A whole-genome assembly of Drosophila

Long walk to genomics: History and current approaches to genome sequencing and assembly

Genomes represent the starting point of genetic studies. Since the discovery of DNA structure, scientists have devoted great efforts to determine their sequence in an exact way. In this review we provide a comprehensive historical background of the improvements in DNA sequencing technologies that have accompanied the major milestones in genome sequencing and assembly, ranging from early sequencing methods to Next-Generation Sequencing platforms. We then focus on the advantages and challenges of the current technologies and approaches, collectively known as Third Generation Sequencing. As these technical advancements have been accompanied by progress in analytical methods, we also review the bioinformatic tools currently employed in de novo genome assembly, as well as some applications of Third Generation Sequencing technologies and high-quality reference genomes.

Analysis of the Complete Genome Sequence of the Widely Studied Strain Bradyrhizobium betae PL7HG1T Reveals the Presence of Photosynthesis Genes and a Putative Plasmid

Here, we present the complete genome sequence of the widely studied strain Bradyrhizobium betae PL7HG1^T, isolated from a tumor on the roots of sugar beet. The genome consists of a 7.2-Mbp circular chromosome containing key photosynthesis genes but not genes for nodulation and nitrogen fixation. A putative plasmid was also detected.

Here, we present the complete genome sequence of the widely studied strain Bradyrhizobium betae PL7HG1^T, isolated from a tumor on the roots of sugar beet. The genome consists of a 7.2-Mbp circular chromosome containing key photosynthesis genes but not genes for nodulation and nitrogen fixation. A putative plasmid was also detected.

Complete Genome Sequence of Cellulomonas sp. Strain Y8, a High-GC-Content Plasmid-Free Heavy Metal-Resistant Bacterium Isolated from Farmland Soil

We report the complete genome sequence of cadmium-resistant Cellulomonas sp. strain Y8, isolated from farmland soil. The 4.5-Mbp genome contains 4,074 genes, with an approximate GC content of 75%. This work might help in understanding how strain Y8 survives under heavy metal stress.

We report the complete genome sequence of cadmium-resistant Cellulomonas sp. strain Y8, isolated from farmland soil. The 4.5-Mbp genome contains 4,074 genes, with an approximate GC content of 75%. This work might help in understanding how strain Y8 survives under heavy metal stress.

Using Apache Spark on genome assembly for scalable overlap-graph reduction

Background

De novo genome assembly is a technique that builds the genome of a specimen using overlaps of genomic fragments without additional work with reference sequence. Sequence fragments (called reads) are assembled as contigs and scaffolds by the overlaps. The quality of the de novo assembly depends on the length and continuity of the assembly. To enable faster and more accurate assembly of species, existing sequencing techniques have been proposed, for example, high-throughput next-generation sequencing and long-reads-producing third-generation sequencing. However, these techniques require a large amounts of computer memory when very huge-size overlap graphs are resolved. Also, it is challenging for parallel computation.

Results

To address the limitations, we propose an innovative algorithmic approach, called Scalable Overlap-graph Reduction Algorithms (SORA). SORA is an algorithm package that performs string graph reduction algorithms by Apache Spark. The SORA’s implementations are designed to execute de novo genome assembly on either a single machine or a distributed computing platform. SORA efficiently compacts the number of edges on enormous graphing paths by adapting scalable features of graph processing libraries provided by Apache Spark, GraphX and GraphFrames.

Conclusions

We shared the algorithms and the experimental results at our project website, https://github.com/BioHPC/SORA. We evaluated SORA with the human genome samples. First, it processed a nearly one billion edge graph on a distributed cloud cluster. Second, it processed mid-to-small size graphs on a single workstation within a short time frame. Overall, SORA achieved the linear-scaling simulations for the increased computing instances.

Complete Genome Sequence of Bacteriocin-Producing Enterococcus faecium HY07

Here, we report the draft genome sequence of the bacteriocin-producing Enterococcus faecium strain HY07, isolated from traditional Chinese fermented sausages. The genome comprises 2,585,631 bp with 2,624 coding sequences, as assigned by NCBI, which may provide fundamental molecular information on elucidating the adaption mechanism of Enterococcus faecium to the meat environment.

Genome Sequences of 17 Pasteurella multocida Strains Involved in Cases of Rabbit Pasteurellosis

This article reports draft genome sequences of 17 Pasteurella multocida strains isolated from naturally infected rabbits. The total lengths of the assembled contigs ranged between 2.21 and 2.48 Mb, and the total number of genes detected on the contigs ranged between 2,088 and 2,416.

This article reports draft genome sequences of 17 Pasteurella multocida strains isolated from naturally infected rabbits. The total lengths of the assembled contigs ranged between 2.21 and 2.48 Mb, and the total number of genes detected on the contigs ranged between 2,088 and 2,416.

Intraspecific Variation in Protists: Clues for Microevolution from Poteriospumella lacustris (Chrysophyceae)

Species delimitation in protists is still a challenge, attributable to the fact that protists are small, difficult to observe and many taxa are poor in morphological characters, whereas most current phylogenetic approaches only use few marker genes to measure genetic diversity. To address this problem, we assess genome-level divergence and microevolution in strains of the protist Poteriospumella lacustris, one of the first free-living, nonmodel organisms to study genome-wide intraspecific variation. Poteriospumella lacustris is a freshwater protist belonging to the Chrysophyceae with an assumed worldwide distribution. We examined three strains from different geographic regions (New Zealand, China, and Austria) by sequencing their genomes with the Illumina and PacBio platforms. The assembled genomes were small with 49-55 Mb but gene-rich with 16,000-19,000 genes, of which ∼8,000 genes could be assigned to functional categories. At least 68% of these genes were shared by all three species. Genetic variation occurred predominantly in genes presumably involved in ecological niche adaptation. Most surprisingly, we detected differences in genome ploidy between the strains (diploidy, triploidy, and tetraploidy). In analyzing intraspecific variation, several mechanisms of diversification were identified including SNPs, change of ploidy and genome size reduction.

Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus

Newly emerged wheat blast disease is a serious threat to global wheat production. Wheat blast is caused by a distinct, exceptionally diverse lineage of the fungus causing rice blast disease. Through sequencing a recent field isolate, we report a reference genome that includes seven core chromosomes and mini-chromosome sequences that harbor effector genes normally found on ends of core chromosomes in other strains. No mini-chromosomes were observed in an early field strain, and at least two from another isolate each contain different effector genes and core chromosome end sequences. The mini-chromosome is enriched in transposons occurring most frequently at core chromosome ends. Additionally, transposons in mini-chromosomes lack the characteristic signature for inactivation by repeat-induced point (RIP) mutation genome defenses. Our results, collectively, indicate that dispensable mini-chromosomes and core chromosomes undergo divergent evolutionary trajectories, and mini-chromosomes and core chromosome ends are coupled as a mobile, fast-evolving effector compartment in the wheat pathogen genome.

The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters

Background

We report the sequencing, assembly and analysis of the genome of the Komodo dragon (Varanus komodoensis), the largest extant lizard, with a focus on antimicrobial host-defense peptides. The Komodo dragon diet includes carrion, and a complex milieu of bacteria, including potentially pathogenic strains, has been detected in the saliva of wild dragons. They appear to be unaffected, suggesting that dragons have robust defenses against infection. While little information is available regarding the molecular biology of reptile immunity, it is believed that innate immunity, which employs antimicrobial host-defense peptides including defensins and cathelicidins, plays a more prominent role in reptile immunity than it does in mammals. .

Results

High molecular weight genomic DNA was extracted from Komodo dragon blood cells. Subsequent sequencing and assembly of the genome from the collected DNA yielded a genome size of 1.6 Gb with 45x coverage, and the identification of 17,213 predicted genes. Through further analyses of the genome, we identified genes and gene-clusters corresponding to antimicrobial host-defense peptide genes. Multiple β-defensin-related gene clusters were identified, as well as a cluster of potential Komodo dragon ovodefensin genes located in close proximity to a cluster of Komodo dragon β-defensin genes. In addition to these defensins, multiple cathelicidin-like genes were also identified in the genome. Overall, 66 β-defensin genes, six ovodefensin genes and three cathelicidin genes were identified in the Komodo dragon genome.

Conclusions

Genes with important roles in host-defense and innate immunity were identified in this newly sequenced Komodo dragon genome, suggesting that these organisms have a robust innate immune system. Specifically, multiple Komodo antimicrobial peptide genes were identified. Importantly, many of the antimicrobial peptide genes were found in gene clusters. We found that these innate immunity genes are conserved among reptiles, and the organization is similar to that seen in other avian and reptilian species. Having the genome of this important squamate will allow researchers to learn more about reptilian gene families and will be a valuable resource for researchers studying the evolution and biology of the endangered Komodo dragon.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6029-y) contains supplementary material, which is available to authorized users.

Bioinformatics of nanopore sequencing

Nanopore sequencing is one of the most exciting new technologies that undergo dynamic development. With its development, a growing number of analytical tools are becoming available for researchers. To help them better navigate this ever changing field, we discuss a range of software available to analyze sequences obtained using nanopore technology.

A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.

Deep repeat resolution-the assembly of the Drosophila Histone Complex

Though the advent of long-read sequencing technologies has led to a leap in contiguity of de novo genome assemblies, current reference genomes of higher organisms still do not provide unbroken sequences of complete chromosomes. Despite reads in excess of 30 000 base pairs, there are still repetitive structures that cannot be resolved by current state-of-the-art assemblers. The most challenging of these structures are tandemly arrayed repeats, which occur in the genomes of all eukaryotes. Untangling tandem repeat clusters is exceptionally difficult, since the rare differences between repeat copies are obscured by the high error rate of long reads. Solving this problem would constitute a major step towards computing fully assembled genomes. Here, we demonstrate by example of the Drosophila Histone Complex that via machine learning algorithms, it is possible to exploit the underlying distinguishing patterns of single nucleotide variants of repeats from very noisy data to resolve a large and highly conserved repeat cluster. The ideas explored in this paper are a first step towards the automated assembly of complex repeat structures and promise to be applicable to a wide range of eukaryotic genomes.

Draft Genome Sequence of Bifidobacterium longum ZJ1, Isolated from a Centenarian in Anhui, China

Here, we present the complete genome sequence of a Bifidobacterium longum isolate, that of strain ZJ1, and this strain showed a cholesterol degradation ability that is greater than that of five strains we chose for comparison (Bifidobacterium longum 536, B. infantis 1912, B. longum 1941, B. breve ATCC 15698, B. infantis ATCC 17930). The draft genome of strain ZJ1 consists of 2,414,672 bp, with 2,042 protein-coding genes, 69 noncoding RNA genes, and 60.16% G+C content.

Here, we present the complete genome sequence of a Bifidobacterium longum isolate, that of strain ZJ1, and this strain showed a cholesterol degradation ability that is greater than that of five strains we chose for comparison (Bifidobacterium longum 536, B. infantis 1912, B. longum 1941, B. breve ATCC 15698, B. infantis ATCC 17930). The draft genome of strain ZJ1 consists of 2,414,672 bp, with 2,042 protein-coding genes, 69 noncoding RNA genes, and 60.16% G+C content.

Whole-Genome Sequences of Four Indian Isolates of Azospirillum brasilense

Azospirillum brasilense is used worldwide as a plant growth-promoting inoculant for agricultural crops. To understand how the genomes of Indian strains of A. brasilense compare with their South American counterparts, we determined the whole-genome sequences of four strains of A. brasilense isolated from the rhizosphere of grasses from India.

Azospirillum brasilense is used worldwide as a plant growth-promoting inoculant for agricultural crops. To understand how the genomes of Indian strains of A. brasilense compare with their South American counterparts, we determined the whole-genome sequences of four strains of A. brasilense isolated from the rhizosphere of grasses from India.

Dramatic changes in gene expression in different forms of Crithidia fasciculata reveal potential mechanisms for insect-specific adhesion in kinetoplastid parasites

Kinetoplastids are a group of parasites that includes several medically-important species. These human-infective species are transmitted by insect vectors in which the parasites undergo specific developmental transformations. For each species, this includes a stage in which parasites adhere to insect tissue via a hemidesmosome-like structure. Although this structure has been described morphologically, it has never been molecularly characterized. We are using Crithidia fasciculata, an insect parasite that produces large numbers of adherent parasites inside its mosquito host, as a model kinetoplastid to investigate both the mechanism of adherence and the signals required for differentiation to an adherent form. An advantage of C. fasciculata is that adherent parasites can be generated both in vitro, allowing a direct comparison to cultured swimming forms, as well as in vivo within the mosquito. Using RNAseq, we identify genes associated with adherence in C. fasciculata. As almost all of these genes have orthologs in other kinetoplastid species, our findings may reveal shared mechanisms of adherence, allowing investigation of a crucial step in parasite development and disease transmission. In addition, dual-RNAseq allowed us to explore the interaction between the parasites and the mosquito. Although the infection is well-tolerated, anti-microbial peptides and other components of the mosquito innate immune system are upregulated. Our findings indicate that C. fasciculata is a powerful model system for probing kinetoplastid-insect interactions.

Kinetoplastids are single-celled parasites that cause devastating human diseases worldwide. Although this group includes many species that infect a variety of hosts, they have a great deal of shared biology. One relatively unexplored aspect of the kinetoplastid life cycle is their ability to adhere to insect tissue. For pathogenic species, adherence is critical for transmission by insect vectors. We have used an insect parasite called Crithidia fasciculata as a model kinetoplastid to reveal shared mechanisms of insect adherence. We have compared gene expression profiles of motile, non-adherent C. fasciculata to those of C. fasciculata adhered to non-living substrates and those attached to the hindgut of mosquitoes. Through this analysis, we have identified a large number of candidate proteins that may mediate adhesion in these and related parasites. In addition, our findings suggest that the mosquito immune system is responding to the presence of parasites in the gut. These results establish a new, robust system to explore the interaction between kinetoplastids and their insect hosts.

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

Short read massive parallel sequencing has emerged as a standard diagnostic tool in the medical setting. However, short read technologies have inherent limitations such as GC bias, difficulties mapping to repetitive elements, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long read single molecule sequencers resolve these obstacles. Moreover, they offer higher consensus accuracies and can detect epigenetic modifications from native DNA. The first commercially available long read single molecule platform was the RS system based on PacBio's single molecule real-time (SMRT) sequencing technology, which has since evolved into their RSII and Sequel systems. Here we capsulize how SMRT sequencing is revolutionizing constitutional, reproductive, cancer, microbial and viral genetic testing.

Sketching and Sublinear Data Structures in Genomics

Large-scale genomics demands computational methods that scale sublinearly with the growth of data. We review several data structures and sketching techniques that have been used in genomic analysis methods. Specifically, we focus on four key ideas that take different approaches to achieve sublinear space usage and processing time: compressed full-text indices, approximate membership query data structures, locality-sensitive hashing, and minimizers schemes. We describe these techniques at a high level and give several representative applications of each.

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

Several new genomics technologies have become available that offer long-read sequencing or long-range mapping with higher throughput and higher resolution analysis than ever before. These long-range technologies are rapidly advancing the field with improved reference genomes, more comprehensive variant identification and more complete views of transcriptomes and epigenomes. However, they also require new bioinformatics approaches to take full advantage of their unique characteristics while overcoming their complex errors and modalities. Here, we discuss several of the most important applications of the new technologies, focusing on both the currently available bioinformatics tools and opportunities for future research.

Locality-sensitive hashing for the edit distance

MOTIVATION

Sequence alignment is a central operation in bioinformatics pipeline and, despite many improvements, remains a computationally challenging problem. Locality-sensitive hashing (LSH) is one method used to estimate the likelihood of two sequences to have a proper alignment. Using an LSH, it is possible to separate, with high probability and relatively low computation, the pairs of sequences that do not have high-quality alignment from those that may. Therefore, an LSH reduces the overall computational requirement while not introducing many false negatives (i.e. omitting to report a valid alignment). However, current LSH methods treat sequences as a bag of k-mers and do not take into account the relative ordering of k-mers in sequences. In addition, due to the lack of a practical LSH method for edit distance, in practice, LSH methods for Jaccard similarity or Hamming similarity are used as a proxy.

RESULTS

We present an LSH method, called Order Min Hash (OMH), for the edit distance. This method is a refinement of the minHash LSH used to approximate the Jaccard similarity, in that OMH is sensitive not only to the k-mer contents of the sequences but also to the relative order of the k-mers in the sequences. We present theoretical guarantees of the OMH as a gapped LSH.

AVAILABILITY AND IMPLEMENTATION

The code to generate the results is available at http://github.com/Kingsford-Group/omhismb2019.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach

Motivation

It is highly desirable to assemble genomes of high continuity and consistency at low cost. The current bottleneck of draft genome continuity using the second generation sequencing (SGS) reads is primarily caused by uncertainty among repetitive sequences. Even though the single-molecule real-time sequencing technology is very promising to overcome the uncertainty issue, its relatively high cost and error rate add burden on budget or computation. Many long-read assemblers take the overlap-layout-consensus (OLC) paradigm, which is less sensitive to sequencing errors, heterozygosity and variability of coverage. However, current assemblers of SGS data do not sufficiently take advantage of the OLC approach.

Results

Aiming at minimizing uncertainty, the proposed method BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can (i) perform reference-assisted assembly based on the genome of a close species (ii) or improve the results of existing assemblies that are obtained based on short or long sequencing reads. The tests on two eukaryote genomes, a wild rice Oryza longistaminata and a parrot Melopsittacus undulatus, show that BAUM achieved substantial improvement on genome size and continuity. Besides, BAUM reconstructed a considerable amount of repetitive regions that failed to be assembled by existing short read assemblers. We also propose statistical approaches to control the uncertainty in different steps of BAUM.

Availability and implementation

http://www.zhanyuwang.xin/wordpress/index.php/2017/07/21/baum.

Supplementary information

Supplementary data are available at Bioinformatics online.

Nanopore sequencing data analysis: state of the art, applications and challenges

The nanopore sequencing process is based on the transit of a DNA molecule through a nanoscopic pore, and since the 90s is considered as one of the most promising approaches to detect polymeric molecules. In 2014, Oxford Nanopore Technologies (ONT) launched a beta-testing program that supplied the scientific community with the first prototype of a nanopore sequencer: the MinION. Thanks to this program, several research groups had the opportunity to evaluate the performance of this novel instrument and develop novel computational approaches for analyzing this new generation of data. Despite the short period of time from the release of the MinION, a large number of algorithms and tools have been developed for base calling, data handling, read mapping, de novo assembly and variant discovery. Here, we face the main computational challenges related to the analysis of nanopore data, and we carry out a comprehensive and up-to-date survey of the algorithmic solutions adopted by the bioinformatic community comparing performance and reporting limits and advantages of using this new generation of sequences for genomic analyses. Our analyses demonstrate that the use of nanopore data dramatically improves the de novo assembly of genomes and allows for the exploration of structural variants with an unprecedented accuracy and resolution. However, despite the impressive improvements reached by ONT in the past 2 years, the use of these data for small-variant calling is still challenging, and at present, it needs to be coupled with complementary short sequences for mitigating the intrinsic biases of nanopore sequencing technology.

Molecular and functional properties of two Spodoptera exigua acetylcholinesterase genes

Acetylcholinesterase (AChE) is a vital enzyme that hydrolyzes acetylcholine. Here, full-length complementary DNAs (cDNAs) of two acetylcholinesterase genes (SeAce1 and SeAce2) were obtained from Spodoptera exigua, a widespread phytophagous pest in agriculture. The complete SeAce1 cDNA comprised 5447 nucleotides including an open reading frame (ORF) encoding 694 amino acids, while SeAce2 cDNA encompassed a 1917-bp ORF which would likely yield 638 amino acids. Both SeAce1 and SeAce2 contained specific characteristics of functional AChE. A phylogenetic tree of all lepidopteran insect Aces showed S. exigua clustered with S. litura, Helicoverpa assulta, and H. armigera, all of which are Noctuidae. In S. exigua, SeAce1 gene expression levels (reverse transcription polymerase chain reaction [RT-PCR] and quantitative RT-PCR) were markedly increased compared with SeAce2 in all developmental phases and tissue types. Both genes were down regulated by inserting the corresponding dsRNAs in 5th instar larvae, which resulted in 56.7% (SeAce1) and 24.6% (SeAce2) death. Downregulation of both SeAce1 and SeAce2 significantly reduced fecundity and vitellogenin gene expression in S. exigua. These results revealed the biological functions of the two Ace genes (SeAce1 and SeAce2), providing novel insights into the development of strategies for controlling insect pests.

GAAP: A Genome Assembly + Annotation Pipeline

Genomic analysis begins with de novo assembly of short-read fragments in order to reconstruct full-length base sequences without exploiting a reference genome sequence. Then, in the annotation step, gene locations are identified within the base sequences, and the structures and functions of these genes are determined. Recently, a wide range of powerful tools have been developed and published for whole-genome analysis, enabling even individual researchers in small laboratories to perform whole-genome analyses on their objects of interest. However, these analytical tools are generally complex and use diverse algorithms, parameter setting methods, and input formats; thus, it remains difficult for individual researchers to select, utilize, and combine these tools to obtain their final results. To resolve these issues, we have developed a genome analysis pipeline (GAAP) for semiautomated, iterative, and high-throughput analysis of whole-genome data. This pipeline is designed to perform read correction, de novo genome (transcriptome) assembly, gene prediction, and functional annotation using a range of proven tools and databases. We aim to assist non-IT researchers by describing each stage of analysis in detail and discussing current approaches. We also provide practical advice on how to access and use the bioinformatics tools and databases and how to implement the provided suggestions. Whole-genome analysis of Toxocara canis is used as case study to show intermediate results at each stage, demonstrating the practicality of the proposed method.

Complete Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens LBUM677

Pseudomonas fluorescens LBUM677 has shown the ability to increase plant biomass and seed oil yield in soybean, canola, and Buglossoides arvensis (corn gromwell) when inoculated in the rhizosphere. Here, we report a draft genome sequence of P. fluorescens LBUM677, with an estimated size of 6.14 Mb.

Pseudomonas fluorescens LBUM677 has shown the ability to increase plant biomass and seed oil yield in soybean, canola, and Buglossoides arvensis (corn gromwell) when inoculated in the rhizosphere. Here, we report a draft genome sequence of P. fluorescens LBUM677, with an estimated size of 6.14 Mb.

Genomic signatures of heterokaryosis in the oomycete pathogen Bremia lactucae

Lettuce downy mildew caused by Bremia lactucae is the most important disease of lettuce globally. This oomycete is highly variable and rapidly overcomes resistance genes and fungicides. The use of multiple read types results in a high-quality, near-chromosome-scale, consensus assembly. Flow cytometry plus resequencing of 30 field isolates, 37 sexual offspring, and 19 asexual derivatives from single multinucleate sporangia demonstrates a high incidence of heterokaryosis in B. lactucae. Heterokaryosis has phenotypic consequences on fitness that may include an increased sporulation rate and qualitative differences in virulence. Therefore, selection should be considered as acting on a population of nuclei within coenocytic mycelia. This provides evolutionary flexibility to the pathogen enabling rapid adaptation to different repertoires of host resistance genes and other challenges. The advantages of asexual persistence of heterokaryons may have been one of the drivers of selection that resulted in the loss of uninucleate zoospores in multiple downy mildews.

Mobilome of Brevibacterium aurantiacum Sheds Light on Its Genetic Diversity and Its Adaptation to Smear-Ripened Cheeses

Brevibacterium aurantiacum is an actinobacterium that confers key organoleptic properties to washed-rind cheeses during the ripening process. Although this industrially relevant species has been gaining an increasing attention in the past years, its genome plasticity is still understudied due to the unavailability of complete genomic sequences. To add insights on the mobilome of this group, we sequenced the complete genomes of five dairy Brevibacterium strains and one non-dairy strain using PacBio RSII. We performed phylogenetic and pan-genome analyses, including comparisons with other publicly available Brevibacterium genomic sequences. Our phylogenetic analysis revealed that these five dairy strains, previously identified as Brevibacterium linens, belong instead to the B. aurantiacum species. A high number of transposases and integrases were observed in the Brevibacterium spp. strains. In addition, we identified 14 and 12 new insertion sequences (IS) in B. aurantiacum and B. linens genomes, respectively. Several stretches of homologous DNA sequences were also found between B. aurantiacum and other cheese rind actinobacteria, suggesting horizontal gene transfer (HGT). A HGT region from an iRon Uptake/Siderophore Transport Island (RUSTI) and an iron uptake composite transposon were found in five B. aurantiacum genomes. These findings suggest that low iron availability in milk is a driving force in the adaptation of this bacterial species to this niche. Moreover, the exchange of iron uptake systems suggests cooperative evolution between cheese rind actinobacteria. We also demonstrated that the integrative and conjugative element BreLI (Brevibacterium Lanthipeptide Island) can excise from B. aurantiacum SMQ-1417 chromosome. Our comparative genomic analysis suggests that mobile genetic elements played an important role into the adaptation of B. aurantiacum to cheese ecosystems.

The Genome of C57BL/6J "Eve", the Mother of the Laboratory Mouse Genome Reference Strain

Isogenic laboratory mouse strains enhance reproducibility because individual animals are genetically identical. For the most widely used isogenic strain, C57BL/6, there exists a wealth of genetic, phenotypic, and genomic data, including a high-quality reference genome (GRCm38.p6). Now 20 years after the first release of the mouse reference genome, C57BL/6J mice are at least 26 inbreeding generations removed from GRCm38 and the strain is now maintained with periodic reintroduction of cryorecovered mice derived from a single breeder pair, aptly named Adam and Eve. To provide an update to the mouse reference genome that more accurately represents the genome of today's C57BL/6J mice, we took advantage of long read, short read, and optical mapping technologies to generate a de novo assembly of the C57BL/6J Eve genome (B6Eve). Using these data, we have addressed recurring variants observed in previous mouse genomic studies. We have also identified structural variations, closed gaps in the mouse reference assembly, and revealed previously unannotated coding sequences. This B6Eve assembly explains discrepant observations that have been associated with GRCm38-based analyses, and will inform a reference genome that is more representative of the C57BL/6J mice that are in use today.

Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data

Long reads obtained from third-generation sequencing platforms can help overcome the long-standing challenge of the de novo assembly of sequences for the genomic analysis of non-model eukaryotic organisms. Numerous long-read-aided de novo assemblies have been published recently, which exhibited superior quality of the assembled genomes in comparison with those achieved using earlier second-generation sequencing technologies. Evaluating assemblies is important in guiding the appropriate choice for specific research needs. In this study, we evaluated 10 long-read assemblers using a variety of metrics on Pacific Biosciences (PacBio) data sets from different taxonomic categories with considerable differences in genome size. The results allowed us to narrow down the list to a few assemblers that can be effectively applied to eukaryotic assembly projects. Moreover, we highlight how best to use limited genomic resources for effectively evaluating the genome assemblies of non-model organisms.

Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges

Marine sponges are recognized as valuable sources of bioactive metabolites and renowned as petri dishes of the sea, providing specialized niches for many symbiotic microorganisms. Sponges of the family Dysideidae are well documented to be chemically talented, often containing high levels of polyhalogenated compounds, terpenoids, peptides, and other classes of bioactive small molecules. This group of tropical sponges hosts a high abundance of an uncultured filamentous cyanobacterium, Hormoscilla spongeliae Here, we report the comparative genomic analyses of two phylogenetically distinct Hormoscilla populations, which reveal shared deficiencies in essential pathways, hinting at possible reasons for their uncultivable status, as well as differing biosynthetic machinery for the production of specialized metabolites. One symbiont population contains clustered genes for expanded polybrominated diphenylether (PBDE) biosynthesis, while the other instead harbors a unique gene cluster for the biosynthesis of the dysinosin nonribosomal peptides. The hybrid sequencing and assembly approach utilized here allows, for the first time, a comprehensive look into the genomes of these elusive sponge symbionts.IMPORTANCE Natural products provide the inspiration for most clinical drugs. With the rise in antibiotic resistance, it is imperative to discover new sources of chemical diversity. Bacteria living in symbiosis with marine invertebrates have emerged as an untapped source of natural chemistry. While symbiotic bacteria are often recalcitrant to growth in the lab, advances in metagenomic sequencing and assembly now make it possible to access their genetic blueprint. A cell enrichment procedure, combined with a hybrid sequencing and assembly approach, enabled detailed genomic analysis of uncultivated cyanobacterial symbiont populations in two chemically rich tropical marine sponges. These population genomes reveal a wealth of secondary metabolism potential as well as possible reasons for historical difficulties in their cultivation.

Complete Genome Sequences of Two USA300-Related Community-Associated Methicillin-Resistant Staphylococcus aureus Clinical Isolates

USA300 is a predominant community-associated methicillin-resistant Staphylococcus aureus strain causing significant morbidity and mortality in North America. We present the full annotated genome sequences of two methicillin-resistant Staphylococcus aureus isolates related to the USA300 pulsotype with the goal of studying the evolutionary relationships of this highly successful strain type.

USA300 is a predominant community-associated methicillin-resistant Staphylococcus aureus strain causing significant morbidity and mortality in North America. We present the full annotated genome sequences of two methicillin-resistant Staphylococcus aureus isolates related to the USA300 pulsotype with the goal of studying the evolutionary relationships of this highly successful strain type.

First report of isolation and complete genome of Vibrio rotiferianus strain SSVR1601 from cage-cultured black rockfish (Sebastes schlegelii) associated with skin ulcer

Vibrio rotiferianus is an important marine pathogen of various aquatic organisms and can be found widely distributed in the marine environment. To further characterize this pathogen, the pathogenic properties and genome of V. rotiferianus SSVR1601 isolated from Sebastes schlegelii with skin ulcer were analysed. SSVR1601 was shown to be short rod-shaped cell with a single polar flagellum. Different degrees of pathological changes in fish kidney, intestine, gills and liver were observed after SSVR1601 challenge. The SSVR1601 genome consists of two chromosomes and two plasmids with a total of 5,717,113 bp, 42.04%-44.93% GC content, 5,269 predicted CDSs, 134 tRNAs and 40 rRNAs. The common virulence factors including OMPs, haemolysin, flagellin, DNase, entF, algU, tcpI, acfB and rfaD were found in strain SSVR1601. Furthermore, factors responsible for iron uptake (fur, fepC and ccmC) and types II, IV and VI secretion systems were detected, which are likely responsible for the pathogenicity of SSVR1601. The antimicrobial resistance genes, bacA, tet34 and norM, were detected based on Antibiotic Resistance Genes Database. The phylogenetic analysis revealed SSVR1601 to be most closely related to V. rotiferianus strains CAIM577 and B64D1.

Drosophila melanogaster and its nephrocytes: A versatile model for glomerular research

Glomerular disorders are a predominant cause of chronic kidney diseases and end-stage renal failure. Especially podocytes, epithelial cells which represent the outermost part of the filtration barrier, are affected by disease and experience a gradual loss of function. Despite recent advances in identifying potential pathways underlying podocyte injury, treatment remains challenging. It is therefore desirable to employ suitable model organisms in order to study glomerular disease and elucidate affected pathways. Due to its diverse ways of genetic manipulation and high genomic conservation, Drosophila melanogaster is a powerful model organism for biomedical research. The fly was recently used to assess podocytopathies by exploiting the nephrocyte system. Nephrocytes are spherical cells within the body cavity of the fly responsible for detoxification and clearance of unwanted substances. More importantly, they share many characteristics with mammalian podocytes. Here, we summarize how to use Drosophila as a model organism for podocyte research. We discuss examples of techniques that can be used to genetically manipulate nephrocytes and provide protocols for nephrocyte isolation and for morphological as well as functional analysis.

Isolation and Characterization of Live Yeast Cells from Ancient Vessels as a Tool in Bio-Archaeology

So far, most of the study of ancient organisms has been based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms—yeast in this case—from ancient pottery vessels used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains that participated in the fermentation process and were absorbed into the clay matrix of the pottery vessels. Moreover, we characterized the isolated yeast strains, their genomes, and the beer they produced. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio- and experimental archaeology that aim to reconstruct ancient artifacts and products.

Ancient fermented food has been studied based on recipes, residue analysis, and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach based on our hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. We developed a pipeline of yeast isolation from clay vessels and screened for yeast cells in beverage-related and non-beverage-related ancient vessels and sediments from several archaeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. The findings that genotypically the isolated yeasts are similar to those found in traditional African beverages and phenotypically they grow similar to modern beer-producing yeast strongly suggest that they are descendants of the original fermenting yeast. These results demonstrate that modern microorganisms can serve as a new tool in bio-archaeology research.

Complete Genome Sequences of Two Methicillin-Susceptible Staphylococcus aureus Clinical Strains Closely Related to Community-Associated Methicillin-Resistant S. aureus USA300

Predominant community-associated methicillin-resistant Staphylococcus aureus strain USA300 is believed to have originated from an ancestral methicillin-susceptible strain, although the details of that evolution remain unknown. To help understand the emergence of this highly successful strain, we sequenced the genomes of two methicillin-susceptible Staphylococcus aureus clinical strains that are very closely related to USA300.

Predominant community-associated methicillin-resistant Staphylococcus aureus strain USA300 is believed to have originated from an ancestral methicillin-susceptible strain, although the details of that evolution remain unknown. To help understand the emergence of this highly successful strain, we sequenced the genomes of two methicillin-susceptible Staphylococcus aureus clinical strains that are very closely related to USA300.

Complete Genome Sequence of Photobacterium damselae Subsp. damselae Strain SSPD1601 Isolated from Deep-Sea Cage-Cultured Sebastes schlegelii with Septic Skin Ulcer

Photobacterium damselae subsp. damselae (PDD) is a Gram-negative bacterium that can infect a variety of aquatic organisms and humans. Based on an epidemiological investigation conducted over the past 3 years, PDD is one of the most important pathogens causing septic skin ulcer in deep-sea cage-cultured Sebastes schlegelii in the Huang-Bohai Sea area and present throughout the year with high abundance. To further understand the pathogenicity of this species, the pathogenic properties and genome of PDD strain SSPD1601 were analyzed. The results revealed that PDD strain SSPD1601 is a rod-shaped cell with a single polar flagellum, and the clinical symptoms were replicated during artificial infection. The SSPD1601 genome consists of two chromosomes and two plasmids, totaling 4,252,294 bp with 3,751 coding sequences (CDSs), 196 tRNA genes, and 47 rRNA genes. Common virulence factors including flagellin, Fur, RstB, hcpA, OMPs, htpB-Hsp60, VasK, and vgrG were found in strain SSPD1601. Furthermore, SSPD1601 is a pPHDD1-negative strain containing the hemolysin gene hlyAch and three putative hemolysins (emrA, yoaF, and VPA0226), which are likely responsible for the pathogenicity of SSPD1601. The phylogenetic analysis revealed SSPD1601 to be most closely related to Phdp Wu-1. In addition, the antibiotic resistance phenotype indicated that SSPD1601 was not sensitive to ceftazidime, pipemidic, streptomycin, cefalexin, bacitracin, cefoperazone sodium, acetylspiramycin, clarithromycin, amikacin, gentamycin, kanamycin, oxacillin, ampicillin, and trimethoprim-sulfamethoxazole, but only the bacitracin resistance gene bacA was detected based on Antibiotic Resistance Genes Database. These results expand our understanding of PDD, setting the stage for further studies of its pathogenesis and disease prevention.

Comparative analysis of de novo assemblers for variation discovery in personal genomes

Current variant discovery approaches often rely on an initial read mapping to the reference sequence. Their effectiveness is limited by the presence of gaps, potential misassemblies, regions of duplicates with a high-sequence similarity and regions of high-sequence divergence in the reference. Also, mapping-based approaches are less sensitive to large INDELs and complex variations and provide little phase information in personal genomes. A few de novo assemblers have been developed to identify variants through direct variant calling from the assembly graph, micro-assembly and whole-genome assembly, but mainly for whole-genome sequencing (WGS) data. We developed SGVar, a de novo assembly workflow for haplotype-based variant discovery from whole-exome sequencing (WES) data. Using simulated human exome data, we compared SGVar with five variation-aware de novo assemblers and with BWA-MEM together with three haplotype- or local de novo assembly-based callers. SGVar outperforms the other assemblers in sensitivity and tolerance of sequencing errors. We recapitulated the findings on whole-genome and exome data from a Utah residents with Northern and Western European ancestry (CEU) trio, showing that SGVar had high sensitivity both in the highly divergent human leukocyte antigen (HLA) region and in non-HLA regions of chromosome 6. In particular, SGVar is robust to sequencing error, k-mer selection, divergence level and coverage depth. Unlike mapping-based approaches, SGVar is capable of resolving long-range phase and identifying large INDELs from WES, more prominently from WGS. We conclude that SGVar represents an ideal platform for WES-based variant discovery in highly divergent regions and across the whole genome.

Genetic Diversity of Salmonella Derby from the Poultry Sector in Europe

Salmonella Derby (S. Derby) is emerging in Europe as a predominant serovar in fattening turkey flocks. This serovar was recorded as being predominant in the turkey sector in 2014 in the United Kingdom (UK). Only two years later, in 2016, it was also recorded in the turkey and broiler sectors in Ireland and Spain. These S. Derby isolates were characterised as members of the multilocus sequence type (MLST) profile 71 (ST71). For the first time, we characterise by whole genome sequencing (WGS) analysis a panel of 90 S. Derby ST71 genomes to understand the routes of transmission of this emerging pathogen within the poultry/turkey food trade. Selected panel included strains isolated as early as 2010 in five leading European g countries for turkey meat production. Twenty-one of the 90 genomes were extracted from a public database-Enterobase. Five of these originated from the United States (n=3), China (n=1) and Taiwan (n=1) isolated between 1986 and 2016. A phylogenomic analysis at the core-genome level revealed the presence of three groups. The largest group contained 97.5% of the European strains and included both, turkey and human isolates that were genetically related by an average of 35 ± 15 single nucleotide polymorphism substitutions (SNPs). To illustrate the diversity, the presence of antimicrobial resistance genes and phages were characteised in 30, S. Derby ST71 genomes, including 11 belonging to this study This study revealed an emergent turkey-related S. Derby ST71 clone circulating in at least five European countries (the UK, Germany, Poland, Italy, and France) since 2010 that causes human gastroenteritis. A matter of concern is the identification of a gyrA mutation involved in resistance to quinolone, present in the Italian genomes. Interestingly, the diversity of phages seems to be related to the geographic origins. These results constitute a baseline for following the spread of this emerging pathogen and identifying appropriate monitoring and prevention measures.

Plant genome sequences: past, present, future

The green plants (Viridiplantae) are an essential kingdom of life, responsible via photosynthesis for the majority of global primary production, and directly utilized by humankind for nutrition, animal feed, fuel, clothing, medicine and other purposes. There are an estimated 391 000 species of land plants, in addition to 8000 species of green algae. Their genomes are unusually diverse compared to those of other kingdoms, ranging in size from ∼10 Mb to over 100 Gb. Knowledge of plant genomes initially lagged behind those of other kingdoms but has greatly increased with the development of new technologies for DNA sequencing; bioinformatic analysis, rather than data production, is increasingly the bottleneck to further knowledge. Recent proposals are now contemplating the sequencing, assembly and annotation of the genomes of all of the world's plant species; meanwhile, low coverage sequencing to measure diversity across collections and wild populations has already become commonplace for many species, especially those utilized as crops.

GMASS: a novel measure for genome assembly structural similarity

BACKGROUND

Thanks to the recent advancements in next-generation sequencing (NGS) technologies, large amount of genomic data, which are short DNA sequences known as reads, has been accumulating. Diverse assemblers have been developed to generate high quality de novo assemblies using the NGS reads, but their output is very different because of algorithmic differences. However, there are not properly structured measures to show the similarity or difference in assemblies.

RESULTS

We developed a new measure, called the GMASS score, for comparing two genome assemblies in terms of their structure. The GMASS score was developed based on the distribution pattern of the number and coverage of similar regions between a pair of assemblies. The new measure was able to show structural similarity between assemblies when evaluated by simulated assembly datasets. The application of the GMASS score to compare assemblies in recently published benchmark datasets showed the divergent performance of current assemblers as well as its ability to compare assemblies.

CONCLUSION

The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo assemblers.

Complete Genome Sequence of "Candidatus Thioglobus sp." Strain NP1, an Open-Ocean Isolate from the SUP05 Clade of Marine Gammaproteobacteria

“Candidatus Thioglobus sp.” strain NP1 is an open-ocean isolate from the SUP05 clade of Gammaproteobacteria. Whole-genome comparisons of strain NP1 to other sequenced isolates from the SUP05 clade indicate that it represents a new species of SUP05 that lacks the ability to fix inorganic carbon using the Calvin-Benson-Bassham cycle.

“Candidatus Thioglobus sp.” strain NP1 is an open-ocean isolate from the SUP05 clade of Gammaproteobacteria. Whole-genome comparisons of strain NP1 to other sequenced isolates from the SUP05 clade indicate that it represents a new species of SUP05 that lacks the ability to fix inorganic carbon using the Calvin-Benson-Bassham cycle.

Local Diversification of Methicillin- Resistant Staphylococcus aureus ST239 in South America After Its Rapid Worldwide Dissemination

The global spread of specific clones of methicillin-resistant Staphylococcus aureus (MRSA) has become a major public health problem, and understanding the dynamics of geographical spread requires worldwide surveillance. Over the past 20 years, the ST239 lineage of MRSA has been recognized as an emerging clone across the globe, with detailed studies focusing on isolates from Europe and Asia. Less is known about this lineage in South America, and, particularly, Brazil where it was the predominant lineage of MRSA in the early 1990s to 2000s. To gain a better understanding about the introduction and spread of ST239 MRSA in Brazil we undertook a comparative phylogenomic analysis of ST239 genomes, adding seven completed, closed Brazilian genomes. Brazilian ST239 isolates grouped in a subtree with those from South American, and Western, romance-language-speaking, European countries, here designated the South American clade. After an initial worldwide radiation in the 1960s and 1970s, we estimate that ST239 began to spread in South America and Brazil in approximately 1988. This clone demonstrates specific genomic changes that are suggestive of local divergence and adaptational change including agrC single-nucleotide polymorphisms variants, and a distinct pattern of virulence-associated genes (mainly the presence of the chp and the absence of sea and sasX). A survey of a geographically and chronologically diverse set of 100 Brazilian ST239 isolates identified this virulence genotype as the predominant pattern in Brazil, and uncovered an unexpectedly high prevalence of agr-dysfunction (30%). ST239 isolates from Brazil also appear to have undergone transposon (IS256) insertions in or near global regulatory genes (agr and mgr) that likely led to rapid reprogramming of bacterial traits. In general, the overall pattern observed in phylogenomic analyses of ST239 is of a rapid initial global radiation, with subsequent local spread and adaptation in multiple different geographic locations. Most ST239 isolates harbor the ardA gene, which we show here to have in vivo anti-restriction activity. We hypothesize that this gene may have improved the ability of this lineage to acquire multiple resistance genes and distinct virulence-associated genes in each local context. The allopatric divergence pattern of ST239 also may suggest strong selective pressures for specific traits in different geographical locations.

Characterization and evolutionary dynamics of complex regions in eukaryotic genomes

Complex regions in eukaryotic genomes are typically characterized by duplications of chromosomal stretches that often include one or more genes repeated in a tandem array or in relatively close proximity. Nevertheless, the repetitive nature of these regions, together with the often high sequence identity among repeats, have made complex regions particularly recalcitrant to proper molecular characterization, often being misassembled or completely absent in genome assemblies. This limitation has prevented accurate functional and evolutionary analyses of these regions. This is becoming increasingly relevant as evidence continues to support a central role for complex genomic regions in explaining human disease, developmental innovations, and ecological adaptations across phyla. With the advent of long-read sequencing technologies and suitable assemblers, the development of algorithms that can accommodate sample heterozygosity, and the adoption of a pangenomic-like view of these regions, accurate reconstructions of complex regions are now within reach. These reconstructions will finally allow for accurate functional and evolutionary studies of complex genomic regions, underlying the generation of genotype-phenotype maps of unprecedented resolution.

The first two mitochondrial genomes of wood wasps (Hymenoptera: Symphyta): Novel gene rearrangements and higher-level phylogeny of the basal hymenopterans

The Symphyta has long been recognized as a paraphyletic grade forming the base of the remaining Hymenopteran, and the superfamily relationships within Symphyta remain controversial. Here, the first two representative mitochondrial genomes from the superfamily Siricoidea and Xiphydrioidea (Hymenoptera: Symphyta) are obtained using next-generation sequencing. The complete mitochondrial genome of Xiphydria sp. is 16,482 bp long with an A + T content of 84.18% while the incomplete one of Tremex columba is 16,847 bp long and A + T content is 81.69%. All 37 typical mitochondrial genes are possessed in both species. The secondary structure of tRNAs and rRNAs for both species are successfully predicted. Compared with the ancestral organization, seven and five tRNA genes are rearranged in mitochondrial genomes of Tremex and Xiphydria, respectively, which are the most rearrangement events within Symphyta. The rearrangement patterns in Tremex and Xiphydria present in this study are all novel to the Symphyta. Phylogenetic relationships among the major lineages of Symphyta are reconstructed using mitochondrial genomes. Both maximum likelihood and Bayesian inference analyses highly support Symphyta is a paraphyletic grade, Xyeloidea + (Tenthredinoidea + (Pamphilioidea + (Xiphydrioidea + (Cephoidea + (Orussoidea + Apocrita))))).

New Approaches for Genome Assembly and Scaffolding

Affordable, high-throughput DNA sequencing has accelerated the pace of genome assembly over the past decade. Genome assemblies from high-throughput, short-read sequencing, however, are often not as contiguous as the first generation of genome assemblies. Whereas early genome assembly projects were often aided by clone maps or other mapping data, many current assembly projects forego these scaffolding data and only assemble genomes into smaller segments. Recently, new technologies have been invented that allow chromosome-scale assembly at a lower cost and faster speed than traditional methods. Here, we give an overview of the problem of chromosome-scale assembly and traditional methods for tackling this problem. We then review new technologies for chromosome-scale assembly and recent genome projects that used these technologies to create highly contiguous genome assemblies at low cost.