Search

The golden-needle mushroom Flammulina filiformis is one of the bulk mushroom products in the world. This study obtained complete mitogenomes of 44 wild isolates collected from nine provinces and two artificially bred cultivars of F. filiformis, together with three Flammulina rossica isolates and one Flammulina fennae isolate for comparison. The mitogenome of F. filiformis ranged from 83,540 bp to 90,938 bp, consisting of 14 conserved protein-coding genes (PCGs), two rRNA genes, and 25 tRNA genes. To the best of our knowledge, it contained the highest proportion of intergenic regions compared to the other known Basidiomycota mitogenomes. Introns and intergenic regions were two major contributing factors to the total size of the F. filiformis mitogenome. The conserved PCG cox3 is located in an intron of another conserved PCG, nad5. This is a unique phenomenon in all known fungal mitogenomes. Gain/loss of introns was observed in cox1, nad5, and rnl. Length polymorphism was widely observed in intergenic regions. Accordingly, primers were designed as useful markers for rapid identification of F. filiformis isolates with differentiated mitogenomes. Our findings provide a basis for further studies related to variety identification and population genetics of this economically important mushroom.

During 2018-2020, we isolated 32 Eurasian avian-like swine influenza A(H1N1) viruses and their reassortant viruses from pigs in China. Genomic testing identified a novel reassortant H3N1 virus, which emerged in late 2020. Derived from G4 Eurasian H1N1 and H3N2 swine influenza viruses. This virus poses a risk for zoonotic infection.

The diversity of Asian horned toads is considered highly underestimated and to contain a large number of undescribed cryptic species. In this work, we describe three new species of Boulenophrys from south China, namely, Boulenophrys yaoshanensis sp. nov. from central Guangxi, Boulenophrys yingdeensis sp. nov. from northern Guangdong, and Boulenophrys yunkaiensis sp. nov. from western Guangdong. These three new species can be distinguished from all recognized congeners by a combination of morphological characteristics and significant genetic divergences. These descriptions increase the number of recognized species of Boulenophrys to 61. In addition, an updated checklist of the Asian horned toads of the subfamily Megophryinae is provided in this study.

In this work, a new species of the genus Tylototriton is described from Guangdong, southern China. Tylototriton sini sp. nov. was recorded as T. asperrimus for decades, and was indicated to represent an independent lineage based on recent molecular phylogenetic analyses. After detailed molecular analysis and morphological comparisons, Tylototriton sini sp. nov. is recognized as a distinct species which can be clearly distinguished from all known congeners by a combination of morphological characteristics and the significant divergence in the mitochondrial gene. Because the genus Tylototriton is of high conservation concern and all formally described members are protected by law, we also provide first data on the conservation status and recommendations for IUCN categorization for Tylototriton sini sp. nov. A suggestion on the species groups division of the genus Tylototriton is also provided based on their morphological differences and phylogenetic relationships.

Microbial sulfate reduction is largely associated with anaerobic methane oxidation and alkane degradation in sulfate-methane transition zone (SMTZ) of deep-sea cold seeps. How the sulfur cycling is mediated by microbes near SMTZ has not been fully understood. In this study, we detected a shallow SMTZ in three of eight sediment cores sampled from two cold seep areas in the South China Sea. One hundred ten genomes representing sulfur-oxidizing bacteria (SOB) and sulfur-reducing bacteria (SRB) strains were identified from three SMTZ-bearing cores. In the layers above SMTZ, SOB were mostly constituted by Campylobacterota, Gammaproteobacteria and Alphaproteobacteria that probably depended on nitrogen oxides and/or oxygen for oxidation of sulfide and thiosulfate in near-surface sediment layers. In the layers below the SMTZ, the deltaproteobacterial SRB genomes and metatranscriptomes revealed CO2 fixation by Wood-Ljungdahl pathway, sulfate reduction and nitrogen fixation for syntrophic or fermentative lifestyle. A total of 68% of the metagenome assembled genomes were not adjacent to known species in a phylogenomic tree, indicating a high diversity of bacteria involved in sulfur cycling. With the large number of genomes for SOB and SRB, our study uncovers the microbial populations that potentially mediate sulfur metabolism and associated carbon and nitrogen cycles, which sheds light on complex biogeochemical processes in deep-sea environments.

Microbially mediated nitrogen cycling in carbon-dominated cold seep environments remains poorly understood. So far anaerobic methanotrophic archaea (ANME-2) and their sulfate-reducing bacterial partners (SEEP-SRB1 clade) have been identified as diazotrophs in deep sea cold seep sediments. However, it is unclear whether other microbial groups can perform nitrogen fixation in such ecosystems. To fill this gap, we analyzed 61 metagenomes, 1428 metagenome-assembled genomes, and six metatranscriptomes derived from 11 globally distributed cold seeps. These sediments contain phylogenetically diverse nitrogenase genes corresponding to an expanded diversity of diazotrophic lineages. Diverse catabolic pathways were predicted to provide ATP for nitrogen fixation, suggesting diazotrophy in cold seeps is not necessarily associated with sulfate-dependent anaerobic oxidation of methane. Nitrogen fixation genes among various diazotrophic groups in cold seeps were inferred to be genetically mobile and subject to purifying selection. Our findings extend the capacity for diazotrophy to five candidate phyla (Altarchaeia, Omnitrophota, FCPU426, Caldatribacteriota and UBA6262), and suggest that cold seep diazotrophs might contribute substantially to the global nitrogen balance.

Recently, a novel duck-origin goose parvovirus (N-GPV) was reported to cause short beak and dwarfism syndrome in ducks. In this study, we performed complete genome sequencing and analyzed three different duck-derived parvoviruses that infected different breeds of ducks. Phylogenetic trees based on gene sequences indicated that they were classical goose parvovirus (C-GPV), Muscovy duck parvovirus (MDPV), and N-GPV. Furthermore, potential recombination events were found. These results improve our understanding of the diversity of duck-derived parvoviruses in Anhui province, eastern China, and provide a reference for the prevention of associated diseases.

In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, thus influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans, to assess viral diversity, virus-host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations, with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.

A definition of the Goniurosaurus yingdeensis group is presented in this study, on the basis of morphological and phylogenetic analyses based on a series of additional specimens. Moreover, a new species of this group, Goniurosaurus variussp. nov., is proposed for northern Guangdong Province, China. The new species can be distinguished from the other two congeners of this group by the following unique characters: one or two internasals; enlarged supraorbital tubercles absent; paravertebral tubercles between limb insertions 27–29; dorsal tubercle rows at midbody 21–24; ten precloacal pores in males and absent in females; body bands with black spots; iris orange-red.

Canine kobuvirus (CaKoV), a newly described virus, is the causative agent of gastroenteritis in dogs. In this study, 57 fecal samples from dogs with diarrhea in Anhui Province, eastern China, were collected. Among these, five samples were identified to be infected with CaKoV, by polymerase chain reaction targeting the CaKoV 3D gene. The five CaKoV strains were subjected to phylogenetic analysis. The sequences of VP1 from the five CaKoV strains were 93.6%–96.1% identical to each other and 91.75%–97.95% identical to other reported CaKoV VP1 sequences. In addition, the complete genome of one strain was successfully amplified and sequenced. The genome consisted of 8223 nucleotides and shared 94.6%–97.0% nucleotide and 93.1%–94.0% amino acid sequence identity with other CaKoV isolates. Phylogenetic analysis revealed that the CaKoV strain from Anhui Province was similar to other Chinese strains, and it was more closely related to feline and mouse kobuviruses than to sheep and bovine kobuviruses. Interestingly, all of the CaKoV-positive samples were coinfected with canine parvovirus. The finding of CaKoV infection in dogs with diarrhea and coinfection with canine parvovirus are a cause for concern and highlight the need for management and preventive measures.

A new species of colubrid snake,Lycodon cathayasp. nov., is described based on two adult male specimens collected from Huaping Nature Reserve, Guangxi, southern China. In a phylogenetic analyses, the new species is shown to be a sister taxon to the clade composed ofL. futsingensisandL. namdongensiswith low statistical support, and can be distinguished from all known congeners by the significant genetic divergence in the mitochondrial cytochromebgene fragment (p-distance ≥ 7.9%), and morphologically by the following combination of characters: (1) dorsal scales in 17–17–15 rows, smooth throughout; (2) supralabials eight, third to fifth in contact with eye, infralabials nine; (3) ventral scales 199–200 (plus two preventral scales), subcaudals 78; (4) loreal single, elongated, in contact with eye or not, not in contact with internasals; (5) a single preocular not in contact with frontal, supraocular in contact with prefrontal, two postoculars; (6) maxillary teeth 10 (4+2+2+2); (7) two anterior temporals, three posterior temporals; (8) precloacal plate entire; (9) ground color from head to tail brownish black, with 31–35 dusty rose bands on body trunk, 13–16 on tail; (10) bands in 1–2 vertebral scales broad in minimum width; (11) bands separate ground color into brownish black ellipse patches arranged in a row along the top of body and tail; (12) elliptical patches in 3–6 scales of the vertebral row in maximum width; (13) ventral surface of body with wide brownish black strip, margined with a pair of continuous narrow greyish white ventrolateral lines. With the description of the new species, 64 congeners are currently known in the genusLycodon, with 16 species occurring in China.

Five Curvularia strains isolated from diseased leaves of lemongrass (Cymbopogon citratus) in Guangxi Province, China, were examined. NCBI-Blast searches of ITS sequences suggested a high degree of similarity (99–100%) to Curvularia akaii, C. akaiiensis, C. bothriochloae, C. heteropogonis and C. sichuanensis. To accurately identify these strains, we further analysed their morphology and phylogenetic relationships based on combinations of ITS, GAPDH, and tef1 gene sequences. Morphological observations indicated that the key character differing from similar species was conidial size, whereas phylogenetic analyses indicated that the five strains represent one species that is also distinct from C. akaii, C. akaiiensis and C. bothriochloae by conidial size and conidiophore length. Thus, the strains examined are found to represent a new species described herein as Curvularia nanningensis. The pathogenicity test on the host and detached leaves confirmed the new species to be pathogenic on Cymbopogon citratus leaves. Standardised requirements for reliable identification of Curvularia pathogens are also proposed.

The maximum ammonia oxidation potential (AOP) of a topsoil in Langhovde, East Antarctica was 22.1±2.4‍ ‍ng N g-1 dry soil h-1 (2‍ ‍mM ammonium, 10°C, n=3). This topsoil exhibited twin AOP peaks (1 and 2‍ ‍mM ammonium) at 10°C, but not at 20°C. Six and ten operational taxonomic units (OTUs) were identified for ammonia-oxidizing bacteria (AOB) and archaea (AOA) amoA, respectively. AOB were classified into Nitrosospira; the two dominant OTUs corresponded to the Mount Everest cluster. AOA were classified into three clusters; Nitrososphaera and Nitrosocosmicus were the two dominant clusters.

Porcine reproductive and respiratory syndrome virus (PRRSV) is an important pathogen that causes huge economic losses to the swine industry worldwide. Here, a novel variant of PRRSV strain named TJnh2021 was isolated from nursery piglets with morbidity rate (75%) and mortality rate (40%) in Tianjin Province of China in 2021. Phylogenetic and molecular evolutionary analyses revealed that TJnh2021 was highly similar to NADC34-like (lineage 1.5, isolated in North America in 2014) in the ORF1ab-ORF2 and ORF6-ORF7 coding regions, as well as to QYYZ-like (lineage 3, isolated in China in 2010) in the ORF3-ORF5, suggestive of a natural recombination event. Recombination analyses revealed that recombination events occurred in two interlineage recombination events between lineages 1.5 and 3, and two breakpoints in ORF2 (nt12196) and ORF5 (nt13628) (with reference to the VR-2332 strain). Animal experiments demonstrated that TJnh2021 caused mortality rates of 40% and exhibited higher pathogenicity in piglets compared to other lineage 1.5 strains reported in China. Taken altogether, NADC34-like PRRSV has undergone genetic exchange with Chinese local PRRSV strains and recombination might be responsible for the variations in pathogenicity and highlight the importance of surveillance of this lineage in China.

Carotenoids are natural functional pigments produced by plants and microorganisms and play essential roles in human health. Cabbage (Brassica oleracea L. var. capitata L.) is an economically important vegetable in terms of production and consumption. It is highly nutritious and contains β-carotene, lutein, and other antioxidant carotenoids. Here, we systematically analyzed carotenoid biosynthetic genes (CBGs) on the whole genome to understand the carotenoid biosynthetic pathway in cabbage. In total, 62 CBGs were identified in the cabbage genome, which are orthologs of 47 CBGs in Arabidopsis thaliana. Out of the 62 CBGs, 46 genes in cabbage were mapped to nine chromosomes. Evolutionary analysis of carotenoid biosynthetic orthologous gene pairs among B. oleracea, B. rapa, and A. thaliana revealed that orthologous genes of B. oleracea underwent a negative selection similar to that of B. rapa. Expression analysis of the CBGs showed functional differentiation of orthologous gene copies in B. oleracea and B. rapa. Exogenous phytohormone treatment suggested that ETH, ABA, and MeJA can promote some important CBGs expression in cabbage. Phylogenetic analysis showed that BoPSYs exhibit high conservatism. Subcellular localization analysis indicated that BoPSYs are located in the chloroplast. This study is the first to study carotenoid biosynthesis genes in cabbage and provides a basis for further research on carotenoid metabolic mechanisms in cabbage.

Hulless barley (Hordeum vulgare L. var. nudum), also called naked barley, is a unique variety of cultivated barley. The genome-wide specific length amplified fragment sequencing (SLAF-seq) method is a rapid deep sequencing technology that is used for the selection and identification of genetic loci or markers. In this study, we collected 300 hulless barley accessions and used the SLAF-seq method to identify candidate genes involved in plant height (PH) and tiller number (TN). We obtained a total of 1407 M paired-end reads, and 228,227 SLAF tags were developed. After filtering using an integrity threshold of >0.8 and a minor allele frequency of >0.05, 14,504,892 single-nucleotide polymorphisms (SNP) loci were screened out. The remaining SNPs were used for the construction of a neighbour-joining phylogenetic tree, and the three subcluster members showed no obvious differentiation among regional varieties. We used a genome wide association study approach to identify 1006 and 113 SNPs associated with TN and PH, respectively. Based on best linear unbiased predictors (BLUP), 41 and 29 SNPs associated with TN and PH, respectively. Thus, several of genes, including Hd3a and CKX5, may be useful candidates for the future genetic breeding of hulless barley. Taken together, our results provide insight into the molecular mechanisms controlling barley architecture, which is important for breeding and yield.

Infections caused by SARS-CoV-2 have brought great harm to human health. After transmission for over two years, SARS-CoV-2 has diverged greatly and formed dozens of different lineages. Understanding the trend of its genome evolution could help foresee difficulties in controlling transmission of the virus. In this study, we conducted an extensive monthly survey and in-depth analysis on variations of nucleotide, amino acid and codon numbers in 311,260 virus samples collected till January 2022. The results demonstrate that the evolution of SARS-CoV-2 is toward increasing U-content and reducing genome-size. C, G and A to U mutations have all contributed to this U-content increase. Mutations of C, G and A at codon position 1, 2 or 3 have no significant difference in most SARS-CoV-2 lineages. Current viruses are more cryptic and more efficient in replication, and are thus less virulent yet more infectious. Delta and Omicron variants have high mutability over other lineages, bringing new threat to human health. This trend of genome evolution may provide a clue for tracing the origin of SARS-CoV-2, because ancestral viruses should have lower U-content and probably bigger genome-size.

Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long- and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.

The Amolops populations in the coastal hills in eastern Guangdong and southern Fujian, China, were controversially recorded as A. hongkongensis or A. daiyunensis before. In this study, based on the morphological examination and phylogenetic analysis of the specimens from these areas, a new species, Amolops teochew sp. nov., is described. Amolops teochew sp. nov. can be distinguished reliably from A. hongkongensis and A. daiyunensis by a combination of characteristics morphologically and distinct divergences genetically. The description of the new species highlights the Amolops diversity in the limited hilly region of southeastern China, which is remarkably higher than that in the more extensive inland region of southeastern China.

Camellia vietnamensis Huang, which belongs to Camellia oleifera, is a traditional Chinese medicinal plant widely planted on Hainan Island. Tea saponin is an important functional component of C. vietnamensis, and squalene is the precursor substance that controls its formation. Squalene synthase (SQS: EC 2.5.1.21) synthesizes squalene from 2 molecules of farnesyl pyrophosphate (FPP). In this study, 1683 bp of the C. vietnamensis SQS gene, designated as CvSQS, was cloned and encoded 414 amino acids. Bioinformatics and phylogenetic tree analysis revealed the high homology of CvSQS with squalene synthases from other plants. For soluble proteins, the carboxy-terminal deleted CvSQS was obtained for expression in Escherichia coli Transetta (DE3), and the recombinant protein with a weight of 42.5 kDa was detected using SDS-PAGE and Western blot. After an enzymatic reaction, the presence of squalene in the product was analyzed using GC-MS detection, which indicated that CvSQS had catalytic activity. The tissue specificity of CvSQS and its presence in seeds at various ripening stages was detected by q-RT PCR. CvSQS had the highest transcriptional level in leaves, followed by seeds, roots, and flowers; the amount of CvSQS in the seeds was highest in September. The identification and functional characterization of CvSQS is essential for further studies on the regulation mechanism of tea saponin in C. vietnamensis.

As one of antimicrobial peptides (AMPs), defensins are involved in invertebrate innate immunity against invading pathogens. In this study, a member of the invertebrate defensins was cloned and characterized from the small abalone Haliotis diversicolor, designated HdDef-2. The HdDef-2 cDNA contained a 201 bp open reading frame encoding 66 amino acids including a signal peptide of 18 amino acids and a mature peptide of 48 amino acids. The mature peptide of HdDef-2 possessed similar features to other AMPs, such as lower molecular mass, net positive charge (+1), and a high hydrophobic residue ratio (45%). In addition, six cysteines in the mature peptide were arranged in the pattern C-X16-C-X3-C-X9-C-X4-C-X1-C and stabilized the α-helix/β-sheet motif (CSαβ) with three disulfide bonds (C1-C4, C2-C5 and C3-C6) in the predicted tertiary structure. Moreover, the similar three-dimensional structure to Anopheles gambiae defensin and a phylogenetic analysis suggest that HdDef-2 may be a new member of the arthropod defensin family. Quantitative real-time PCR analysis revealed that HdDef-2 transcripts were constitutively expressed in the mantle, gill, hepatopancreas, and foot, with the highest level in the hepatopancreas. It was observed that HdDef-2 transcripts were significantly induced in the hepatopancreas after infection by Vibrio harveyi. These results indicate that HdDef-2 may be involved in the immune response against invading pathogenic bacteria, but future work is needed to verify its antimicrobial activity in protein level and elucidate the underlying mechanisms.

Porcine parvovirus 7 (PPV7), a new serotype of the porcine parvovirus, was discovered in swine of the USA in 2016. Recently, PPV7 was detected in Anhui province, China. Twenty-four of the 120 lung samples were PPV7-positive. Three PPV7 strains were sequenced and named PPV7/China/AHbz, PPV7/China/AHhf, and PPV7/China/AHmas, respectively. The complete genome and NS1 gene nucleotides of the three PPV7 strains showed 80.0%-98.4% and 94.4%-98.7% sequence identity, respectively, to the other PPV7 strains obtained from NCBI. The three PPV7 strains from Anhui share a common origin with a PPV7 GX49 strain isolated in Guangxi. These results help to understand the molecular epidemiology of PPV7.

Two new species, Castanediellabrevis and C.monoseptata, are described, illustrated and compared with other Castanediella taxa. Evidence for the new species is provided by morphological comparison and sequence data analyses. Castanediellabrevis can be distinguished from other Castanediella species by the short hyaline conidiophores and fusiform, aseptate hyaline conidia, while C.monoseptata differs from other Castanediella species by its unbranched conidiophores and fusiform, curved, 0–1-sepatate, hyaline conidia. Phylogenetic analysis of combined ITS and LSU sequence data was carried out to determine the phylogenetic placement of the species. A synopsis of hitherto described Castanediella species is provided. In addition, Castanediella is also compared with morphologically similar-looking genera such as Idriella, Idriellopsis, Microdochium, Neoidriella, Paraidriella and Selenodriella.

Background Brassica oleracea exhibits extensive phenotypic diversity. As an important trait, petal color varies among different B. oleracea cultivars, enabling the study of the genetic basis of this trait. In a previous study, the gene responsible for petal color in B. oleracea was mapped to a 503-kb region on chromosome 3, but the candidate gene has not yet been identified. Results In the present study, we report that the candidate gene was further delineated to a 207-kb fragment. BoCCD4, a homolog of the Arabidopsis carotenoid cleavage dioxygenase 4 (CCD4) gene, was selected for evaluation as the candidate gene. Sequence analysis of the YL-1 inbred line revealed three insertions/deletions and 34 single-nucleotide polymorphisms in the coding region of BoCCD4. Functional complementation showed that BoCCD4 from the white-petal inbred line 11–192 can rescue the yellow-petal trait of YL-1. Expression analysis revealed that BoCCD4 is exclusively expressed in petal tissue of white-petal plants, and phylogenetic analysis indicated that CCD4 homologs may share evolutionarily conserved roles in carotenoid metabolism. These findings demonstrate that BoCCD4 is responsible for white/yellow petal color variation in B. oleracea. Conclusions This study demonstrated that function loss of BoCCD4, a homolog of Arabidopsis CCD4, is responsible for yellow petal color in B. oleracea. Electronic supplementary material The online version of this article (10.1186/s12864-019-5596-2) contains supplementary material, which is available to authorized users.

Mycovirus infection is a universal phenomenon in the major fungus groups. So far, however, mycoviruses have not been described in the phytopathogenic fungus Leptosphaeria biglobosa, the causal agent of phoma stem canker (blackleg). Here, we report the complete genome sequence of a novel mitovirus, Leptosphaeria biglobosa mitovirus 1 (LbMV1), isolated from the strain H3-38 of L. biglobosa. The LbMV1 genome comprises 2568 nucleotides with a low G+C content of 30%. Using the mitochondrial genetic code, the genome of LbMV1 was found to contain a single large open reading frame that encodes a predicted protein of 756 amino acids. Multiple alignment of the predicted protein sequence showed the highest similarity (51% identity) to the putative RNA-dependent RNA polymerase of Ophiostoma mitovirus 4. In addition, phylogenetic analysis grouped LbMV1 within the genus Mitovirus of the family Narnaviridae. Our results suggest that the double-stranded RNA found in strain H3-38 is the replicating genome of the mitovirus LbMV1, its deletion represents the first evidence of a mycovirus infecting L. biglobosa.

Although interplays between plant and coevolved microorganisms are believed to drive landscape formation and ecosystem services, the relationships between the mycobiome and phytochemical evolution and the evolutionary characteristics of plant-mycobiome interaction patterns are still unclear. The present study explored fungal communities from 405 multiniche samples of three Holarctic disjunct Panax species. The overall mycobiomes showed compartment-dominated variations and dynamic universality. Neutral models were fitted for each compartment at the Panax genus (I) and species (II) levels to infer the community assembly mechanism and identify fungal subgroups potentially representing different plant-fungi interaction results, i.e., the potentially selected, opposed, and neutral taxa. Selection contributed more to the endosphere than to external compartments. The nonneutral taxa showed significant phylogenetic clustering. In Model I, the opposed subgroups could best reflect Panax saponin diversities (r = 0.69), and genera with highly positive correlations to specific saponins were identified using machine learning. Although mycobiomes in the three species differed significantly, subgroups in Model II were phylogenetically clustered based on potential interaction type rather than plant species, indicating potentially conservative plant-fungi interactions. In summary, the finding of strong links between invaders and saponin diversity can help explore the underlying mechanisms of saponin biosynthesis evolution from microbial insights, which is important to understanding the formation of the current landscape. The potential conservatism of plant-fungi interaction patterns suggests that the related genetic modules and selection pressures were convergent across Panax species, advancing our understanding of plant interplay with biotic environments.

The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms inhabiting several hydrothermally inactive seafloor deposits among globally distributed deep-sea vent fields. Despite of geographically distant vent fields, similar microbial community patterns were observed with the dominance of Gammaproteobacteria, Bacteroidota and previously overlooked Candidatus Patescibacteria. Metabolically flexible Gammaproteobacteria are major potential primary producers utilizing mainly sulfur, iron and hydrogen as electron donors coupled with oxygen and nitrate respiration for chemolithoautotrophic growth. In addition to heterotrophic microorganisms like free-living Bacteroidota, Ca. Patescibacteria potentially perform fermentative recycling of organic carbon. Finally, we provided evidence that many functional genes that are central to energy metabolism have been laterally transferred among members within the community and largely within the same class. Taken together, these findings shed light on microbial ecology and evolution in inactive seafloor sulfide deposits after the cessation of hydrothermal activities.

Main conclusion Chitinase family genes were involved in the response of Brassica oleracea to Fusarium wilt, powdery mildew, black spot and downy mildew. Abstract Abstract Chitinase, a category of pathogenesis-related proteins, is believed to play an important role in defending against external stress in plants. However, a comprehensive analysis of the chitin-binding gene family has not been reported to date in cabbage (Brassica oleracea L.), especially regarding the roles that chitinases play in response to various diseases. In this study, a total of 20 chitinase genes were identified using a genome-wide search method. Phylogenetic analysis was employed to classify these genes into two groups. The genes were distributed unevenly across six chromosomes in cabbage, and all of them contained few introns (≤ 2). The results of collinear analysis showed that the cabbage genome contained 1–5 copies of each chitinase gene (excluding Bol035470) identified in Arabidopsis. The heatmap of the chitinase gene family showed that these genes were expressed in various tissues and organs. Two genes (Bol023322 and Bol041024) were relatively highly expressed in all of the investigated tissues under normal conditions, exhibiting the expression characteristics of housekeeping genes. In addition, under four different stresses, namely, Fusarium wilt, powdery mildew, black spot and downy mildew, we detected 9, 5, 8 and 8 genes with different expression levels in different treatments, respectively. Our results may help to elucidate the roles played by chitinases in the responses of host plants to various diseases.

The diversity of Panophrys horned toads is considered highly underestimated with a large number of undescribed cryptic species. In this work, we describe four Panophrys species from eastern China which were proposed as cryptic species by molecular data in previous study, additionally provide new information on the biogeography of these four species. Panophrys daiyunensis sp. nov. from southern Fujian, Panophrys daoji sp. nov. from eastern Zhejiang, Panophrys sanmingensis sp. nov. from the hilly area among Fujian, Jiangxi and Guangdong, and Panophrys tongboensis sp. nov. from northeastern Jiangxi, can be distinguished from all recognized congeners by a combination of morphological characteristics. The descriptions of these four new species take the recognized species of Panophrys to 51, which is the largest genus within the Asian horned toads subfamily Megophryinae. Considered as an appropriate arrangement for the Asian horned toads currently and applied in this study to describe the new species, the generic recognition of Panophrys is also discussed.

Gut microbial transformations of flavonoids, an enormous class of polyphenolic compounds abundant in plant-based diets, are closely associated with human health. However, the enzymes that initiate the gut microbial metabolism of flavones and flavonols, the two most abundant groups of flavonoids, as well as their underlying molecular mechanisms of action remain unclear. Here, we discovered a flavone reductase (FLR) from the gut bacterium, Flavonifractor plautii ATCC 49531 (originally assigned as Clostridium orbiscindens DSM 6740), which specifically catalyses the hydrogenation of the C2–C3 double bond of flavones/flavonols and initiates their metabolism as a key step. Crystal structure analysis revealed the molecular basis for the distinct catalytic property of FLR. Notably, FLR and its widespread homologues represent a class of ene-reductases that has not been previously identified. Genetic and biochemical analyses further indicated the importance of FLR in gut microbial consumption of dietary and medicinal flavonoids, providing broader insight into gut microbial xenobiotic transformations and possible guidance for personalized nutrition and medicine., Flavonoids are abundant polyphenols in plants but it is not well understood how their metabolism is initiated by microbes in the human gut. Here, the authors identify and characterise an ene-reductase from the gut bacterium, Flavonifractor plautii ATCC 49531 that catalyses the hydrogenation of the C2–C3 double bond of flavones and flavonols and present its crystal structure.

A single nucleotide mutation of BoCER2 is the primary cause of the wax deficiency in cabbage. An effective allele-specific KASP marker was developed for marker-assisted selection of glossiness. TL28-1 is a novel spontaneous wax-deficient mutant with a glossy phenotype identified from cabbage. In this study, the genetic analysis suggested that the wax-deficient trait of TL28-1 was controlled by a single recessive gene. All wax monomers longer than 28 carbons were significantly decreased in TL28-1. Fine-mapping results showed that the wax-deficient locus wdtl28 was located at an 80-kb interval between BOL01-20 and BOL01-24 markers on chromosome 1. According to the genome annotation of B. oleracea, the ECERIFERUM2- LIKE (CER2-LIKE) gene, BoCER2, was identified as the candidate gene. Phylogenetic analysis showed that BoCER2 and other CER2-LIKEs from vascular plants formed a clade within the BAHD superfamily of acyltransferases. The BoCER2 transcript was detected in various tissues, including stem, leaf, flower, and silique, but not in the cabbage roots. Subcellular localization indicated that BoCER2 protein functions in the endoplasmic reticulum. Further sequence analysis showed that a single nucleotide mutation (G to A) is present in the BoCER2 coding sequence in TL28-1, leading to a stop codon (TGA), hence premature translation termination. Linkage analysis showed that the homozygotic mutational BoCER2 co-segregated with wax deficiency. Moreover, the complementation test suggested that BoCER2 from wild type can rescue the wax deficiency of TL28-1. These results indicate that BoCER2 mutation hinders the elongation of very-long-chain fatty acid precursors in TL28-1, leading to wax deficiency. The allele-specific KASP marker designed in this study could be effective for marker-assisted selection of glossiness.

Bambusa rigida is a tropical woody bamboo widely distributed in Sichuan and southeastern of China with important economic and ecological values. We performed a complete chloroplast (cp) genome of B. rigida using Illumina NovaSeq PE150 platform. The length of complete cp sequence is 139,500 bp in size with a pair of inverted repeat (IR) regions of 43,587 bp, which separates a large single-copy (LSC) region of 83,036 bp and a small single-copy (SSC) region of 12,875 bp. Plastid genome contains 132 genes, including 84 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 30 cp genomes indicates that B. rigida is closely related to Bambusa ventricosa in Bambuseae.

Background In the last few years, many microfungi—including plant-associated species—have been reported from various habitats and substrates in Italy. In this study of pleosporalean fungi, we researched terrestrial habitats in the Provinces of Arezzo (Tuscany region), Forli-Cesena and Ravenna (Emilia-Romagna region) in Italy. New information Our research on Italian pleosporalean fungi resulted in the discovery of a new species, Italica heraclei ( Phaeosphaeriaceae ). In addition, we present a new host record for Pseudoophiobolus mathieui ( Phaeosphaeriaceae ) and the second Italian record of Phomatodes nebulosa ( Didymellaceae ). Species boundaries were defined, based on morphological study and multi-locus phylogenetic reconstructions using Maximum Likelihood and Bayesian Inference analyses. Our findings expand the knowledge on host and distribution ranges of pleosporalean fungi in Italy.

BackgroundAn outbreak of acute gastroenteritis occurred in a kindergarten located Shenzhen City on March 4, 2018. We were invited to investigate to the risk factors associated with this outbreak.MethodsWe conducted retrospective cohort-studies on three different groups of subjects in order to figure out the difference of incidence of acute gastroenteritis among subjects of different activities on March 2: group one consisted of people who attended the Lantern festival activities; group two consisted of children and employees who ate breakfast and bread provided by the kindergarten; and groups three consisted of children and employees who did not eat breakfast or bread provided by the kindergarten. Fecal, anal swabs, dishware swabs and hand swabs specimens were collected in the study. Bacteria known to cause acute gastroenteritis were cultured. Viruses associated with acute gastroenteritis were tested using real-time PCR. Capsid gene fragment of 557 bp of norovirus was amplified and sequenced. The phylogenetic tree was constructed with MEGA 7.0 using neighbor-joining method based on capsid gene fragment of norovirus.ResultsA total of 143 suspected cases were identified in this outbreak. Diarrhea happened more often in adults than in children while emesis and bellyache were more frequently found in children than in adults. Higher AGE incidence was observed in group 2, children and employees who had breakfast in the kindergarten on March 2, as well as in group 3, and among employees who eating bread involved in breakfast provided on March 2. Five anal swab specimens were positive for norovirus. All noroviruses belongs to group II.3 and have an identity more than 99%.ConclusionA chef, as an asymptomatic carrier with norovirus, was the infectious resource in this outbreak. He contaminated breakfast food provided on March 2. Although morning check is implemented in kindergartens of China, employees are often excluded in morning check. Our finding highlights the importance of morning check covering employees and periodical training for cooks.

A new canine picornavirus (CanPV) variant, designated as dog/SH1901/CHN/2019, was detected in a pool of various canine fecal samples in the mainland of China using a viral metagenomic analysis, and its nearly complete genome sequence was determined and analyzed. Sequence analyses revealed that it had a standard picornavirus genome organization, a type I internal ribosome entry site (IRES) in the 5'UTR. However, dog/SH1901/CHN/2019 has generated a serial of unique aa mutations and 7aa insertion when compared with the closely related CanPVs. Phylogenetic analysis and pairwise sequence comparisons based on the P1, 2C, 3C, and 3D protein sequences showed that dog/SH1901/ CHN/2019 was closely related to CanPV strains 244 F, 325 F and 6D, which clustered into an independent evolutionary clade and distantly related to CanPV strain A128thr of the genus Mischivirus, which indicated the unclassified CanPV strains may belong to a novel species or genus in the family Picornaviridae. This study extends our knowledge on the evolution and genetic diversity of CanPVs.

Tembusu virus (TMUV) is a positive-sense RNA virus that is associated with severe reduction in egg production and even death in ducks. TMUV infection shows high incidence and is a threat to the global duck industry. However, the possible origin, genotype, and codon usage bias of TMUV are not very clear. Here, we addressed these questions by analyzing the available genomic sequences from China. The results showed that the ancestor of avian TMUV was most likely a mosquito TMUV. Moreover, three TMUV clades were identified by three different phylogenetic analysis methods. The TMUV genome exhibits a stronger mutation pressure than natural selection pressure. Our findings provide important insights that reveal the ongoing TMUV spread in China and can aid in future prevention and control.

The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers. We analyzed 897 transcriptomes from three Cetartiodactyla lineages: ruminants, camels and cetaceans, as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen functional innovations. We identified genes with relatively high expression in the rumen, of which many appeared to be recruited from other tissues. These genes show functional enrichment in ketone body metabolism, regulation of microbial community, and epithelium absorption, which are the most prominent biological processes involved in rumen innovations. Several modes of genetic change underlying rumen functional innovations were uncovered, including coding mutations, genes newly evolved, and changes of regulatory elements. We validated that the key ketogenesis rate-limiting gene (HMGCS2) with five ruminant-specific mutations was under positive selection and exhibits higher synthesis activity than those of other mammals. Two newly evolved genes (LYZ1 and DEFB1) are resistant to Gram-positive bacteria and thereby may regulate microbial community equilibrium. Furthermore, we confirmed that the changes of regulatory elements accounted for the majority of rumen gene recruitment. These results greatly improve our understanding of rumen evolution and organ evo-devo in general.