April 21, 2020  |  

Complete genome sequence and evolution analysis of Psychrobacter sp. YP14 from Gammaridea Gastrointestinal Microbiota of Yap Trench

Psychrobacter sp. YP14, a moderately psychrophilic bacterium belonging to the class Gammaproteobacteria, was isolated from Gammaridea Gastrointestinal Microbiota of Yap Trench. The strain has one circular chromosome of 2,895,311 bp with a 44.66% GC content, consisting of 2333 protein-coding genes, 53 tRNA genes and 9 rRNA genes. Four plasmids were completely assembled and their sizes were 13,712 bp, 19711 bp, 36270 bp, 8194 bp, respectively. In particular, a putative open reading frame (ORF) for dienelactone hydrolase (DLH) related to degradation of chlorinated aromatic hydrocarbons. To get an better understanding of the evolution of Psychrobacter sp. YP14 in this genus, six Psychrobacter strains (G, PRwf-1, DAB_AL43B, AntiMn-1,P11G5, P2G3), with publicly available complete genome, were selected and comparative genomics analysis were performed among them. The closest phylogenetic relationship was identified between strains G and K5 based on 16s gene and ANI (average nucleotide identity) values. Analysis of the pan-genome structure found that YP14 has fewer COG clusters associated with transposons and prophage which indicates fewer sequence rearrangements compared with PRwf-1. Besides, stress response-related genes of strain YP14 demonstrates that it has less strategies to cope with extreme environment, which is consistent with its intestinal habitat. The difference of metabolism and strategies coped with stress response of YP14 are more conducive to the study of microbial survival and metabolic mechanisms in deep sea environment.


April 21, 2020  |  

Genome Sequence Resource of a Puccinia striiformis Isolate infecting wheatgrass.

Stripe rust caused by Puccinia striiformis is a disastrous disease of cereal crops and various grasses. To date, fourteen stripe rust genomes are publicly available, including thirteen P. striiformis f. sp. tritici and one P. striiformis f. sp. hordei. In this study, one isolate (11-281) of P. striiformis collected from wheatgrass (Agropyron cristatum), which is avirulent to most of standard differential genotypes of wheat and barley, was sequenced, assembled, and annotated. The sequences were assembled to a draft genome of 84.75 Mb, which is comparable to previously sequenced P. striiformis f. sp. tritici and P. striiformis f. sp. hordei isolates. The draft genome comprised 381 scaffolds and contained 1,829 predicted secreted proteins. The high quality draft genome of the isolate is a valuable resource in shedding light on the evolution and pathogenicity of P. striiformis.


April 21, 2020  |  

Genome data of Fusarium oxysporum f. sp. cubense race 1 and tropical race 4 isolates using long-read sequencing.

Fusarium wilt of banana is caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. cubense (Foc). We generated two chromosome-level assemblies of Foc race 1 and tropical race 4 strains using single-molecule real-time sequencing. The Foc1 and FocTR4 assemblies had 35 and 29 contigs with contig N50 lengths of 2.08 Mb and 4.28 Mb, respectively. These two new references genomes represent a greater than 100-fold improvement over the contig N50 statistics of the previous short read-based Foc assemblies. The two high-quality assemblies reported here will be a valuable resource for the comparative analysis of Foc races at the pathogenic levels.


April 21, 2020  |  

Comparative genomic analysis unravels the transmission pattern and intra-species divergence of acute hepatopancreatic necrosis disease (AHPND)-causing Vibrio parahaemolyticus strains.

Acute hepatopancreatic necrosis disease (AHPND) is a recently discovered shrimp disease that has become a severe threat to global shrimp-farming industry. The causing agents of AHPND were identified as Vibrio parahaemolyticus and other vibrios harboring a plasmid encoding binary toxins PirAvp/PirBvp. However, the epidemiological involvement of environmental vibrios in AHPND is poorly understood. In this study, with an aim to reveal the possible transmission route of AHPND-causing V. parahaemolyticus, we sequenced and analyzed the genomes of four pairs of V. parahaemolyticus strains from four representative regions of shrimp farming in China, each including one strain isolated from diseased shrimp during an AHPND outbreak and one strain isolated from sediment before AHPND outbreaks. Our results showed that all the four shrimp-isolated and three of the sediment-isolated strains encode and secret PirAvp/PirBvp toxins and, therefore, are AHPND-causing strains. In silico multilocus sequence typing and high-resolution phylogenomic analysis based on single-nucleotide polymorphisms, as well as comparison of genomic loci in association with prophages and capsular polysaccharides (CPSs) consistently pointed to a close genetic relationship between the shrimp- and sediment-isolated strains obtained from the same region. In addition, our analyses revealed that the sequences associated with prophages, CPSs, and type VI secretion system-1 are highly divergent among strains from different regions, implying that these genes may play vital roles in environmental adaptation for AHPND-causing V. parahaemolyticus and thereby be potential targets for AHPND control. Summing up, this study provides the first direct evidence regarding the transmission route of AHPND-causing V. parahaemolyticus and underscores that V. parahaemolyticus in shrimp are most likely originated from local environment. The importance of environmental disinfection measures in shrimp farming was highlighted.


April 21, 2020  |  

Complete chloroplast genome sequences of Kaempferia galanga and Kaempferia elegans: Molecular structures and comparative analysis.

Kaempferia galanga and Kaempferia elegans, which belong to the genus Kaempferia family Zingiberaceae, are used as valuable herbal medicine and ornamental plants, respectively. The chloroplast genomes have been used for molecular markers, species identification and phylogenetic studies. In this study, the complete chloroplast genome sequences of K. galanga and K. elegans are reported. Results show that the complete chloroplast genome of K. galanga is 163,811 bp long, having a quadripartite structure with large single copy (LSC) of 88,405 bp and a small single copy (SSC) of 15,812 bp separated by inverted repeats (IRs) of 29,797 bp. Similarly, the complete chloroplast genome of K. elegans is 163,555 bp long, having a quadripartite structure in which IRs of 29,773 bp length separates 88,020 bp of LSC and 15,989 bp of SSC. A total of 111 genes in K. galanga and 113 genes in K. elegans comprised 79 protein-coding genes and 4 ribosomal RNA (rRNA) genes, as well as 28 and 30 transfer RNA (tRNA) genes in K. galanga and K. elegans, respectively. The gene order, GC content and orientation of the two Kaempferia chloroplast genomes exhibited high similarity. The location and distribution of simple sequence repeats (SSRs) and long repeat sequences were determined. Eight highly variable regions between the two Kaempferia species were identified and 643 mutation events, including 536 single-nucleotide polymorphisms (SNPs) and 107 insertion/deletions (indels), were accurately located. Sequence divergences of the whole chloroplast genomes were calculated among related Zingiberaceae species. The phylogenetic analysis based on SNPs among eleven species strongly supported that K. galanga and K. elegans formed a cluster within Zingiberaceae. This study identified the unique characteristics of the entire K. galanga and K. elegans chloroplast genomes that contribute to our understanding of the chloroplast DNA evolution within Zingiberaceae species. It provides valuable information for phylogenetic analysis and species identification within genus Kaempferia.


April 21, 2020  |  

The genome of the medicinal plant Andrographis paniculata provides insight into the biosynthesis of the bioactive diterpenoid neoandrographolide.

Andrographis paniculata is a herbaceous dicot plant widely used for its anti-inflammatory and anti-viral properties across its distribution in China, India and other Southeast Asian countries. A. paniculata was used as a crucial therapeutic treatment during the influenza epidemic of 1919 in India, and is still used for the treatment of infectious disease in China. A. paniculata produces large quantities of the anti-inflammatory diterpenoid lactones andrographolide and neoandrographolide, and their analogs, which are touted to be the next generation of natural anti-inflammatory medicines for lung diseases, hepatitis, neurodegenerative disorders, autoimmune disorders and inflammatory skin diseases. Here, we report a chromosome-scale A. paniculata genome sequence of 269 Mb that was assembled by Illumina short reads, PacBio long reads and high-confidence (Hi-C) data. Gene annotation predicted 25 428 protein-coding genes. In order to decipher the genetic underpinning of diterpenoid biosynthesis, transcriptome data from seedlings elicited with methyl jasmonate were also obtained, which enabled the identification of genes encoding diterpenoid synthases, cytochrome P450 monooxygenases, 2-oxoglutarate-dependent dioxygenases and UDP-dependent glycosyltransferases potentially involved in diterpenoid lactone biosynthesis. We further carried out functional characterization of pairs of class-I and -II diterpene synthases, revealing the ability to produce diversified labdane-related diterpene scaffolds. In addition, a glycosyltransferase able to catalyze O-linked glucosylation of andrograpanin, yielding the major active product neoandrographolide, was also identified. Thus, our results demonstrate the utility of the combined genomic and transcriptomic data set generated here for the investigation of the production of the bioactive diterpenoid lactone constituents of the important medicinal herb A. paniculata. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.


April 21, 2020  |  

Complete Genome Sequence of Bacillus cereus CC-1, A Novel Marine Selenate/Selenite Reducing Bacterium Producing Metallic Selenides Nanomaterials.

Metallic selenides nanomaterials are widely used in many fields, especially for photothermal therapy and thermoelectric devices. However, the traditional chemogenic methods are energy-intensive and environmentally unfriendly. In this study, the first complete genome data of a metallic selenides producing bacterium Bacillus cereus CC-1 was reported. This strain can not only reduce selenite and selenate into elemental selenium nanoparticles (SeNPs), but also synthesize several metallic selenides nanoparticles when adding metal ions (Pb2+, Ag+ and Bi3+) and selenite simultaneously. The size of the genome is 5,308,319 bp with 36.07% G+C content. Several putative genes responsible for heavy metal resistance, salt resistance, and selenate reduction were found. This genome data provide fundamental information, which support the use of this strain for the production of biocompatible photothermal and thermoelectric nanomaterials under mild conditions.


April 21, 2020  |  

A high-quality draft genome assembly of Sinella curviseta: A soil model organism (Collembola).

Sinella curviseta, among the most widespread springtails (Collembola) in Northern Hemisphere, has often been treated as a model organism in soil ecology and environmental toxicology. However, little information on its genetic knowledge severely hinders our understanding of its adaptations to the soil habitat. We present the largest genome assembly within Collembola using ~44.86?Gb (118X) of single-molecule real-time Pacific Bioscience Sequel sequencing. The final assembly of 599 scaffolds was ~381.46?Mb with a N50 length of 3.28?Mb, which captured 95.3% complete and 1.5% partial arthropod Benchmarking Universal Single-Copy Orthologs (n?=?1066). Transcripts and circularized mitochondrial genome were also assembled. We predicted 23,943 protein-coding genes, of which 83.88% were supported by transcriptome-based evidence and 82.49% matched protein records in UniProt. In addition, we also identified 222,501 repeats and 881 noncoding RNAs. Phylogenetic reconstructions for Collembola support Tomoceridae sistered to the remaining Entomobryomorpha with the position of Symphypleona not fully resolved. Gene family evolution analyses identified 9,898 gene families, of which 156 experienced significant expansions or contractions. Our high-quality reference genome of S. curviseta provides the genetic basis for future investigations in evolutionary biology, soil ecology, and ecotoxicology. © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.


April 21, 2020  |  

Identification and pathogenicity of an XDR Streptococcus suis isolate that harbours the phenicol-oxazolidinone resistance genes optrA and cfr, and the bacitracin resistance locus bcrABDR.

One hundred and seven Streptococcus suis isolates were collected from healthy pigs or asymptomatic carriers in Jiangsu, China in 2016-2017. Thirty-eight percent of the isolates were linezolid-resistant and all carried the optrA gene. Among them, one isolate, SFJ44, was resistant to all 20 of the antibiotics tested, except for ceftiofur, and thus exhibited an extensively-drug-resistant phenotype. This isolate carried the optrA gene and the bacitracin resistance locus bcrABDR on an antibiotic-resistance-associated genomic island (ARGI1), and harboured the resistance genes cfr, aadE, sat4, spw-like, aphA3, mef(A), msr(D), erm(A)-like, erm(B), tetAB(P)’, tet(M) and catQ on ARGI2~4. The IS1216E-bcrABDR-ISEnfa1 segment showed >99.9% sequence identity to corresponding sequences from other species. The cfr gene was located on ARGI4, and two IS6 family insertion sequences, IS1216E and ISTeha2, were found upstream and downstream of cfr-?ISEnfa5, respectively. A circular intermediate of bcrABDR-ISEnfa1 was detected, suggesting the role of ISEnfa1 in dissemination of bcrABDR. Other antibiotic resistance genes might be acquired from different Gram-positive pathogens. Infection of zebrafish showed that SFJ44 exhibited a virulence level comparable to serotype 2 hypervirulent strain SC070731, highlighting the need for surveillance of the pathogenicity of multi-drug-resistant S. suis isolates. This is the first report of the co-existence of optrA and cfr, and of the bcrABDR locus in streptococci. As it has been suggested that S. suis may act as an antibiotic resistance reservoir contributing to the spread of resistance genes to major streptococcal pathogens, the potential dissemination of these resistance genes among Gram-positive bacteria is of concern and routine surveillance should be strengthened.Copyright © 2019 Elsevier Ltd. All rights reserved.


April 21, 2020  |  

Genome-wide analysis of methyl jasmonate-regulated isoform expression in the medicinal plant Andrographis paniculata

Alternative splicing can increase the complexity of the transcriptome and proteome. The most common mechanism of alternative splicing in plants is intron retention (IR), and the expression levels of IR isoforms can be differentially regulated when facing abiotic stress. The full-length transcriptome of the medicinal plant Andrographis paniculata was sequenced using both Illumina- and SMRT-based RNA-seq and a total of 4846 IR isoforms were identified. The expression levels of 310/296 IR isoforms were up-regulated, and 629/659 IR isoforms were down-regulated at 24?h/48?h after methyl jasmonate (MeJA) treatment, respectively. In the (E,E,E)-geranylgeranyl diphosphate (GGPP) biosynthesis pathway which contributes to the andrographolide biosynthesis, eight genes were alternatively spliced, resulting in a total of 25 isoforms, of which 12 are IR isoforms. After MeJA treatment, four of these IR isoforms showed significant differential expression. RT-PCR and qRT-PCR experiments confirmed the existence of five IR isoforms. This research deepens our understanding of the A. paniculata transcriptome and can assist in the future study of andrographolide biosynthesis.


April 21, 2020  |  

Complete chloroplast genome sequence of Hedychium coronarium

The first complete chloroplast genome of Hedychium coronarium (Zingiberaceae) was reported in this study. The H. coronarium chloroplast genome was 163,949bp in length and comprised a pair of inverted repeat (IR) regions of 29,780bp each, a large single-copy (LSC) region of 88,581bp and a small single-copy (SSC) region of 15,808bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species), and eight rRNA genes (four rRNA species). The nucleotide composition was asymmetric (31.68% A, 18.35% C, 17.74% G, 32.23% T) with an overall AT content of 63.92%. Phylogenetic analysis showed that H. coronarium was classified into a monophyletic group within the genus Hedychium in family Zingiberaceae.


April 21, 2020  |  

Complete chloroplast genome of the plant Stahlianthus Involucratus (Zingiberaceae)

The first complete chloroplast genome of Stahlianthus involucratus (Zingiberaceae) was reported in this study. The S. involucratus chloroplast genome was 163,300bp in length and consisted of one large sin- gle copy (LSC) region of 87,498bp, one small single copy (SSC) region of 15,568bp, and a pair of inverted repeat (IR) regions 30,117bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species) and 8 rRNA genes (4 rRNA species). The phylogenetic analysis based on single nucleotide polymorphisms strongly supported that S. involucratus, Curcuma roscoeana and Curcuma longa formed a cluster in group CurcumaII within family Zingiberaceae.


April 21, 2020  |  

Characterization and phylogenetic analysis of the complete chloroplast genome sequence of Costus viridis (Costaceae)

The first complete chloroplast genome of Costus viridis (Costaceae) was reported in the current study. The C. viridis genome was 168,966bp in length and comprised a pair of inverted repeat (IR) regions of 29,166bp each, a large single-copy (LSC) region of 92,189bp, and a small single-copy (SSC) region of 18,445bp. It encoded 133 genes, including 87 protein-coding genes (79 PCG species), 38 tRNA genes (28 tRNA species), and eight rRNA genes (four rRNA species). The overall AT content was 63.75%. Phylogenetic analysis showed that C. viridis was closely related to species Costus osae within the genus Costus in family Costaceae.


April 21, 2020  |  

The sequence and de novo assembly of Takifugu bimaculatus genome using PacBio and Hi-C technologies.

Takifugu bimaculatus is a native teleost species of the southeast coast of China where it has been cultivated as an important edible fish in the last decade. Genetic breeding programs, which have been recently initiated for improving the aquaculture performance of T. bimaculatus, urgently require a high-quality reference genome to facilitate genome selection and related genetic studies. To address this need, we produced a chromosome-level reference genome of T. bimaculatus using the PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The genome was assembled into 2,193 contigs with a total length of 404.21?Mb and a contig N50 length of 1.31?Mb. After chromosome-level scaffolding, 22 chromosomes with a total length of 371.68?Mb were constructed. Moreover, a total of 21,117 protein-coding genes and 3,471 ncRNAs were annotated in the reference genome. The highly accurate, chromosome-level reference genome of T. bimaculatus provides an essential genome resource for not only the genome-scale selective breeding of T. bimaculatus but also the exploration of the evolutionary basis of the speciation and local adaptation of the Takifugu genus.


April 21, 2020  |  

Evaluation of reference genes for normalizing RT-qPCR in leaves and suspension cells of Cephalotaxus hainanensis under various stimuli.

Reverse transcription quantitative real-time PCR (RT-qPCR) is a widely used approach for investigating gene expression levels in plants because of its high reproducibility, sensitivity, accuracy and rapidness. Evaluation of reference genes for normalizing RT-qPCR data is a necessary step, especially in new plant varieties. Cephalotaxus hainanensis is a precious medicinal plant belonging to the family of Cephalotaxaceae and no RT-qPCR studies have been reported on it.In this study, 9 candidate reference genes were selected from the transcriptome data of C. hainanensis; 3 statistical algorithms (geNorm, NormFinder, BestKeeper) were applied to evaluate their expression stabilities through 180 samples under 6 stimuli treatments in leaves and leaf-derived suspension cultured cells; a comprehensive stabilities ranking was also performed by RefFinder. The results showed that suitable reference genes in C. hainanensis should be selected for normalization relative to different experimental sets. 18S showed a higher stability than other candidate reference genes which ranked at the top two suitable genes under all experimental setups in this study.This study is the first to evaluate the stability of reference genes in C. hainanensis and supply an important foundation to use the RT-qPCR for an accurate and far-reaching gene expression analysis in C. hainanensis.


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