Complete mitochondrial genome of an oleaginous microalga Vischeria punctata (Eustigmatophyceae: Chlorobotryaceae) and phylogenetic analysis.

Vischeria punctata, as first described by Vischer in 1945, is a member of the family Chlorobotryaceae, within the order Eustigmatales. This species is recognized for its potential as a source of biofuels and other high-value products. In the present investigation, the whole genome of V. punctata was sequenced utilizing the Illumina HiSeq 4000 platform, enabling the assembly and annotation of its complete mitochondrial genome. The resulting circular genome spans 41,528 base pairs (bp) with a guanine-cytosine (GC) content of 27.3%. This genome encompasses 36 protein-coding genes, alongside 28 transfer RNA (tRNA), and three ribosomal RNA (rRNA) genes. The evolutionary trajectory of V. punctata was further explored by constructing a phylogenetic tree derived from the mitochondrial 33 gene dataset of 16 Ochrophyta species. Comparative analysis reveals that V. punctata bears closer ties to Vischeria sp. CAUP Q202 than to Vischeria stellata strain SAG 33.83, suggesting shared evolutionary pathways and phenotypic traits. This investigation constitutes the inaugural study into the mitochondrial evolution and phylogenetic patterning of the mitogenome in V. punctata. The outcomes from this research bolster our understanding of the genetic diversity and evolutionary processes within the class Eustigmatophyceae. In particular, the mitochondrial genome of V. punctata serves as a valuable resource in elucidating these aspects.

Discovery of a novel small molecule with efficacy in protecting against inflammation in vitro and in vivo by enhancing macrophages activation.

Immune response and inflammation highly contribute to many metabolic syndromes such as inflammatory bowel disease (IBD), ageing and cancer with disruption of host metabolic homeostasis and the gut microbiome. Icariin-1 (GH01), a small-molecule flavonoid derived from Epimedium, has been shown to protect against systemic inflammation. However, the molecular mechanisms by which GH01 ameliorates ulcerative colitis via regulation of microbiota-mediated macrophages polarization remain elusive. In this study, we found that GH01 effectively ameliorated dextran sulfate sodium (DSS)-induced colitis symptoms in mice. Disruption of intestinal barrier function, commensal microbiota and its metabolites were also significantly restored by GH01 in a dose-dependent manner. Of note, we also found that GH01 enhanced phagocytic ability of macrophages and switched macrophage phenotype from M1 to M2 both in vitro and in vivo. Such macrophage polarization was highly associated with intestinal barrier integrity and the gut microbial community. Consequently, GH01 exhibited strong anti-inflammatory capacity by inhibiting TLR4 and NF-κB pathways and proinflammatory factors (IL-6). These findings suggested that GH01 might be a potential nutritional intervention strategy for IBD treatment with the gut microbial community-meditated macrophage as the therapeutic targets.

[Characteristics of the chloroplast genome of Dracaena marginata and phylogenetic analysis].

Dracaena marginata is a widely cultivated horticultural plant in the world, which has high ornamental and medicinal value. In this study, the whole genome of leaves from D. marginata was sequenced by Illumina HiSeq 4000 platform. The chloroplast genome were assembled for functional annotation, sequence characteristics and phylogenetic analysis. The results showed that the chloroplast genome of D. marginata composed of four regions with a size of 154 926 bp, which was the smallest chloroplast genome reported for Dracaena species to date. A total of 132 genes were identified, including 86 coding genes, 38 tRNA genes and 8 rRNA genes. Codon bias analysis found that the codon usage bias was weak and there was a bias for using A/U base endings. 46 simple sequence repeat and 54 repeats loci were detected in the chloroplast genome, with the maximum detection rate in the large single copy region and inverted repeat region, respectively. The inverted repeats boundaries of D. marginata and Dracaena were highly conserved, whereas gene location differences occurred. Phylogenetic analysis revealed that D. serrulata and D. cinnabari form a monophyletic clade, which was the closest relationship and conformed to the morphological classification characteristics. The analysis of the chloroplast genome of D. marginata provides important data basis for species identification, genetic diversity and chloroplast genome engineering of Dracaena.

The complete mitochondrial genome of Cuminum cyminum (Apiales: Apiaceae) and phylogenetic analysis.

Cumin (Cuminum cyminum L). belongs to the family Apiaceae and the order Apiales, which is a widely grown spice and medicinal plant in Xinjiang province, China. In the current study, whole genome sequencing of C. cyminum was performed using the Illumina HiSeq 4000 platform, and the complete mitogenome sequence was assembled and annotated. We found that the single circular mitogenome of C. cyminum was 246,721 bp in length, and has about 45.5% GC content. It comprised 73 genes in the coding region (35 protein-coding genes, 18 tRNA genes, 3 rRNA genes, and 15 open-reading frames) and a non-coding region. Phylogenetic analysis indicated that C. cyminum is closely related to Daucus carota and the subtribes Daucinae. The mitogenome of C. cyminum revealed its phylogenetic relationships with other species in the Apiaceae family, which would further help in understanding its evolution.

The genomes of Vischeria oleaginous microalgae shed light on the molecular basis of hyper-accumulation of lipids.

BACKGROUND: With the urgent need to reduce carbon emissions, and the dwindling reserves of easily exploitable fossil fuel, microalgae-based biofuels that can be used for transport systems and CO2 abatement have attracted great attention worldwide in recent years. One useful characteristic of microalgae is their ability to accumulate high levels of lipid content, in particular under conditions of nitrogen deprivation, with numerous species identified so far. However, a trade-off between levels of lipid accumulation and biomass productivity hinders the commercial applicability of lipids from microalgae. Here, we sequenced the genomes of Vischeria sp. CAUP H4302 and Vischeria stellata SAG 33.83, which can accumulate high content of lipids rich in nutraceutical fatty acids and with excellent biomass yield in nitrogen-limiting culture. RESULTS: A whole-genome duplication (WGD) event was revealed in V. sp. CAUP H4302, which is a rare event in unicellular microalgae. Comparative genomic analyses showed that a battery of genes encoding pivotal enzymes involved in fatty acids and triacylglycerol biosynthesis, storage polysaccharide hydrolysis, and nitrogen and amino acid-related metabolisms are expanded in the genus Vischeria or only in V. sp. CAUP H4302. The most highlighted is the expansion of cyanate lyase genes in the genus Vischeria, which may enhance their detoxification ability against the toxic cyanate by decomposing cyanate to NH3 and CO2, especially under nitrogen-limiting conditions, resulting in better growth performance and sustained accumulation of biomass under the aforementioned stress conditions. CONCLUSIONS: This study presents a WGD event in microalgae, providing new insights into the genetic and regulatory mechanism underpinning hyper-accumulation of lipids and offering potentially valuable targets for future improvements in oleaginous microalgae by metabolic engineering.

Comparative Genomic Analysis of a Methylorubrum rhodesianum MB200 Isolated from Biogas Digesters Provided New Insights into the Carbon Metabolism of Methylotrophic Bacteria.

Methylotrophic bacteria are widely distributed in nature and can be applied in bioconversion because of their ability to use one-carbon source. The aim of this study was to investigate the mechanism underlying utilization of high methanol content and other carbon sources by Methylorubrum rhodesianum strain MB200 via comparative genomics and analysis of carbon metabolism pathway. The genomic analysis revealed that the strain MB200 had a genome size of 5.7 Mb and two plasmids. Its genome was presented and compared with that of the 25 fully sequenced strains of Methylobacterium genus. Comparative genomics revealed that the Methylorubrum strains had closer collinearity, more shared orthogroups, and more conservative MDH cluster. The transcriptome analysis of the strain MB200 in the presence of various carbon sources revealed that a battery of genes was involved in the methanol metabolism. These genes are involved in the following functions: carbon fixation, electron transfer chain, ATP energy release, and resistance to oxidation. Particularly, the central carbon metabolism pathway of the strain MB200 was reconstructed to reflect the possible reality of the carbon metabolism, including ethanol metabolism. Partial propionate metabolism involved in ethyl malonyl-CoA (EMC) pathway might help to relieve the restriction of the serine cycle. In addition, the glycine cleavage system (GCS) was observed to participate in the central carbon metabolism pathway. The study revealed the coordination of several metabolic pathways, where various carbon sources could induce associated metabolic pathways. To the best of our knowledge, this is the first study providing a more comprehensive understanding of the central carbon metabolism in Methylorubrum. This study provided a reference for potential synthetic and industrial applications of this genus and its use as chassis cells.

Potential application of a newly isolated microalga Desmodesmus sp. GXU-A4 for recycling Molasses vinasse.

The development of cost-effective and energy-efficient technologies for the stabilization of organic wastewater by microalgae has been essential and sought after. In the current study, GXU-A4 was isolated from an aerobic tank treating molasses vinasse (MV) and identified as Desmodesmus sp. based on its morphology, rbcL, and ITS sequences. It exhibited good growth with a high lipid content and chemical oxygen demand (COD) when grown using MV and the anaerobic digestate of MV (ADMV) as the growth medium. Three distinct COD concentrations for wastewater were established. Accordingly, GXU-A4 removed more than 90% of the COD from molasses vinasse (MV1, MV2, and MV3) with initial COD concentrations of 1193 mgL-1, 2100 mgL-1, and 3180 mgL-1, respectively. MV1 attained the highest COD and color removal rates of 92.48% and 64.63%, respectively, and accumulated 47.32% DW (dry weight) of lipids and 32.62% DW of carbohydrates, respectively. Moreover, GXU-A4 grew rapidly in anaerobic digestate of MV (ADMV1, ADMV2, and ADMV3) with initial COD concentrations of 1433 mgL-1, 2567 mgL-1, and 3293 mgL-1, respectively. Under ADMV3 conditions, the highest biomass reached 13.81 g L-1 and accumulated 27.43% DW of lipids and 38.70% DW of carbohydrates, respectively. Meanwhile, the removal rates of NH4-N and chroma in ADMV3 reached 91.10% and 47.89%, respectively, significantly reducing the concentration of ammonia nitrogen and color in ADMV. Thus, the results demonstrate that GXU-A4 has a high fouling tolerance, a rapid growth rate in MV and ADMV, the ability to achieve biomass accumulation and nutrient removal from wastewater, and a high potential for MV recycling.

A Newly Isolated Strain of Haematococcus pluvialis GXU-A23 Improves the Growth Performance, Antioxidant and Anti-Inflammatory Status, Metabolic Capacity and Mid-intestine Morphology of Juvenile Litopenaeus vannamei.

Haematococcus pluvialis can be used as a green additive in aquafeeds due to it contains rich astaxanthin and polyunsaturated fatty acid. In the present study, a newly strain of H. pluvialis GXU-A23 with high concentration of astaxanthin was firstly isolated by a newly culture strategy in our laboratory. In addition, H. pluvialis GXU-A23 was applied in the Litopenaeus vannamei feed for determining whether it has positive effects on the growth performance, antioxidant and anti-inflammatory status, metabolic capacity and mid-intestine morphology of juvenile L. vannamei. Shrimp with 0.63 g approximately initial body weight were fed diets supplemented with/without 50 g/kg H. pluvialis GXU-A23. After 8 weeks feeding intervention, significantly higher growth performance of L. vannamei was obtained in the H. pluvialis GXU-A23 treatment group compared to the control group (p < 0.05). At the same time, L. vannamei fed with H. pluvialis GXU-A23 acquired significantly better antioxidant and anti-inflammatory status than the control group (p < 0.05). In addition, higher RNA expression level of hepatopancreas digestive enzyme, hepatopancreas lipid and glucose metabolic enzymes as well as better mid-intestine morphology were found in the H. pluvialis GXU-A23 treatment group than the control group (p < 0.05). These results indicated that 50 g/kg H. pluvialis GXU-A23 was suitable for the L. vannamei feed, which could improve the growth performance, antioxidant and anti-inflammatory status, metabolic capacity and mid-intestine morphology of juvenile L. vannamei.

Dietary Klebsormidium sp. Supplementation Improves Growth Performance, Antioxidant and Anti-Inflammatory Status, Metabolism, and Mid-Intestine Morphology of Litopenaeus Vannamei.

Filamentous microalga Klebsormidium sp. has huge potential to become a natural and healthy additive in aquatic feed since it contains various bioactive nutrients, such as linoleic acid (LA), carotenoids, and chlorophylls. Therefore, an eight-week feeding experiment was performed to evaluate the effects of dietary Klebsormidium sp. on the growth performance, antioxidant and anti-inflammatory status, metabolism, and mid-intestine morphology of Litopenaeus vannamei. Two isonitrogenous and isolipid diets supplemented with and without 5% Klebsormidium sp. were prepared. Results showed that L. vannamei fed with Klebsormidium sp. had better growth performance and feed utilization by optimizing mid-intestine morphology and improving the carbohydrate metabolism. In addition, Klebsormidium sp. also enhanced the antioxidant capacity of L. vannamei by downregulating antioxidant parameters (hepatopancreas T-SOD, hepatopancreas GSH-PX, hemolymph T-SOD, hemolymph MDA) and RNA expression levels of antioxidant genes (gsh-px and cat). Furthermore, the supplementations of dietary Klebsormidium sp. significantly improved hepatopancreas health by downregulating RNA expression levels of pro-inflammatory related genes (relish and rho). Therefore, a dose of 5% Klebsormidium sp. is recommended for the daily diet of L. vannamei to improve the growth performance, antioxidant and anti-inflammatory status, metabolism, and mid-intestine morphology of shrimp.

Resistance of anaerobic activated sludge acclimated by different feeding patterns: response to different stress shocks.

Anaerobic activated sludge plays a key role in the anaerobic digestion (AD) treatment of wastewater. The ability of anaerobic activated sludge to endure stress shock determines the performance of AD. In this study, the resistance of anaerobic activated sludge acclimated by three feeding patterns (continuous, semi-continuous, and pulse) to four stress shocks, including low pH influent, high OLR (organic loading rate), high ammonium and high sulfate, was investigated respectively. The results showed that the anaerobic activated sludge acclimated by semi-continuous feeding had the best resistance to high OLR shock, followed by pulse feeding, and then continuous feeding. There was no significant difference in the resistance of the three activated sludge to the other stress shocks. Under stress shock, the microbial community structure and abundance of specific functional microorganisms in the activated sludge acclimated by different feeding patterns varied, while the relative abundance of Methanosarcinaceae in the anaerobic activated sludge increased. The variation in the relative abundance of specific functional microorganisms was in charge of the differences in the resistance of anaerobic activated sludge. Overall, the results presented herein provide reference for improving the stability and effectiveness of activated sludge under adverse conditions.

Improving the efficiency of anaerobic digestion of Molasses alcohol wastewater using Cassava alcohol wastewater as a mixed feedstock.

Cassava alcohol wastewater (CAW) was utilized as a mixed feedstock to explore whether the addition of CAW could improve the anaerobic digestion of Molasses alcohol wastewater (MAW). The result showed that the rate of removal of the soluble chemical oxygen demand in the M treatment mixed with CAW was 70.13 ± 0.16%, which was significantly higher than that of the C treatment (only MAW), which was 61.23 ± 0.36%. Co-digestion in the M treatment resulted in higher methane production, achieving 23.89% increase in methane yield compared to C treatment. The addition of CAW helps to alleviate the accumulation of volatile fatty acids (397.06 ± 141.82 mg·L-1), enhance the stability of system and promote the establishment of stable and active microbial communities. Microbial community structure analysis indicated that hydrolytic bacteria such as Bacteroidetes, Firmicutes, and Proteobacteria, and acetoclastic methanogens, including Methanosaeta and Methanosarcina were more abundant in the co-digests.

The complete mitochondrial genome of Ophiocordyceps gracilis and its comparison with related species.

In this study, the complete mitochondrial genome of O. gracilis was sequenced and assembled before being compared with related species. As the second largest mitogenome reported in the family Ophiocordycipitaceae, the mitogenome of O. gracilis (voucher OG201301) is a circular DNA molecule of 134,288 bp that contains numerous introns and longer intergenomic regions. UCA was detected as anticodon in tRNA-Sec of O. gracilis, while comparative mitogenome analysis of nine Ophiocordycipitaceae fungi indicated that the order and contents of PCGs and rRNA genes were considerably conserved and could descend from a common ancestor in Ophiocordycipitaceae. In addition, the expansion of mitochondrial organization, introns, gene length, and order of O. gracilis were determined to be similar to those of O. sinensis, which indicated common mechanisms underlying adaptive evolution in O. gracilis and O. sinensis. Based on the mitochondrial gene dataset (15 PCGs and 2 RNA genes), a close genetic relationship between O. gracilis and O. sinensis was revealed through phylogenetic analysis. This study is the first to investigate the molecular evolution, phylogenetic pattern, and genetic structure characteristics of mitogenome in O. gracilis. Based on the obtained results, the mitogenome of O. gracilis can increase understanding of the genetic diversity and evolution of cordycipitoid fungi.

Transcriptomic analysis unravels the modulating mechanisms of the biomass and value-added bioproducts accumulation by light spectrum in Eustigmatos cf. Polyphem (Eustigmatophyceae).

Light spectrum can influence microalgal growth and metabolites accumulation significantly. However, the related mechanism has not been fully elucidated. Here, an oleaginous microalga Eustigmatos cf. polyphem, which also featured with high content of palmitoleic acid (POA) and ß-carotene, was cultured with LEDs-based red light (RL) and blue light (BL). The results showed that the biomass, total lipid content and POA content were much higher under RL than these under BL, regardless of nitrogen concentration. However, the ß-carotene content under RL was significantly lower than that under BL. Transcriptomic analysis revealed that photosynthesis, central carbon metabolism, fatty acid and glycerolipid biosynthesis were elevated, supporting the fast cell growth and high lipid content with POA under RL. In contrast, upregulation of key enzymes in carotenoids biosynthesis and suppression of ß-carotene conversion promoted ß-carotene accumulation under BL. These findings provide a feasible strategy for promoting lipids, POA and ß-carotene in E. cf. polyphem.

Biomass, lipid accumulation kinetics, and the transcriptome of heterotrophic oleaginous microalga Tetradesmus bernardii under different carbon and nitrogen sources.

BACKGROUND: Heterotrophic cultivation of microalgae has been proposed as a viable alternative method for novel high-value biomolecules, enriched biomass, and biofuel production because of their allowance of high cell density levels, as well as simple production technology. Tetradesmus bernardii, a newly isolated high-yielding oleaginous microalga under photoautotrophic conditions, is able to grow heterotrophically, meaning that it can consume organic carbon sources in dark condition. We investigated the effect of different carbon/nitrogen (C/N) ratios on the growth and lipid accumulation of T. bernardii in heterotrophic batch culture under two nitrogen sources (NaNO3 and CO(NH2)2). In addition, we conducted time-resolved transcriptome analysis to reveal the metabolic mechanism of T. bernardii in heterotrophic culture. RESULTS: T. bernardii can accumulate high biomass concentrations in heterotrophic batch culture where the highest biomass of 46.09 g/L was achieved at 100 g/L glucose concentration. The rate of glucose to biomass exceeded 55% when the glucose concentration was less than 80 g/L, and the C/N ratio was 44 at urea treatment. The culture was beneficial to lipid accumulation at a C/N ratio between 110 and 130. NaNO3 used as a nitrogen source enhanced the lipid content more than urea, and the highest lipid content was 45% of dry weight. We performed RNA-seq to analyze the time-resolved transcriptome of T. bernardii. As the nitrogen was consumed in the medium, nitrogen metabolism-related genes were significantly up-regulated to speed up the N metabolic cycle. As chloroplasts were destroyed in the dark, the metabolism of cells was transferred from chloroplasts to cytoplasm. However, storage of carbohydrate in chloroplast remained active, mainly the synthesis of starch, and the precursor of starch synthesis in heterotrophic culture may largely come from the absorption of organic carbon source (glucose). With regard to lipid metabolism, the related genes of fatty acid synthesis in low nitrogen concentration increased gradually with the extension of cultivation time. CONCLUSION: T. bernardii exhibited rapid growth and high lipid accumulation in heterotrophic culture. It may be a potential candidate for biomass and biofuel production. Transcriptome analysis showed that multilevel regulation ensured the conversion from carbon to the synthesis of carbohydrate and lipid.

Evaluation and Transcriptome Analysis of the Novel Oleaginous Microalga Lobosphaera bisecta (Trebouxiophyceae, Chlorophyta) for Arachidonic Acid Production.

Arachidonic acid (AA) is an omega-6 long-chain polyunsaturated fatty acid and is important for human health. The coccoid green microalga Lobosphaera bisecta has been reported to be able to accumulate high AA content under certain conditions. Nutrient management and light intensity had significant effects on the biomass and accumulation of lipids and AA in L. bisecta SAG2043. Both a high nitrogen concentration (18 mM) and high light intensity (bilateral light-300 µmol m-2 s-1) were beneficial to the growth of L. bisecta, and the replacement of culture medium further enhanced the biomass, which reached 8.9 g L-1. Low nitrogen concentration (3.6 mM) and high light significantly promoted the accumulation of lipids and AA. The highest lipid and AA content reached 54.0% and 10.8% of dry weight, respectively. Lipid compositions analysis showed that 88.2% of AA was distributed within the neutral lipids. We then reconstructed the lipid metabolic pathways of L. bisecta for the first time, and demonstrated that the upregulation of a key desaturase and elongase in the Δ6 pathway was conducive to the accumulation of fatty acids toward AA synthesis. L. bisecta SAG2043 exhibits high biomass, lipid and AA production. It may be a potential candidate for AA production.

Integrated biorefinery strategy for tofu wastewater biotransformation and biomass valorization with the filamentous microalga Tribonema minus.

This study focused on the feasibility of using different concentrations of tofu wastewater (TW) as alternative media for Tribonema minus cultures to produce valuable biorefinery feedstock. T. minus grew mixotrophically in 100% TW with larger carbohydrate (30.99% of dry weight (DW)), protein (15.56% of DW) and chrysolaminarin (6.93% of DW) accumulations than that of in mBG-11 medium. The highest biomass concentration, 7.77 g/L, was achieved in 100% TW, and nutrient removal efficiencies of T. minus at this concentration ranged from 60.49% to 93.60%. Although smaller neutral lipid and palmitoleic acid amounts were detected in 100% TW, their productivities reached 133.77 and 67.19 mg/L/d, respectively, due to the largest biomass yield contribution, which were comparable to those in mBG-11 medium. These findings demonstrated that TW is a promising alternative medium, and an integrated TW biotransformation and biomass valorization process is proposed to achieve better economic performance and environmental sustainability.

Phylogeographic structures of the host insects of Ophiocordyceps sinensis.

A fungus-insect complex, known as DongChong XiaCao, is formed from the infection of the hepialid larvae by the fungus Ophiocordyceps sinensis, which is endemic to the Qinghai-Tibetan Plateau (QTP). Due to previously limited sample collection size, the data about the diversity and structure of the host insect was insufficient and lacked details. The purpose of this study was aimed to discuss the diversity and phylogeography of the host insects of O. sinensis with a large-scale sampling. The mitochondrial cytochrome oxidase I gene (cox1) was sequenced and analyzed among 710 samples representing 88 geographic locations. 205 haplotypes of cox1 were identified from all the 710 samples and 4 phylogenetic clades with 12 subclades were identified. Instead of the single latitude-based divergence suggested previously, three distribution patterns were deduced to correspond to the phylogeographic structures, including but not limited to the co-existence of a wide and specific local phylogeographic distribution structures. Two separate genetic diversity and differentiation centers, namely the northwestern Yunnan and the southeastern Tibet were identified. Dating analyses from three calibrations supported that the divergence of the 4 clades occurred in the Oligocene-Miocene period (30.54-13.66 million years ago) (Ma), which were connected with the second and third geological movements of the QTP (17-25, 8-13 Ma). Our results provide a more detailed understanding of the divergence and distribution patterns of the host insects of O. sinensis.

Comparative transcriptome analysis of a long-time span two-step culture process reveals a potential mechanism for astaxanthin and biomass hyper-accumulation in Haematococcus pluvialis JNU35.

BACKGROUND: Among all organisms tested, Haematococcus pluvialis can accumulate the highest levels of natural astaxanthin. Nitrogen starvation and high irradiance promote the accumulation of starch, lipid, and astaxanthin in H. pluvialis, yet their cell division is significantly retarded. Accordingly, adaptive regulatory mechanisms are very important and necessary to optimize the cultivation conditions enabling an increase in biomass; as well as promoting astaxanthin accumulation by H. pluvialis. To clarify the intrinsic mechanism of high-level astaxanthin and biomass accumulation in the newly isolated strain, H. pluvialis JNU35, nitrogen-sufficiency and nitrogen-depletion conditions were employed. Time-resolved comparative transcriptome analysis was also conducted by crossing the two-step culture process. RESULTS: In the present study, we report the overall growth and physiological, biochemical, and transcriptomic characteristics of H. pluvialis JNU35 in response to nitrogen variation. From eight sampling time-points (2 days, 4 days, 8 days, 10 days, 12 days, 14 days, 16 days, and 20 days), 25,480 differentially expressed genes were found. These genes included the significantly responsive unigenes associated with photosynthesis, astaxanthin biosynthesis, and nitrogen metabolic pathways. The expressions of all key and rate-limiting genes involved in astaxanthin synthesis were significantly upregulated. The photosynthetic pathway was found to be attenuated, whereas the ferredoxin gene was upregulated, which might activate the cyclic electron-transport chain as compensation. Moreover, the expressions of genes related to nitrogen transport and assimilation were upregulated. The expressions of genes in the proteasome pathway were also upregulated. In contrast, the chloroplasts and nonessential proteins were gradually degraded, activating the specific ornithine-urea cycle pathway. These changes may promote the sustained accumulation of astaxanthin and biomass. CONCLUSIONS: To the best of our knowledge, this paper is the first to investigate the long-term differences of gene expression from two-step culture process in the astaxanthin producer, H. pluvialis JNU35. According to our results, ß-carotene ketolase (bkt1 and bkt2) serves as the key enzyme regulating astaxanthin accumulation in H. pluvialis JNU35. The cyclic electron-transport chain and novel nitrogen metabolic process were used adaptively as the regulatory mechanism compensating for different levels of stress. The in-depth study of these metabolic pathways and related key genes can reveal the underlying relationship between cell growth and astaxanthin accumulation in H. pluvialis JNU35.

The complete mitochondrial genome of wood-rotting fungus Xylaria hypoxylon.

Xylaria hypoxylon is a noticeable black fungus, and also habitual to cluster on rotting wood. In this study, the high-quality whole-genome of X. hypoxylon strain SFY20170806 was sequenced on the Illumina sequencing platform. The complete mitochondrial genome of X. hypoxylon was assembled and annotated. The single circular structure of 129,366 bp length is the largest species found in the order Xylariales. The overall GC content is 29.7% and gene composition includes 13 protein-coding genes (PCGs), 30 transfer RNA genes(tRNA), 2 ribosomal RNA genes(rRNA) and 6 open reading frames (ORF). Phylogenetic tree was constructed to validate the evolutionary relationship based on the complete mitogenomes from twelve taxa of four species of Xylariales, four species of Hypocreales, two species of Helotiales, one species of Microascales and X. hypoxylon. Phylogenetic analysis demonstrated that X. hypoxylon has a special evolutionary status and close genetic relationship with Annulohypoxylon stygium.

Complete mitochondrial genome of the important bio-control fungus Purpureocillium lilacinum (Ophiocordycipitaceae, Hypocreales) and its phylogenetic analysis.

Purpureocillium lilacinum is widely used as commercialized bio-control agents for controlling plant parasitic nematodes, as well as other insects and plant pathogens. In this study, the complete mitogenome of P. lilacinum was determined using the next-generation sequencing technology. The mitogenome is a circular molecule of 23,495 bp containing 15 protein-coding genes (PCGs), 2 rRNA (rnl and rns) genes and 22 tRNA genes. The overall base composition is 35.5% A, 36.0% T, 12.9% C and 15.6% G, with a CG content of 28.5%. Phylogenetic analysis inferred from 14 concatenated PCGs of 47 taxa shows that P. lilacinum is clustered with the genus Tolypocladium of Ophiocordycipitaceae and forms a separate clade with strong statistical support. This study contributes to our understanding about sytematics and evolutionary biology of cordycipitoid fungi.