scholarly journals Genome Sequencing of Musa acuminata Dwarf Cavendish Reveals a Duplication of a Large Segment of Chromosome 2

2019 ◽  
Vol 10 (1) ◽  
pp. 37-42
Author(s):  
Mareike Busche ◽  
Boas Pucker ◽  
Prisca Viehöver ◽  
Bernd Weisshaar ◽  
Ralf Stracke
Keyword(s):  
Sequence Data ◽  
Musa Acuminata ◽  
Genomic Diversity ◽  
Genome Comparison ◽  
Sequence Variant ◽  
Chromosome 2 ◽  
Large Segment ◽  
Reference Genome Assembly ◽  
Illumina Sequence ◽  
Functional Relevance

Different Musa species, subspecies, and cultivars are currently investigated to reveal their genomic diversity. Here, we compare the genome sequence of one of the commercially most important cultivars, Musa acuminata Dwarf Cavendish, against the Pahang reference genome assembly. Numerous small sequence variants were detected and the ploidy of the cultivar presented here was determined as triploid based on sequence variant frequencies. Illumina sequence data also revealed a duplication of a large segment on the long arm of chromosome 2 in the Dwarf Cavendish genome. Comparison against previously sequenced cultivars provided evidence that this duplication is unique to Dwarf Cavendish. Although no functional relevance of this duplication was identified, this example shows the potential of plants to tolerate such aneuploidies.

scholarly journals Genome sequencing of Musa acuminata Dwarf Cavendish reveals a duplication of a large segment of chromosome 2

2019 ◽  
Author(s):  
Mareike Busche ◽  
Boas Pucker ◽  
Prisca Viehöver ◽  
Bernd Weisshaar ◽  
Ralf Stracke
Keyword(s):  
Sequence Data ◽  
Musa Acuminata ◽  
Genomic Diversity ◽  
Genome Comparison ◽  
Sequence Variant ◽  
Chromosome 2 ◽  
Large Segment ◽  
Reference Genome Assembly ◽  
Illumina Sequence ◽  
Functional Relevance

AbstractDifferent Musa species, subspecies, and cultivars are currently investigated to reveal their genomic diversity. Here, we compare the genome sequence of one of the commercially most important cultivars, Musa acuminata Dwarf Cavendish, against the Pahang reference genome assembly. Numerous small sequence variants were detected and the ploidy of the cultivar presented here was determined as triploid based on sequence variant frequencies. Illumina sequence data also revealed a duplication of a large segment on the long arm of chromosome 2 in the Dwarf Cavendish genome. Comparison against previously sequenced cultivars provided evidence that this duplication is unique to Dwarf Cavendish. Although no functional relevance of this duplication was identified, this example shows the potential of plants to tolerate such aneuploidies.

scholarly journals A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

2016 ◽  
Vol 1 ◽  
pp. 4 ◽  
Author(s):  
Sarah Auburn ◽  
Ulrike Böhme ◽  
Sascha Steinbiss ◽  
Hidayat Trimarsanto ◽  
Jessica Hostetler ◽  
...  
Keyword(s):  
South America ◽  
Plasmodium Vivax ◽  
Sequence Data ◽  
Ex Vivo ◽  
Vital Role ◽  
Asia Pacific ◽  
Reference Sequence ◽  
Manual Curation ◽  
Illumina Sequence

Plasmodium vivax is now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuous ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite’s biology and epidemiology. To date, molecular studies of P. vivax have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds.  Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres.  An extensive repertoire of over 1200 Plasmodium interspersed repeat (pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality.

scholarly journals ntEdit: scalable genome sequence polishing

2019 ◽  
Vol 35 (21) ◽  
pp. 4430-4432 ◽  
Author(s):  
René L Warren ◽  
Lauren Coombe ◽  
Hamid Mohamadi ◽  
Jessica Zhang ◽  
Barry Jaquish ◽  
...  
Keyword(s):  
Human Genome ◽  
Genome Sequence ◽  
Sequence Data ◽  
Bloom Filter ◽  
Supplementary Information ◽  
Routine Practice ◽  
High Coverage ◽  
Illumina Sequence ◽  
Genome Assemblies ◽  
Indel Rate

Abstract Motivation In the modern genomics era, genome sequence assemblies are routine practice. However, depending on the methodology, resulting drafts may contain considerable base errors. Although utilities exist for genome base polishing, they work best with high read coverage and do not scale well. We developed ntEdit, a Bloom filter-based genome sequence editing utility that scales to large mammalian and conifer genomes. Results We first tested ntEdit and the state-of-the-art assembly improvement tools GATK, Pilon and Racon on controlled Escherichia coli and Caenorhabditis elegans sequence data. Generally, ntEdit performs well at low sequence depths (<20×), fixing the majority (>97%) of base substitutions and indels, and its performance is largely constant with increased coverage. In all experiments conducted using a single CPU, the ntEdit pipeline executed in <14 s and <3 m, on average, on E.coli and C.elegans, respectively. We performed similar benchmarks on a sub-20× coverage human genome sequence dataset, inspecting accuracy and resource usage in editing chromosomes 1 and 21, and whole genome. ntEdit scaled linearly, executing in 30–40 m on those sequences. We show how ntEdit ran in <2 h 20 m to improve upon long and linked read human genome assemblies of NA12878, using high-coverage (54×) Illumina sequence data from the same individual, fixing frame shifts in coding sequences. We also generated 17-fold coverage spruce sequence data from haploid sequence sources (seed megagametophyte), and used it to edit our pseudo haploid assemblies of the 20 Gb interior and white spruce genomes in <4 and <5 h, respectively, making roughly 50M edits at a (substitution+indel) rate of 0.0024. Availability and implementation https://github.com/bcgsc/ntedit Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Mutations Associated with Reduced Surotomycin Susceptibility in Clostridium difficile and Enterococcus Species

2015 ◽  
Vol 59 (7) ◽  
pp. 4139-4147 ◽  
Author(s):  
Hannah M. Adams ◽  
Xiang Li ◽  
Carmela Mascio ◽  
Laurent Chesnel ◽  
Kelli L. Palmer
Keyword(s):  
Clostridium Difficile ◽  
Sequence Data ◽  
Acyl Carrier Protein ◽  
Serial Passage ◽  
Restriction Endonuclease Analysis ◽  
Health Concern ◽  
Content Type ◽  
Cyclic Lipopeptide ◽  
Illumina Sequence

ABSTRACTClostridium difficileinfection (CDI) is an urgent public health concern causing considerable clinical and economic burdens. CDI can be treated with antibiotics, but recurrence of the disease following successful treatment of the initial episode often occurs. Surotomycin is a rapidly bactericidal cyclic lipopeptide antibiotic that is in clinical trials for CDI treatment and that has demonstrated superiority over vancomycin in preventing CDI relapse. Surotomycin is a structural analogue of the membrane-active antibiotic daptomycin. Previously, we utilizedin vitroserial passage experiments to deriveC. difficilestrains with reduced surotomycin susceptibilities. The parent strains used included ATCC 700057 and clinical isolates from the restriction endonuclease analysis (REA) groups BI and K. Serial passage experiments were also performed with vancomycin-resistant and vancomycin-susceptibleEnterococcus faeciumandEnterococcus faecalis. The goal of this study is to identify mutations associated with reduced surotomycin susceptibility inC. difficileand enterococci. Illumina sequence data generated for the parent strains and serial passage isolates were compared. We identified nonsynonymous mutations in genes coding for cardiolipin synthase inC. difficileATCC 700057, enoyl-(acyl carrier protein) reductase II (FabK) and cell division protein FtsH2 inC. difficileREA type BI, and a PadR family transcriptional regulator inC. difficileREA type K. Among the 4 enterococcal strain pairs, 20 mutations were identified, and those mutations overlap those associated with daptomycin resistance. These data give insight into the mechanism of action of surotomycin againstC. difficile, possible mechanisms for resistance emergence during clinical use, and the potential impacts of surotomycin therapy on intestinal enterococci.

scholarly journals The speciation and hybridization history of the genusSalmonella

2019 ◽  
Author(s):  
Alexis Criscuolo ◽  
Sylvie Issenhuth-Jeanjean ◽  
Xavier Didelot ◽  
Kaisa Thorell ◽  
James Hale ◽  
...  
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Binary Fission ◽  
Bacterial Lineage ◽  
Food Borne ◽  
European Nucleotide Archive ◽  
Reference Collection ◽  
Illumina Sequence ◽  
History Of ◽  
Food Borne Infections

AbstractBacteria and archaea make up most of natural diversity but the mechanisms that underlie the origin and maintenance of prokaryotic species are poorly understood. We investigated the speciation history of the genusSalmonella, an ecologically diverse bacterial lineage, within whichS. entericasubsp.entericais responsible for important human food-borne infections. We performed a survey of diversity across a large reference collection using multilocus sequence typing, followed by genome sequencing of distinct lineages. We identified eleven distinct phylogroups, three of which were previously undescribed. Strains assigned toS. entericasubsp.salamaeare polyphyletic, with two distinct lineages that we designate Salamae A and Salamae B. Strains of subspecieshoutenaeare subdivided into two groups, Houtenae A and B and are both related to Selander’s group VII. A phylogroup we designate VIII was previously unknown. A simple binary fission model of speciation cannot explain observed patterns of sequence diversity. In the recent past, there have been large scale hybridization events involving an unsampled ancestral lineage and three distantly related lineages of the genus that have given rise to Houtenae A, Houtenae B and VII. We found no evidence for ongoing hybridization in the other eight lineages but detected more subtle signals of ancient recombination events. We are unable to fully resolve the speciation history of the genus, which might have involved additional speciation-by-hybridization or multi-way speciation events. Our results imply that traditional models of speciation by binary fission and divergence may not apply inSalmonella.Data summaryIllumina sequence data were submitted to the European Nucleotide Archive under project number PRJEB2099 and are available from INSDC (NCBI/ENA/DDBJ) under accession numbers ERS011101 to ERS011146. The MLST sequence and profile data generated in this study have been publicly available on theSalmonellaMLST web site between 2010 and the migration of theSalmonellaMLST website to EnteroBase (https://enterobase.warwick.ac.uk/), and subsequently from there.

scholarly journals Life-history traits and habitat availability shape genomic diversity in birds: implications for conservation

2021 ◽  
Vol 288 (1961) ◽  
Author(s):  
Anna Brüniche-Olsen ◽  
Kenneth F. Kellner ◽  
Jerrold L. Belant ◽  
J. Andrew DeWoody
Keyword(s):  
Life History ◽  
Life History Traits ◽  
Management Practices ◽  
Sequence Data ◽  
Extinction Risk ◽  
Conservation Status ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Habitat Availability

More than 25% of species assessed by the International Union for Conservation of Nature (IUCN) are threatened with extinction. Understanding how environmental and biological processes have shaped genomic diversity may inform management practices. Using 68 extant avian species, we parsed the effects of habitat availability and life-history traits on genomic diversity over time to provide a baseline for conservation efforts. We used published whole-genome sequence data to estimate overall genomic diversity as indicated by historical long-term effective population sizes ( N e ) and current genomic variability ( H ), then used environmental niche modelling to estimate Pleistocene habitat dynamics for each species. We found that N e and H were positively correlated with habitat availability and related to key life-history traits (body mass and diet), suggesting the latter contribute to the overall genomic variation. We found that H decreased with increasing species extinction risk, suggesting that H may serve as a leading indicator of demographic trends related to formal IUCN conservation status in birds. Our analyses illustrate that genome-wide summary statistics estimated from sequence data reflect meaningful ecological attributes relevant to species conservation.

scholarly journals International High-Risk Clones Among Extended-Spectrum β-Lactamase–Producing Escherichia coli in Dhaka, Bangladesh

2021 ◽  
Vol 12 ◽  
Author(s):  
Razib Mazumder ◽  
Arif Hussain ◽  
Ahmed Abdullah ◽  
Md. Nazrul Islam ◽  
Md. Tuhin Sadique ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
High Risk ◽  
Sequence Data ◽  
Diarrhoeal Disease ◽  
Resistance Mechanisms ◽  
Genome Comparison ◽  
E Coli ◽  
Extended Spectrum ◽  
Genome Phylogeny ◽  
Cephalosporin Resistance

Background:Escherichia coli is a major extended-spectrum β-lactamase (ESBL)–producing organism responsible for the rapid spread of antimicrobial resistance (AMR) that has compromised our ability to treat infections. Baseline data on population structure, virulence, and resistance mechanisms in E. coli lineages from developing countries such as Bangladesh are lacking.Methods: Whole-genome sequencing was performed for 46 ESBL–E. coli isolates cultured from patient samples at the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b)-Dhaka. Sequence data were analyzed to glean details of AMR, virulence, and phylogenetic and molecular markers of E. coli lineages.Results: Genome comparison revealed presence of all major high-risk clones including sequence type 131 (ST131) (46%), ST405 (13%), ST648 (7%), ST410 (4.3%), ST38 (2%), ST73 (2%), and ST1193 (2%). The predominant ESBL gene and plasmid combination were blaCTX–M–15 and FII-FIA-FIB detected in diverse E. coli phylogroups and STs. The blaNDM–5 (9%) gene was present in prominent E. coli STs. One (2%) mcr-1–positive ST1011 E. coli, coharboring blaCTXM–55 gene, was detected. The extraintestinal pathogenic E. coli genotype was associated with specific E. coli lineages. The single nucleotide polymorphism (SNP)-based genome phylogeny largely showed correlation with phylogroups, serogroups, and fimH types. Majority of these isolates were susceptible to amikacin (93%), imipenem (93%), and nitrofurantoin (83%).Conclusion: Our study reveals a high diversity of E. coli lineages among ESBL-producing E. coli from Dhaka. This study suggests ongoing circulation of ST131 and all major non-ST131 high-risk clones that are strongly associated with cephalosporin resistance and virulence genes. These findings warrant prospective monitoring of high-risk clones, which would otherwise worsen the AMR crises.

scholarly journals Group-Specific Carbon Fixation Activity Measurements Reveal Distinct Responses to Oxygen Among Hydrothermal vent Campylobacteria

2020 ◽  
Author(s):  
Jesse McNichol ◽  
Stefan Dyksma ◽  
Marc Mußmann ◽  
Jeffrey S. Seewald ◽  
Sean P. Sylva ◽  
...  
Keyword(s):  
Community Composition ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Carbon Fixation ◽  
Genomic Diversity ◽  
Sequence Variant ◽  
Activity Measurements ◽  
Initial Starting

AbstractMolecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that Campylobacteria (prev. Epsilonproteobacteria) often dominate the microbial community and that three subgroups - Arcobacter, Sulfurimonas and Sulfurovum - frequently coexist. In this study, we used replicated radiocarbon incubations of deep-sea hydrothermal fluids to investigate the activities of each group under three distinct incubation conditions. In order to quantify group-specific radiocarbon incorporation, we used newly designed oligonucleotide probes for Arcobacter, Sulfurimonas, and Sulfurovum to quantify their activity using catalyzed-reporter deposition fluorescence in-situ hybridization (CARD-FISH) combined with fluorescence-activated cell sorting. All three groups actively fixed CO2 in short-term (~ 20 h) incubations with either nitrate, oxygen, or no additions (control) at similar per-cell carbon fixation rates. Oxygen additions had the largest effect on community composition and overall cell numbers, and caused a pronounced shift in community composition at the amplicon sequence variant (ASV) level after only 20 h of incubation for all three groups. Interestingly, the effect of oxygen on carbon fixation rates appeared to depend on the initial starting community. Higher carbon fixation rates in oxygen-amended treatments were noted for all three taxa after an unintended disturbance to the sample site that may have selected for more oxygen-tolerant phylotypes. When viewed from a coarse taxonomic level, our data support assertions that these chemoautotrophic groups are functionally redundant in terms of their core metabolic capabilities since they were simultaneously active under all incubation conditions. In contrast, the higher resolution of amplicon sequencing allowed us to reveal finer-scale differences in growth that likely reflect adaptation of physiologically-distinct subtypes to varying oxygen concentrations in situ. Despite this progress, we still know remarkably little about the factors that maintain genomic diversity and allow for stable co-existence among these three campylobacterial groups. Moving forward, we suggest that more subtle biological factors such as enzyme substrate specificity, motility, cell morphology, and tolerance to environmental stress should be more thoroughly investigated to better understand ecological niche differentiation at deep-sea hydrothermal vents.

scholarly journals Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism

mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Disa Bäckström ◽  
Natalya Yutin ◽  
Steffen L. Jørgensen ◽  
Jennah Dharamshi ◽  
Felix Homa ◽  
...  
Keyword(s):  
Deep Sea ◽  
Genomic Diversity ◽  
Genome Comparison ◽  
Phylogenomic Analysis ◽  
Dna Viruses ◽  
Deep Sea Sediments ◽  
Giant Viruses ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Loki’S Castle ◽  
Virus Genomes

ABSTRACT The nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes (proposed order, “Megavirales”) include the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, and Mimiviridae, as well as still unclassified pithoviruses, pandoraviruses, molliviruses, and faustoviruses. Several of these virus groups include giant viruses, with genome and particle sizes exceeding those of many bacterial and archaeal cells. We explored the diversity of the NCLDV in deep sea sediments from the Loki’s Castle hydrothermal vent area. Using metagenomics, we reconstructed 23 high-quality genomic bins of novel NCLDV, 15 of which are related to pithoviruses, 5 to marseilleviruses, 1 to iridoviruses, and 2 to klosneuviruses. Some of the identified pithovirus-like and marseillevirus-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth of the respective groups. The discovered viruses, including putative giant members of the family Marseilleviridae, have a broad range of apparent genome sizes, in agreement with the multiple, independent origins of gigantism in different branches of the NCLDV. Phylogenomic analysis reaffirms the monophyly of the pithovirus-iridovirus-marseillevirus branch of the NCLDV. Similarly to other giant viruses, the pithovirus-like viruses from Loki’s Castle encode translation systems components. Phylogenetic analysis of these genes indicates a greater bacterial contribution than had been detected previously. Genome comparison suggests extensive gene exchange between members of the pithovirus-like viruses and Mimiviridae. Further exploration of the genomic diversity of Megavirales in additional sediment samples is expected to yield new insights into the evolution of giant viruses and the composition of the ocean megavirome. IMPORTANCE Genomics and evolution of giant viruses are two of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diversity of the nucleocytoplasmic large DNA viruses of eukaryotes. The results support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches.

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