zooplankton samples in the vicinity of a coral reef island with environmental gradients. To investigate the spatiotemporal dynamics of zooplankton diversity patterns and the effect of PCR amplification biases across these complex communities, we first took metatranscriptomics approach. Comprehensive computational analyses revealed a clear pattern of higher/lower homogeneity in smaller/larger zooplankton compositions across samples respectively. Our study thus suggests changes in the role of dispersal across the sizes. Next, we applied in silico PCR to the metatranscriptomics datasets, in order to estimate the extent of PCR amplification bias. Irrespective of stringency criteria, we observed clear separations of size fraction sample clusters in both metatranscriptomics and in silico datasets. In contrast, the pattern-smaller-fractioned communities had higher compositional homogeneity than larger ones-was observed in the metatranscriptomics data but not in the in silico datasets. To investigate this discrepancy further, we analysed the mismatches of widely used mitochondrial CO1 primers and identified priming site mismatches likely driving PCR-based biases. Our results suggest the use of metatranscriptomics or, although less ideal, redesigning the CO1 primers is necessary to circumvent these issues.

Long-Read Genome Sequencing of Abscondita cerata (Coleoptera: Lampyridae), the Endemic Firefly of Taiwan.

Abscondita cerata is the most abundant and widely distributed endemic firefly species in Taiwan and is considered a key environmental and ecological indicator organism. In this study, we report the first long-read genome sequencing of Abs. cerata sequenced by Nanopore technology. The draft genome size, 967 Mb, was measured through a hybrid approach that consisted of assembling using 11.25-Gb Nanopore long reads and polishing using 9.47-Gb BGI PE100 short reads. The drafted genome was assembled into 4,855 contigs, with the N50 reaching 325.269 kb length. The assembled genome was predicted to possess 55,206 protein-coding genes, of which 20,862 (37.78%) were functionally annotated with public databases. 47.11% of the genome sequences consisted of repeat elements; among them DNA transposons accounted for the largest proportion (26.79%). A BUSCO (Benchmarking Universal Single Copy Orthologs) evaluation demonstrated that the genome and gene completeness were 84.8% and 79%, respectively. The phylogeny constructed using 1,792 single copy genes was consistent with previous studies. The comparative transcriptome between adult male head and lantern tissues revealed (1) the vision of Abs. cerata is primarily UV-sensitive to environmental twilight, which determines when it begins its nocturnal activity, (2) the major expressed OR56d receptor may be correlated to suitable humidity sensing, and (3) Luc1-type luciferase is responsible for Abs. cerata's luminescent spectrum.

Novel Ganoderma triterpenoid saponins from the biotransformation-guided purification of a commercial Ganoderma extract.

Ganoderma sp. contains high amounts of diverse triterpenoids; however, few triterpenoid saponins could be isolated from the medicinal fungus. To produce novel Ganoderma triterpenoid saponins, biotransformation-guided purification (BGP) process was applied to a commercial Ganoderma extract. The commercial Ganoderma extract was partially separated into three fractions by preparative high-performance liquid chromatography, and the separated fractions were then directly biotransformed by a Bacillus glycosyltransferase (BsUGT489). One of the biotransformed products could be further purified and identified as a novel saponin: ganoderic acid C2 (GAC2)-3-O-ß-glucoside by nucleic magnetic resonance (NMR) and mass spectral analyses. Based on the structure of the saponin, the predicted precursor should be the GAC2, which was confirmed to be biotransformed into four saponins, GAC2-3-O-ß-glucoside, GAC2-3,15-O-ß-diglucoside and two unknown GAC2 monoglucosides, revealed by NMR and mass spectral analyses. GAC2-3-O-ß-glucoside and GAC2-3,15-O-ß-diglucoside possessed 17-fold and 200-fold higher aqueous solubility than that of GAC2, respectively. In addition, GAC2-3-O-ß-glucoside retained the most anti-α-glucosidase activity of GAC2 and was comparable with that of the anti-diabetes drug (acarbose). The present study showed that the BGP process is an efficient strategy to survey novel and bioactive molecules from crude extracts of natural products.

Luminescent characteristics and mitochondrial COI barcodes of nine cohabitated Taiwanese fireflies.

Background: Over 50 Taiwanese firefly species have been discovered, but scientists lack information regarding most of their genetics, bioluminescent features, and cohabitating phenomena. In this study, we focus on morphological species identification and phylogeny reconstructed by COI barcoding, as well as luminescent characteristics of cohabited Taiwanese firefly species to determine the key factors that influenced how distinct bioluminescent species evolved to coexist and proliferate within the same habitat. Methods: In this study, 366 specimens from nine species were collected in northern Taiwan from April to August, 2016-2019. First, the species and sex of the specimens were morphologically and genetically identified. Then, their luminescent spectra and intensities were recorded using a spectrometer and a power meter, respectively. The habitat temperature, relative humidity, and environmental light intensity were also measured. The cytochrome oxidase I (COI) gene sequence was used as a DNA barcode to reveal the phylogenetic relationships of cohabitated species. Results: Nine species-eight adult species (Abscondita chinensis, Abscondita cerata, Aquatica ficta, Luciola curtithorax, Luciola kagiana, Luciola filiformis, Curtos sauteri, and Curtos costipennis) and one larval Pyrocoelia praetexta-were morphologically identified. The nine species could be found in April-August. Six of the eight adult species shared an overlap occurrence period in May. Luminescent spectra analysis revealed that the λ max of studied species ranged from 552-572 nm (yellow-green to orange-yellow). The average luminescent intensity range of these species was about 1.2-14 lux (182.1-2,048 nW/cm2) for males and 0.8-5.8 lux (122.8-850 nW/cm2) for females, and the maximum luminescent intensity of males was 1.01-7.26-fold higher than that of females. Compared with previous studies, this study demonstrates that different λ max, species-specific flash patterns, microhabitat choices, nocturnal activity time, and/or an isolated mating season are key factors that may lead to the species-specific courtship of cohabitated fireflies. Moreover, we estimated that the fireflies start flashing or flying when the environmental light intensity decreased to 6.49-28.1 lux. Thus, based on a rough theoretical calculation, the sensing distance between male and female fireflies might be 1.8-2.7 m apart in the dark. In addition, the mitochondrial COI barcode identified species with high resolution and suggested that most of the studied species have been placed correctly with congeners in previous phylogenies. Several cryptic species were revealed by the COI barcode with 3.27%-12.3% variation. This study renews the idea that fireflies' luminescence color originated from the green color of a Lampyridae ancestor, then red-shifted to yellow-green in Luciolinae, and further changed to orange-yellow color in some derived species.

Long-read Sequencing Data Reveals Dynamic Evolution of Mitochondrial Genome Size and the Phylogenetic Utility of Mitochondrial DNA in Hercules Beetles (Dynastes; Scarabaeidae).

The evolutionary dynamics and phylogenetic utility of mitochondrial genomes (mitogenomes) have been of particular interest to systematists and evolutionary biologists. However, certain mitochondrial features, such as the molecular evolution of the control region in insects, remain poorly explored due to technological constraints. Using a combination of long- and short-read sequencing data, we assembled ten complete mitogenomes from ten Hercules beetles. We found large-sized mitogenomes (from 24 to 28 kb), which are among the largest in insects. The variation in genome size can be attributed to copy-number evolution of tandem repeats in the control region. Furthermore, one type of tandem repeat was found flanking the conserved sequence block in the control region. Importantly, such variation, which made up around 30% of the size of the mitogenome, may only become detectable should long-read sequencing technology be applied. We also found that, although different mitochondrial loci often inferred different phylogenetic histories, none of the mitochondrial loci statistically reject a concatenated mitochondrial phylogeny, supporting the hypothesis that all mitochondrial loci share a single genealogical history. We on the other hand reported statistical support for mito-nuclear phylogenetic discordance in 50% of mitochondrial loci. We argue that long-read DNA sequencing should become a standard application in the rapidly growing field of mitogenome sequencing. Furthermore, mitochondrial gene trees may differ even though they share a common genealogical history, and ND loci could be better candidates for phylogenetics than the commonly used COX1.

A Novel Soy Isoflavone Derivative, 3'-Hydroxyglycitin, with Potent Antioxidant and Anti-α-Glucosidase Activity.

This study demonstrated the enzymatic hydroxylation of glycitin to 3'-hydroxyglycitin, confirming the structure by mass and nucleic magnetic resonance spectral analyses. The bioactivity assays further revealed that the new compound possessed over 100-fold higher 1,1-diphenyl-2-picrylhydrazine free-radical scavenging activity than the original glycitin, although its half-time of stability was 22.3 min. Furthermore, the original glycitin lacked anti-α-glucosidase activity, whereas the low-toxic 3'-hydroxyglycitin displayed a 10-fold higher anti-α-glucosidase activity than acarbose, a standard clinical antidiabetic drug. The inhibition mode of 3'-hydroxyglycitin was noncompetitive, with a Ki value of 0.34 mM. These findings highlight the potential use of the new soy isoflavone 3'-hydroxyglycitin in biotechnology industries in the future.

A New Stilbene Glucoside from Biotransformation-Guided Purification of Chinese Herb Ha-Soo-Oh.

Ha-Soo-Oh is a traditional Chinese medicine prepared from the roots of Polygonum multiflorum Thunb. The herb extract has been widely used in Asian countries as a tonic agent and nutritional supplement for centuries. To identify new bioactive compounds in Chinese herbs, the biotransformation-guided purification (BGP) process was applied to Ha-Soo-Oh with Bacillus megaterium tyrosinase (BmTYR) as a biocatalyst. The result showed that a major biotransformed compound could be purified using the BGP process with preparative high-performance liquid chromatography (HPLC), and it was confirmed as a new compound, 2,3,5,3',4'-pentahydroxystilbene-2-O-ß-glucoside (PSG) following mass and nucleic magnetic resonance (NMR) spectral analyses. PSG was further confirmed as a biotransformation product from 2,3,5,4'-tetrahydroxystilbene-2-O-ß-glucoside (TSG) by BmTYR. The new PSG exhibited 4.7-fold higher 1,1-diphenyl-2-picrylhydrazine (DPPH) free radical scavenging activity than that of TSG. The present study highlights the potential usage of BGP in herbs to discover new bioactive compounds in the future.

Enzymatic Synthesis of Novel and Highly Soluble Puerarin Glucoside by Deinococcus geothermalis Amylosucrase.

Puerarin (daidzein-8-C-glucoside) is an isoflavone isolated from several leguminous plants of the genus Pueraria. Puerarin possesses several pharmacological properties; however, the poor solubility of puerarin limits its applications. To resolve this poor solubility, Deinococcus geothermalis amylosucrase (DgAS) was used to modify puerarin into more soluble derivatives. The results showed that DgAS could biotransform puerarin into a novel compound: puerarin-4'-O-α-glucoside. The biotransformation reaction was manipulated at different temperatures, pH values, sucrose concentrations, reaction times, and enzyme concentrations. The results showed that the optimal reaction condition was biotransformed by 200 µg/mL DgAS with 20% (w/v) sucrose at pH 6 and incubated at 40 °C for 48 h, and the optimal production yield was 35.1%. Puerarin-4'-O-α-glucoside showed 129-fold higher solubility than that of puerarin and, thus, could be further applied for pharmacological use in the future.

Novel Glycosylation by Amylosucrase to Produce Glycoside Anomers.

Glycosylation occurring at either lipids, proteins, or sugars plays important roles in many biological systems. In nature, enzymatic glycosylation is the formation of a glycosidic bond between the anomeric carbon of the donor sugar and the functional group of the sugar acceptor. This study found novel glycoside anomers without an anomeric carbon linkage of the sugar donor. A glycoside hydrolase (GH) enzyme, amylosucrase from Deinococcus geothermalis (DgAS), was evaluated to glycosylate ganoderic acid F (GAF), a lanostane triterpenoid from medicinal fungus Ganoderma lucidum, at different pH levels. The results showed that GAF was glycosylated by DgAS at acidic conditions pH 5 and pH 6, whereas the activity dramatically decreased to be undetectable at pH 7 or pH 8. The biotransformation product was purified by preparative high-performance liquid chromatography and identified as unusual α-glucosyl-(2→26)-GAF and ß-glucosyl-(2→26)-GAF anomers by mass and nucleic magnetic resonance (NMR) spectroscopy. We further used DgAS to catalyze another six triterpenoids. Under the acidic conditions, two of six compounds, ganoderic acid A (GAA) and ganoderic acid G (GAG), could be converted to α-glucosyl-(2→26)-GAA and ß-glucosyl-(2→26)-GAA anomers and α-glucosyl-(2→26)-GAG and ß-glucosyl-(2→26)-GAG anomers, respectively. The glycosylation of triterpenoid aglycones was first confirmed to be converted via a GH enzyme, DgAS. The novel enzymatic glycosylation-formed glycoside anomers opens a new bioreaction in the pharmaceutical industry and in the biotechnology sector.

Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum.

High-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and interpretation of mitogenomes. In this study, we present the results from sampling and sequencing of six gastropod mitogenomes (Aplysia argus, Cellana orientalis, Cellana toreuma, Conus ebraeus, Conus miles and Tylothais aculeata) from a graduate level biodiversity course. The students were able to produce mitogenomes from sampling to annotation using existing protocols and programs. Approximately 4 Gb of sequence was produced from 16 Flongle and one MinION flow cells, averaging 235 Mb and N50 = 4.4 kb per flow cell. Five of the six 14.1-18 kb mitogenomes were circlised containing all 13 core protein coding genes. Additional Illumina sequencing revealed that the ONT assemblies spanned over highly AT rich sequences in the control region that were otherwise missing in Illumina-assembled mitogenomes, but still contained a base error of one every 70.8-346.7 bp under the fast mode basecalling with the majority occurring at homopolymer regions. Our findings suggest that the portable MinION device can be used to rapidly produce low-cost mitogenomes onsite and tailored to genomics-based training in biodiversity research.

Omics and mechanistic insights into di-(2-ethylhexyl) phthalate degradation in the O2-fluctuating estuarine sediments.

Di-(2-ethylhexyl) phthalate (DEHP) represents the most used phthalate plasticizer with an annual production above the millions of tons worldwide. Due to its inadequate disposal, outstanding chemical stability, and extremely low solubility (3 mg/L), endocrine-disrupting DEHP often accumulates in urban estuarine sediments at concentrations above the predicted no-effect concentration (20-100 mg/kg). Our previous study suggested that microbial DEHP degradation in estuarine sediments proceeds synergistically where DEHP side-chain hydrolysis to form phthalic acid represents a bottleneck. Here, we resolved this bottleneck and deconstructed the microbial synergy in O2-fluctuating estuarine sediments. Metagenomic analysis and RNA sequencing suggested that orthologous genes encoding extracellular DEHP hydrolase NCU65476 in Acidovorax sp. strain 210-6 are often flanked by the co-expressed composite transposon and are widespread in aquatic environments worldwide. Therefore, we developed a turbidity-based microplate assay to characterize NCU65476. The optimized assay conditions (with 1 mM Ca2+ and pH 6.0) increased the DEHP hydrolysis rate by a factor of 10. Next, we isolated phthalic acid-degrading Hydrogenophaga spp. and Thauera chlorobenzoica from Guandu estuarine sediment to study the effect of O2(aq) on their metabolic synergy with strain 210-6. The results of co-culture experiments suggested that after DEHP side-chain hydrolysis by strain 210-6, phthalic acid can be degraded by Hydrogenophaga sp. when O2(aq) is above 1 mg/L or degraded by Thauera chlorobenzoica anaerobically. Altogether, our data demonstrates that DEHP could be degraded synergistically in estuarine sediments via divergent pathways responding to O2 availability. The optimized conditions for NCU65476 could facilitate the practice of DEHP bioremediation in estuarine sediments.

Species-Specific Flash Patterns Track the Nocturnal Behavior of Sympatric Taiwanese Fireflies.

It is highly challenging to evaluate the species' content and behavior changes in wild fireflies, especially for a sympatric population. Here, the flash interval (FI) and flash duration (FD) of flying males from three sympatric species (Abscondita cerata, Luciola kagiana, and Luciola curtithorax) were investigated for their potentials in assessing species composition and nocturnal behaviors during the A. cerata mating season. Both FI and FD were quantified from the continuous flashes of adult fireflies (lasting 5-30 s) via spatiotemporal analyses of video recorded along the Genliao hiking trail in Taipei, Taiwan. Compared to FD patterns and flash colors, FI patterns exhibited the highest species specificity, making them a suitable reference for differentiating firefly species. Through the case study of a massive occurrence of A. cerata (21 April 2018), the species contents (~85% of the flying population) and active periods of a sympatric population comprising A. cerata and L. kagiana were successfully evaluated by FI pattern matching, as well as field specimen collections. Our study suggests that FI patterns may be a reliable species-specific luminous marker for monitoring the behavioral changes in a sympatric firefly population in the field, and has implication values for firefly conservation.

Genetic diversity of the regionally endangered Chinese ricefish (Oryzias sinensis) in Taiwan, with comments on its conservation status.

The Chinese ricefish (Oryzias sinensis) is a freshwater fish that is regionally endangered in Taiwan. To evaluate its conservation status and further formulate conservation plans for this species in Taiwan, this study analyzed the fish collected from all known localities, including a newly discovered population. The phylogenetic trees based on D-loop and COI divided the Chinese ricefish into two major clades: Taiyangpi-Shuanglienpi and Taiping-Gongliao. This study showed that both the Shuanglienpi and Taiyangpi wild populations had significantly higher Hd and π values, while the Shuanglienpi restored population only had one haplotype from the wild. However, their genetic diversity may have decreased over the past few decades. The Gongliao and Taiping populations shared the same haplotype as a population from a previous study. We propose that the Gongliao and Taiping populations were founded by a few individuals and might have originated from a single introduction event from southeastern mainland China. Low genetic diversity was clearly observed in the Taiping, Gongliao and Shuanglienpi restored populations. Based on the present investigation and previous studies, the invasive poeciliid fish (such as mosquitofish and green swordtail) contribute the most to the decline of the Chinese ricefish population and genetic diversity in Taiwan.

Chub movement is attracted by the collision sounds associated with spawning activities.

Cyprinids (carps, chubs and minnows) possess well-developed hearing and high sensitivity to sound pressure. The sensitive hearing may assist cyprinids with searching for food, territory defense, and mating behavior. Many paired fishes violently shake in sand and gravel while spawning in rivers. However, no study has examined the ecological importance of the collision sound made by the behavior. This study examined whether cohabitated chubs (Opsariichthys evolans and Zacco platypus) use the collision sound as a signal to locate spawning events so they can be a male satellite or egg eater. Three types of sounds (i.e., collision sound, music noise and ambient noise) were played with or without jerkbaits at the midstream of the Keelung River, Taiwan during the spawning season in 2018 and 2019. Generalized linear mixed models were then built to examine the effects of the sound types and the presence of jerkbaits on the number of individuals that the two chubs attracted. Results showed significantly different levels of attractiveness among the three sound types, with the collision sound attracting most fishes, including both females and males, followed by music noise and ambient noise. The presence of jerkbaits increased the number of fishes attracted, but the effect was only statistically marginally significant. These results suggest that the collision sound as an acoustic signal may be more important than a visual signal for the chubs to locate spawning events of other mating pairs, probably because of the longer transmission distance of the former. The present study demonstrates the ecological meanings of the collision sounds made in association with spawning activities of the chubs and implies that the native chub's spawning activities may be affected by the introduced Z. platypus. More studies on the interactions between these cohabitated chubs will benefit the conservation of native chubs.

Improving Aqueous Solubility of Natural Antioxidant Mangiferin through Glycosylation by Maltogenic Amylase from Parageobacillus galactosidasius DSM 18751.

Mangiferin is a natural antioxidant C-glucosidic xanthone originally isolated from the Mangifera indica (mango) plant. Mangiferin exhibits a wide range of pharmaceutical activities. However, mangiferin's poor solubility limits its applications. To resolve this limitation of mangiferin, enzymatic glycosylation of mangiferin to produce more soluble mangiferin glucosides was evaluated. Herein, the recombinant maltogenic amylase (MA; E.C. 3.2.1.133) from a thermophile Parageobacillus galactosidasius DSM 18751T (PgMA) was cloned into Escherichia coli BL21 (DE3) via the expression plasmid pET-Duet-1. The recombinant PgMA was purified via Ni2+ affinity chromatography. To evaluate its transglycosylation activity, 17 molecules, including mangiferin (as sugar acceptors), belonging to triterpenoids, saponins, flavonoids, and polyphenol glycosides, were assayed with ß-CD (as the sugar donor). The results showed that puerarin and mangiferin are suitable sugar acceptors in the transglycosylation reaction. The glycosylation products from mangiferin by PgMA were isolated using preparative high-performance liquid chromatography. Their chemical structures were glucosyl-α-(1→6)-mangiferin and maltosyl-α-(1→6)-mangiferin, determined by mass and nucleic magnetic resonance spectral analysis. The newly identified maltosyl-α-(1→6)-mangiferin showed 5500-fold higher aqueous solubility than that of mangiferin, and both mangiferin glucosides exhibited similar 1,1-diphenyl-2-picrylhydrazyl free radical scavenging activities compared to mangiferin. PgMA is the first MA with glycosylation activity toward mangiferin, meaning mangiferin glucosides have potential future applications.

Enzymatic Synthesis of Novel Vitexin Glucosides.

Vitexin is a C-glucoside flavone that exhibits a wide range of pharmaceutical activities. However, the poor solubility of vitexin limits its applications. To resolve this limitation, two glycoside hydrolases (GHs) and four glycosyltransferases (GTs) were assayed for glycosylation activity toward vitexin. The results showed that BtGT_16345 from the Bacillus thuringiensis GA A07 strain possessed the highest glycosylation activity, catalyzing the conversion of vitexin into new compounds, vitexin-4'-O-ß-glucoside (1) and vitexin-5-O-ß-glucoside (2), which showed greater aqueous solubility than vitexin. To our knowledge, this is the first report of vitexin glycosylation. Based on the multiple bioactivities of vitexin, the two highly soluble vitexin derivatives might have high potential for pharmacological usage in the future.

Complete Genome Sequence of the Soil-Isolated Psychrobacillus sp. Strain AK 1817, Capable of Biotransforming the Ergostane Triterpenoid Antcin K.

The soil bacterium Psychrobacillus sp. strain AK 1817 was isolated from a tropical soil sample collected in Taiwan. Strain AK 1817 biotransforms the ergostane triterpenoid antcin K from the fungus Antrodia cinnamomea. The genome was sequenced using the PacBio RS II platform and consists of one chromosome of 4,096,020 bp, comprising 3,907 protein-coding genes, 75 tRNAs, 30 rRNAs, 5 noncoding RNAs (ncRNAs), and 100 pseudogenes.

Glycosylation of Ganoderic Acid G by Bacillus Glycosyltransferases.

Ganoderma lucidum is a medicinal fungus abundant in triterpenoids, its primary bioactive components. Although numerous Ganoderma triterpenoids have already been identified, rare Ganoderma triterpenoid saponins were recently discovered. To create novel Ganoderma saponins, ganoderic acid G (GAG) was selected for biotransformation using four Bacillus glycosyltransferases (GTs) including BtGT_16345 from the Bacillus thuringiensis GA A07 strain and three GTs (BsGT110, BsUGT398, and BsUGT489) from the Bacillus subtilis ATCC 6633 strain. The results showed that BsUGT489 catalyzed the glycosylation of GAG to GAG-3-o-ß-glucoside, while BsGT110 catalyzed the glycosylation of GAG to GAG-26-o-ß-glucoside, which showed 54-fold and 97-fold greater aqueous solubility than that of GAG, respectively. To our knowledge, these two GAG saponins are new compounds. The glycosylation specificity of the four Bacillus GTs highlights the possibility of novel Ganoderma triterpenoid saponin production in the future.

Characterization of the complete mitochondrial genome of Abscondita cerata (Olivier, 1911) (Coleoptera: Lampyridae) and its phylogenetic implications.

We sequenced and assembled the complete mitochondrial genome of Abscondita cerata from Nankang, Taipei City, Taiwan. The complete mitogenome of A. cerata is 16,964 bp long, and contains 13 protein-coding, 22 tRNA, and two rDNA genes. Nucleotide compositions of the mitogenome of the A. cerata are A: 43.93%, T: 36.74%, C: 11.05%, and G: 8.28%. The AT and GC skewness of the mitogenome sequence are 0.0891 and -0.1434, showing the genome composition skewness toward adenine and cytosine. The clade including all Lampyridae species is well supported. The result indicates that Luciolinae is a monophyletic group but Lampyrinae is not a monophyletic group, as Lamprigera yunnana, which was originally classified into Lampyrinae, is sister to Luciolinae. The genus Lamprigera may share a unique phylogenetic position in Lampyridae. The genus Luciola is a polyphyletic group and the genus Abscondita is a monophyletic group. A. cerata is the sister species to A. chinensis in China. Mitogenomic data from this study will provide useful molecular markers for further studies on the population genetics, speciation, and conservation of endemic species A. cerata in Taiwan.