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July 7, 2019

Cupriavidus malaysiensis sp. nov., a novel poly(3-hydroxybutyrate-co-4-hydroxybutyrate) accumulating bacterium isolated from the Malaysian environment.

Bacterial classification on the basis of a polyphasic approach was conducted on three poly(3 hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] accumulating bacterial strains that were isolated from samples collected from Malaysian environments; Kulim Lake, Sg. Pinang river and Sg. Manik paddy field. The Gram-negative, rod-shaped, motile, non-sporulating and non-fermenting bacteria were shown to belong to the genus Cupriavidus of the Betaproteobacteria on the basis of their 16S rRNA gene sequence analyses. The sequence similarity value with their near phylogenetic neighbour, Cupriavidus pauculus LMG3413T, was 98.5%. However, the DNA-DNA hybridization values (8-58%) and ribotyping analysis both enabled these strains to be differentiated from related Cupriavidus species with validly published names. The RiboPrint patterns of the three strains also revealed that the strains were genetically related even though they displayed a clonal diversity. The major cellular fatty acids detected in these strains included C15:0 ISO 2OH/C16:1 ?7c, hexadecanoic (16:0) and cis-11-octadecenoic (C18:1 ?7c). Their G+C contents ranged from 68.0  to 68.6 mol%, and their major isoprenoid quinone was Ubiquinone Q-8. Of these three strains, only strain USMAHM13 (= DSM 25816 = KCTC 32390) was discovered to exhibit yellow pigmentation that is characteristic of the carotenoid family. Their assembled genomes also showed that the three strains were not identical in terms of their genome sizes that were 7.82, 7.95 and 8.70 Mb for strains USMAHM13, USMAA1020 and USMAA2-4, respectively, which are slightly larger than that of Cupriavidus necator H16 (7.42 Mb). The average nucleotide identity (ANI) results indicated that the strains were genetically related and the genome pairs belong to the same species. On the basis of the results obtained in this study, the three strains are considered to represent a novel species for which the name Cupriavidus malaysiensis sp. nov. is proposed. The type strain of the species is USMAA1020T (= DSM 19416T = KCTC 32390T).

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July 7, 2019

De novo mutations resolve disease transmission pathways in clonal malaria

Detecting de novo mutations in viral and bacterial pathogens enables researchers to reconstruct detailed networks of disease transmission and is a key technique in genomic epidemiology. However, these techniques have not yet been applied to the malaria parasite, Plasmodium falciparum, in which a larger genome, slower generation times, and a complex life cycle make them difficult to implement. Here, we demonstrate the viability of de novo mutation studies in P. falciparum for the first time. Using a combination of sequencing, library preparation, and genotyping methods that have been optimized for accuracy in low-complexity genomic regions, we have detected de novo mutations that distinguish nominally identical parasites from clonal lineages. Despite its slower evolutionary rate compared with bacterial or viral species, de novo mutation can be detected in P. falciparum across timescales of just 1-2?years and evolutionary rates in low-complexity regions of the genome can be up to twice that detected in the rest of the genome. The increased mutation rate allows the identification of separate clade expansions that cannot be found using previous genomic epidemiology approaches and could be a crucial tool for mapping residual transmission patterns in disease elimination campaigns and reintroduction scenarios.

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July 7, 2019

Comparative genomic analysis of Lactobacillus plantarum GB-LP4 and identification of evolutionarily divergent genes in high-osmolarity environment.

Lactobacillus plantarum is one of the widely-used probiotics and there have been a large number of advanced researches on the effectiveness of this species. However, the difference between previously reported plantarum strains, and the source of genomic variation among the strains were not clearly specified. In order to understand further on the molecular basis of L. plantarum on Korean traditional fermentation, we isolated the L. plantarum GB-LP4 from Korean fermented vegetable and conducted whole genome assembly. With comparative genomics approach, we identified the candidate genes that are expected to have undergone evolutionary acceleration. These genes have been reported to associate with the maintaining homeostasis, which are generally known to overcome instability in external environment including low pH or high osmotic pressure. Here, our results provide an evolutionary relationship between L. plantarum species and elucidate the candidate genes that play a pivotal role in evolutionary acceleration of GB-LP4 in high osmolarity environment. This study may provide guidance for further studies on L. plantarum.

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July 7, 2019

Whole-genome sequence of Mycoplasma bovis strain Ningxia-1.

A genome sequence of the Mycoplasma bovis Ningxia-1 strain was tested by Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing technology. The strain was isolated from a lesioned calf lung in 2013 in Pengyang, Ningxia, China. The single circular chromosome of 1,033,629 bp shows differences between complete Mycoplasma bovis genome in insertion-like sequences (ISs), integrative conjugative elements (ICEs), lipoproteins (LPs), variable surface lipoproteins (VSPs), pathogenicity islands (PAIs), etc. Copyright © 2018 Sun et al.

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July 7, 2019

Complete genomic analysis of multidrug-resistance Pseudomonas aeruginosa Guangzhou-Pae617, the host of megaplasmid pBM413.

We previously described the novel qnrVC6 and blaIMP-45carrying megaplasmid pBM413. This study aimed to investigate the complete genome of multidrug-resistance P. aeruginosa Guangzhou-Pae617, a clinical isolate from the sputum of a patient who was suffering from respiratory disease in Guangzhou, China.The genome was sequenced using Illumina Hiseq 2500 and PacBio RS II sequencers and assembled de novo using HGAP. The genome was automatically and manually annotated.The genome of P. aeruginosa Guangzhou-Pae617 is 6,430,493 bp containing 5881 predicted genes with an average G + C content of 66.43%. The genome showed high similarity to two new sequenced P. aeruginosa strains isolated from New York, USA. From the whole genome sequence, we identified a type IV pilin, two large prophages, 15 antibiotic resistant genes, 5 genes involved in the “Infectious diseases” pathways, and 335 virulence factors.The antibiotic resistance and virulence factors in the genome of P. aeruginosa strain Guangzhou-Pae617 were identified by complete genomic analysis. It contributes to further study on antibiotic resistance mechanism and clinical control of P. aeruginosa. Copyright © 2018 Elsevier Ltd. All rights reserved.

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July 7, 2019

Complete genome sequence of Planococcus faecalis AJ003T, the type species of the genus Planococcus and a microbial C30 carotenoid producer.

A novel type strain, Planococcus faecalis AJ003T, isolated from the feces of Antarctic penguins, synthesizes a rare C30 carotenoid, glycosyl-4,4′-diaponeurosporen-4′-ol-4-oic acid. The complete genome of P. faecalis AJ003Tcomprises a single circular chromosome (3,495,892?bp; 40.9% G?+?C content). Annotation analysis has revealed 3511 coding DNA sequences and 99 RNAs; seven genes associated with the MEP pathway and five genes involved in the carotenoid pathway have been identified. The functionality and complementation of 4,4′-diapophytoene synthase (CrtM) and two copies of heterologous 4,4′-diapophytoene desaturase (CrtN) involved in carotenoid biosynthesis were analyzed in Escherichia coli. Copyright © 2017 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of Flavobacterium kingsejongi WV39, a type species of the genus Flavobacterium and a microbial C40 carotenoid zeaxanthin producer.

A novel species, Flavobacterium kingsejongi WV39, isolated from feces of Antarctic penguins and a type species of the genus Flavobacterium, is yellow because it synthesizes a C40 carotenoid zeaxanthin. The complete genome of F. kingsejongi WV39 is made up of a single circular chromosome (4,224,053bp, 39.8% G+C content). Annotation analysis revealed 3,955 coding sequences, 72 RNAs (18 rRNA+54 tRNA), and five genes involved in zeaxanthin biosynthesis. The key gene encoding ß-carotenoid hydroxylase (CrtZ), which is the last enzyme in the zeaxanthin biosynthetic pathway, was cloned and subjected to complementary analysis in a heterologous E. coli strain. The CrtZ of F. kingsejongi WV39 showed a higher activity than other reported CrtZs. Copyright © 2017 Elsevier B.V. All rights reserved.

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July 7, 2019

RepLong: de novo repeat identification using long read sequencing data.

The identification of repetitive elements is important in genome assembly and phylogenetic analyses. The existing de novo repeat identification methods exploiting the use of short reads are impotent in identifying long repeats. Since long reads are more likely to cover repeat regions completely, using long reads is more favorable for recognizing long repeats.In this study, we propose a novel de novo repeat elements identification method namely RepLong based on PacBio long reads. Given that the reads mapped to the repeat regions are highly overlapped with each other, the identification of repeat elements is equivalent to the discovery of consensus overlaps between reads, which can be further cast into a community detection problem in the network of read overlaps. In RepLong, we first construct a network of read overlaps based on pair-wise alignment of the reads, where each vertex indicates a read and an edge indicates a substantial overlap between the corresponding two reads. Secondly, the communities whose intra connectivity is greater than the inter connectivity are extracted based on network modularity optimization. Finally, representative reads in each community are extracted to form the repeat library. Comparison studies on Drosophila melanogaster and human long read sequencing data with genome-based and short-read-based methods demonstrate the efficiency of RepLong in identifying long repeats. RepLong can handle lower coverage data and serve as a complementary solution to the existing methods to promote the repeat identification performance on long-read sequencing data.The software of RepLong is freely available at https://github.com/ruiguo-bio/replong.ywsun@szu.edu.cn or zhuzx@szu.edu.cn.Supplementary data are available at Bioinformatics online.

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July 7, 2019

Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations.

Mutations, the fuel of evolution, are first manifested as rare DNA changes within a population of cells. Although next-generation sequencing (NGS) technologies have revolutionized the study of genomic variation between species and individual organisms, most have limited ability to accurately detect and quantify rare variants among the different genome copies in heterogeneous mixtures of cells or molecules. We describe the technical challenges in characterizing subclonal variants using conventional NGS protocols and the recent development of error correction strategies, both computational and experimental, including consensus sequencing of single DNA molecules. We also highlight major applications for low-frequency mutation detection in science and medicine, describe emerging methodologies and provide our vision for the future of DNA sequencing.

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July 7, 2019

Recent progress and prospects for advancing arachnid genomics

Arachnids exhibit tremendous species richness and adaptations of biomedical, industrial, and agricultural importance. Yet genomic resources for arachnids are limited, with the first few spider and scorpion genomes becoming accessible in the last four years. We review key insights from these genome projects, and recommend additional genomes for sequencing, emphasizing taxa of greatest value to the scientific community. We suggest greater sampling of spiders whose genomes are understudied but hold important protein recipes for silk and venom production. We further recommend arachnid genomes to address significant evolutionary topics, including the phenotypic impact of genome duplications. A barrier to high-quality arachnid genomes are assemblies based solely on short-read data, which may be overcome by long-range sequencing and other emerging methods.

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July 7, 2019

Lepidoptera genomes: current knowledge, gaps and future directions.

Butterflies and moths (Lepidoptera) are one of the most ecologically diverse and speciose insect orders. With recent advances in genomics, new Lepidoptera genomes are regularly being sequenced, and many of them are playing principal roles in genomics studies, particularly in the fields of phylo-genomics and functional genomics. Thus far, assembled genomes are only available for <10 of the 43 Lepidoptera superfamilies. Nearly all are model species, found in the speciose clade Ditrysia. Community support for Lepidoptera genomics is growing with successful management and dissemination of data and analytical tools in centralized databases. With genomic studies quickly becoming integrated with ecological and evolutionary research, the Lepidoptera community will unquestionably benefit from new high-quality reference genomes that are more evenly distributed throughout the order. Copyright © 2018 Elsevier Inc. All rights reserved.

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July 7, 2019

Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000RAD and 15000RAD.

The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000RADand 15000RAD) for the dromedary (Camelus dromedarius) as a permanent genetic resource for camel genome researchers worldwide. For the 5000RADpanel, a total of 245 female camel-hamster radiation hybrid clones were collected, of which 186 were screened with 44 custom designed marker loci distributed throughout camel genome. The overall mean retention frequency (RF) of the final set of 93 hybrids was 47.7%. For the 15000RADpanel, 238 male dromedary-hamster radiation hybrid clones were collected, of which 93 were tested using 44 PCR markers. The final set of 90 clones had a mean RF of 39.9%. This 15000RADpanel is an important high-resolution complement to the main 5000RADpanel and an indispensable tool for resolving complex genomic regions. This valuable genetic resource of dromedary RH panels is expected to be instrumental for constructing a high resolution camel genome map. Construction of the set of RH panels is essential step toward chromosome level reference quality genome assembly that is critical for advancing camelid genomics and the development of custom genomic tools.

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July 7, 2019

Current advances in genome sequencing of common wheat and its ancestral species

Common wheat is an important and widely cultivated food crop throughout the world. Much progress has been made in regard to wheat genome sequencing in the last decade. Starting from the sequencing of single chromosomes/chromosome arms whole genome sequences of common wheat and its diploid and tetraploid ancestors have been decoded along with the development of sequencing and assembling technologies. In this review, we give a brief summary on international progress in wheat genome sequencing, and mainly focus on reviewing the effort and contributions made by Chinese scientists.

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July 7, 2019

Inferring synteny between genome assemblies: a systematic evaluation.

Genome assemblies across all domains of life are being produced routinely. Initial analysis of a new genome usually includes annotation and comparative genomics. Synteny provides a framework in which conservation of homologous genes and gene order is identified between genomes of different species. The availability of human and mouse genomes paved the way for algorithm development in large-scale synteny mapping, which eventually became an integral part of comparative genomics. Synteny analysis is regularly performed on assembled sequences that are fragmented, neglecting the fact that most methods were developed using complete genomes. It is unknown to what extent draft assemblies lead to errors in such analysis.We fragmented genome assemblies of model nematodes to various extents and conducted synteny identification and downstream analysis. We first show that synteny between species can be underestimated up to 40% and find disagreements between popular tools that infer synteny blocks. This inconsistency and further demonstration of erroneous gene ontology enrichment tests raise questions about the robustness of previous synteny analysis when gold standard genome sequences remain limited. In addition, assembly scaffolding using a reference guided approach with a closely related species may result in chimeric scaffolds with inflated assembly metrics if a true evolutionary relationship was overlooked. Annotation quality, however, has minimal effect on synteny if the assembled genome is highly contiguous.Our results show that a minimum N50 of 1 Mb is required for robust downstream synteny analysis, which emphasizes the importance of gold standard genomes to the science community, and should be achieved given the current progress in sequencing technology.

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July 7, 2019

Complete genome sequences of four toxigenic Clostridium difficile clinical isolates from patients of the lower Hudson Valley, New York, USA.

Complete genome sequences of four toxigenicClostridium difficileisolates from patients in the lower Hudson Valley, New York, USA, were achieved. These isolates represent four common sequence types (ST1, ST2, ST8, and ST42) belonging to two distinct phylogenetic clades. All isolates have a 4.0- to 4.2-Mb circular chromosome, and one carries a phage. Copyright © 2018 Yin et al.

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